3 Dee - Database of Protein Domain Definitions


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The current cluster is formed at a score of 0.134

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Classes% of representative set
undefined 25.31
Small proteins 36.73
Peptides 18.78
Alpha and beta (a/b) 0.41
Alpha and beta (a+b) 3.27
All beta 4.08
All alpha 11.43
Breakdown into folds% of cluster % of class
undefined
undefined from 3Dee 25.31 9.75
Small proteins
Acid protease presegment from 3Dee 0.41 0.87
Ascaris trypsin inhibitor from 3Dee 0.41 0.87
BPTI-like from SCOP 1.22 2.61
Blood coagulation inhibitor (disintegrin) from SCOP 0.41 0.87
Classic zinc finger from 3Dee 8.98 19.13
Complement control module from 3Dee 0.41 0.87
Defensin-like from SCOP 1.63 3.48
EGF-like module from 3Dee 1.63 3.48
Endothelin-like from 3Dee 0.41 0.87
Fibronectin type I module from SCOP 0.82 1.74
Fibronectin type II module from 3Dee 0.41 0.87
Glucocorticoid receptor-like (DNA-binding domain) from SCOP 0.82 1.74
HIV zinc finger-like domains from 3Dee 0.41 0.87
Insulin-like from SCOP 1.63 3.48
Ligand-binding domain of low-density lipoprotein receptor from SCOP 0.41 0.87
Metallothionein from SCOP 1.63 3.48
Neurotoxin III (ATX III) from SCOP 0.41 0.87
Ovomucoid/PCI-1 like inhibitors from SCOP 0.41 0.87
Protein kinase cystein-rich domain (cys2) from 3Dee 0.41 0.87
Proteinase inhibitor PMP-C from SCOP 0.41 0.87
Rubredoxin-like from SCOP 1.22 2.61
Small inhibitors, toxins, lectins from 3Dee 9.39 20.00
Thrombin inhibitors from 3Dee 0.82 1.74
Trefoil from SCOP 0.41 0.87
Zn2/Cys6 DNA-binding domain from SCOP 0.82 1.74
beta-Galactosidase, N terminal fragment from 3Dee 0.41 0.87
mu-Conotoxin GIIIa from 3Dee 0.41 0.87
Peptides
Alzheimer's disease amyloid peptides from 3Dee 0.82 4.08
Antifreeze polypeptide HPLC-6 from 3Dee 2.45 12.24
Atrial natriuretic peptide from 3Dee 0.41 2.04
Coagulation factor IX fragment (residues 1-47) from 3Dee 0.41 2.04
Coagulation factor VIII, membrane-binding peptide from 3Dee 0.41 2.04
Ferredoxin chloroplastic transit peptide from 3Dee 0.41 2.04
Gelsolin fragment (residues 150-169) from 3Dee 0.41 2.04
Glucagon from 3Dee 0.41 2.04
Liposaccharide-binding protein CAP18 (residues 106-137) from 3Dee 0.41 2.04
Mellitin from 3Dee 0.82 4.08
Pancreatic polypeptide from 3Dee 0.41 2.04
Parathyroid hormone fragment (residues 1-37) from 3Dee 0.41 2.04
Phospholamban, cytoplasmic domain residues 1-25 from 3Dee 0.41 2.04
Polymorphic antigen SPAM-H1 (residues 90-127) from 3Dee 0.41 2.04
Protein kinases (PK) Inhibitor from 3Dee 0.82 4.08
RP71935 from 3Dee 0.41 2.04
Simple Helix from 3Dee 0.41 2.04
Simple helix from 3Dee 4.49 22.45
Tertiapin from 3Dee 0.41 2.04
Transmembrane helical fragments from 3Dee 2.45 12.24
Vacuolar targeting peptide from NA-PROPI (residues 29-54) from 3Dee 0.41 2.04
two helices from 3Dee 0.82 4.08
Alpha and beta (a/b)
Insertion in Thioredoxin-like Domain of Glutathione Peroxidase from 3Dee 0.41 0.36
Alpha and beta (a+b)
A DNA topoisomerase I domain from 3Dee 0.41 0.52
Anti-LPS factor/recA domain from SCOP 0.41 0.52
C-type lectin from 3Dee 1.22 1.55
Lysozyme-like Domain II from 3Dee 0.82 1.04
S-adenosylmethionine synthetase. MAT inner domain from 3Dee 0.41 0.52
All beta
P-loop containing nucleotide triphosphate hydrolases small insert from 3Dee 0.82 0.89
Viral coat and capsid proteins from SCOP 3.27 3.57
All alpha
4-helical cytokines fragment from 3Dee 0.41 0.49
Anticodon-binding (C-terminal) domain of glutamyl-tRNA Domain I from 3Dee 0.41 0.49
Ectatomin, A & B chains from SCOP 0.41 0.49
Helix-loop-helix DNA-binding domain from SCOP 0.41 0.49
Heme-linked catalases N-terminal fragment from 3Dee 0.41 0.49
Hemocyanin, middle domain I from 3Dee 1.63 1.97
Immunoglobulin-binding protein A, fragment B from 3Dee 0.41 0.49
Long alpha-hairpin from SCOP 0.41 0.49
Oligomers of long helices from 3Dee 4.08 4.93
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase domain from 3Dee 0.82 0.99
Pheromone proteins from 3Dee 0.41 0.49
Prokaryotic histone-like protein from 3Dee 0.41 0.49
Pyruvate oxidase and decarboxylase, C terminal domain from 3Dee 0.41 0.49
beta-Lactamase/D-ala carboxypeptidasea inserted domain from 3Dee 0.41 0.49
small domain attached to TIM barrel from 3Dee 0.41 0.49

It is formed by merging the following clusters

Cluster 0

All domains in cluster 0 sub-divide into single membered clusters

1fmd4-1 [seq. related domains] All beta Viral coat and capsid proteins

Cluster 1

Descend tree into cluster 1

1rvf4-1 [seq. related domains] All beta Viral coat and capsid proteins
2mev4-1 [seq. related domains] All beta Viral coat and capsid proteins
1bgmp-1 [seq. related domains] Small proteins beta-Galactosidase, N terminal fragment
2bltb-2 [seq. related domains] All alpha beta-Lactamase/D-ala carboxypeptidasea inserted domain
1reqc-1 [seq. related domains] undefined undefined

Cluster 2

Descend tree into cluster 2

1vlk-2 [seq. related domains] All alpha 4-helical cytokines fragment
1yua-1 [seq. related domains] Alpha and beta (a+b) A DNA topoisomerase I domain
1htrp-1 [seq. related domains] Small proteins Acid protease presegment
1aml-1 [seq. related domains] Peptides Alzheimer's disease amyloid peptides
1amc-1 [seq. related domains] Peptides Alzheimer's disease amyloid peptides
2recf-2 [seq. related domains] Alpha and beta (a+b) Anti-LPS factor/recA domain
1gln-3 [seq. related domains] All alpha Anticodon-binding (C-terminal) domain of glutamyl-tRNA Domain I
1a2xb-1 [seq. related domains] Peptides Antifreeze polypeptide HPLC-6
1htn-1 [seq. related domains] Peptides Antifreeze polypeptide HPLC-6
1toh-2 [seq. related domains] Peptides Antifreeze polypeptide HPLC-6
1coi-1 [seq. related domains] Peptides Antifreeze polypeptide HPLC-6
1wfbb-1 [seq. related domains] Peptides Antifreeze polypeptide HPLC-6
1tiic-1 [seq. related domains] Peptides Antifreeze polypeptide HPLC-6
1atb-1 [seq. related domains] Small proteins Ascaris trypsin inhibitor
1anp-1 [seq. related domains] Peptides Atrial natriuretic peptide
1tcp-1 [seq. related domains] Small proteins BPTI-like
1tocu-2 [seq. related domains] Small proteins BPTI-like
1ca0i-1 [seq. related domains] Small proteins BPTI-like
2ech-1 [seq. related domains] Small proteins Blood coagulation inhibitor (disintegrin)
1preb-1 [seq. related domains] Alpha and beta (a+b) C-type lectin
1ixxf-2 [seq. related domains] Alpha and beta (a+b) C-type lectin
1bcpi-1 [seq. related domains] Alpha and beta (a+b) C-type lectin
7znf-1 [seq. related domains] Small proteins Classic zinc finger
1tf3a-3 [seq. related domains] Small proteins Classic zinc finger
2adr-1 [seq. related domains] Small proteins Classic zinc finger
1ubdc-4 [seq. related domains] Small proteins Classic zinc finger
1sp2-1 [seq. related domains] Small proteins Classic zinc finger
1a1ja-1 [seq. related domains] Small proteins Classic zinc finger
1ubdc-3 [seq. related domains] Small proteins Classic zinc finger
1tf6d-5 [seq. related domains] Small proteins Classic zinc finger
1sp1-1 [seq. related domains] Small proteins Classic zinc finger
1arf-1 [seq. related domains] Small proteins Classic zinc finger
2adr-2 [seq. related domains] Small proteins Classic zinc finger
1tf6d-4 [seq. related domains] Small proteins Classic zinc finger
1ubdc-1 [seq. related domains] Small proteins Classic zinc finger
1tf6d-6 [seq. related domains] Small proteins Classic zinc finger
1znm-1 [seq. related domains] Small proteins Classic zinc finger
1tf3a-1 [seq. related domains] Small proteins Classic zinc finger
1tf3a-2 [seq. related domains] Small proteins Classic zinc finger
1tf6d-1 [seq. related domains] Small proteins Classic zinc finger
1bbo-1 [seq. related domains] Small proteins Classic zinc finger
1znf-1 [seq. related domains] Small proteins Classic zinc finger
1a1ja-3 [seq. related domains] Small proteins Classic zinc finger
1ubdc-2 [seq. related domains] Small proteins Classic zinc finger
1mgx-1 [seq. related domains] Peptides Coagulation factor IX fragment (residues 1-47)
1fac-1 [seq. related domains] Peptides Coagulation factor VIII, membrane-binding peptide
1vve-1 [seq. related domains] Small proteins Complement control module
2bds-1 [seq. related domains] Small proteins Defensin-like
1dfnb-1 [seq. related domains] Small proteins Defensin-like
1apf-1 [seq. related domains] Small proteins Defensin-like
1bnb-1 [seq. related domains] Small proteins Defensin-like
1faxl-1 [seq. related domains] Small proteins EGF-like module
1zaq-1 [seq. related domains] Small proteins EGF-like module
1xdtr-1 [seq. related domains] Small proteins EGF-like module
1tpg-2 [seq. related domains] Small proteins EGF-like module
1ecib-1 [seq. related domains] All alpha Ectatomin, A & B chains
1edn-1 [seq. related domains] Small proteins Endothelin-like
1fct-1 [seq. related domains] Peptides Ferredoxin chloroplastic transit peptide
1fbr-2 [seq. related domains] Small proteins Fibronectin type I module
1tpn-1 [seq. related domains] Small proteins Fibronectin type I module
1pdc-1 [seq. related domains] Small proteins Fibronectin type II module
1sol-1 [seq. related domains] Peptides Gelsolin fragment (residues 150-169)
1gcn-1 [seq. related domains] Peptides Glucagon
5gata-1 [seq. related domains] Small proteins Glucocorticoid receptor-like (DNA-binding domain)
1iml-1 [seq. related domains] Small proteins Glucocorticoid receptor-like (DNA-binding domain)
1mfs-1 [seq. related domains] Small proteins HIV zinc finger-like domains
1mdyb-1 [seq. related domains] All alpha Helix-loop-helix DNA-binding domain
8cata-1 [seq. related domains] All alpha Heme-linked catalases N-terminal fragment
1oxy-2 [seq. related domains] All alpha Hemocyanin, middle domain I
1hc2-2 [seq. related domains] All alpha Hemocyanin, middle domain I
1nol-2 [seq. related domains] All alpha Hemocyanin, middle domain I
1ll1-2 [seq. related domains] All alpha Hemocyanin, middle domain I
1zdd-1 [seq. related domains] All alpha Immunoglobulin-binding protein A, fragment B
1gp1b-2 [seq. related domains] Alpha and beta (a/b) Insertion in Thioredoxin-like Domain of Glutathione Peroxidase
1bona-1 [seq. related domains] Small proteins Insulin-like
6rlxc-1 [seq. related domains] Small proteins Insulin-like
6rlxd-1 [seq. related domains] Small proteins Insulin-like
1bonb-1 [seq. related domains] Small proteins Insulin-like
1ajj-1 [seq. related domains] Small proteins Ligand-binding domain of low-density lipoprotein receptor
1lyp-1 [seq. related domains] Peptides Liposaccharide-binding protein CAP18 (residues 106-137)
1sera-1 [seq. related domains] All alpha Long alpha-hairpin
256l-2 [seq. related domains] Alpha and beta (a+b) Lysozyme-like Domain II
1lsg-2 [seq. related domains] Alpha and beta (a+b) Lysozyme-like Domain II
1gp2a-1 [seq. related domains] Peptides Mellitin
2mltb-1 [seq. related domains] Peptides Mellitin
1dmf-1 [seq. related domains] Small proteins Metallothionein
4mt2-1 [seq. related domains] Small proteins Metallothionein
1dmd-1 [seq. related domains] Small proteins Metallothionein
4mt2-2 [seq. related domains] Small proteins Metallothionein
1ans-1 [seq. related domains] Small proteins Neurotoxin III (ATX III)
1hup-1 [seq. related domains] All alpha Oligomers of long helices
2ifo-1 [seq. related domains] All alpha Oligomers of long helices
1fdm-1 [seq. related domains] All alpha Oligomers of long helices
1scma-1 [seq. related domains] All alpha Oligomers of long helices
1a02j-1 [seq. related domains] All alpha Oligomers of long helices
2dgca-1 [seq. related domains] All alpha Oligomers of long helices
1ltic-1 [seq. related domains] All alpha Oligomers of long helices
1a02f-1 [seq. related domains] All alpha Oligomers of long helices
1gcmc-1 [seq. related domains] All alpha Oligomers of long helices
4ifm-1 [seq. related domains] All alpha Oligomers of long helices
1tih-1 [seq. related domains] Small proteins Ovomucoid/PCI-1 like inhibitors
1ankb-2 [seq. related domains] All beta P-loop containing nucleotide triphosphate hydrolases small insert
1zip-2 [seq. related domains] All beta P-loop containing nucleotide triphosphate hydrolases small insert
1ron-1 [seq. related domains] Peptides Pancreatic polypeptide
1zwg-1 [seq. related domains] Peptides Parathyroid hormone fragment (residues 1-37)
1bbl-1 [seq. related domains] All alpha Peripheral subunit-binding domain of 2-oxo acid dehydrogenase domain
1ebdc-1 [seq. related domains] All alpha Peripheral subunit-binding domain of 2-oxo acid dehydrogenase domain
1erd-1 [seq. related domains] All alpha Pheromone proteins
1plp-1 [seq. related domains] Peptides Phospholamban, cytoplasmic domain residues 1-25
1psm-1 [seq. related domains] Peptides Polymorphic antigen SPAM-H1 (residues 90-127)
1hns-1 [seq. related domains] All alpha Prokaryotic histone-like protein
1tbo-1 [seq. related domains] Small proteins Protein kinase cystein-rich domain (cys2)
1cdkj-1 [seq. related domains] Peptides Protein kinases (PK) Inhibitor
1fmoi-1 [seq. related domains] Peptides Protein kinases (PK) Inhibitor
1pmc-1 [seq. related domains] Small proteins Proteinase inhibitor PMP-C
1powb-4 [seq. related domains] All alpha Pyruvate oxidase and decarboxylase, C terminal domain
1rpc-1 [seq. related domains] Peptides RP71935
1med-1 [seq. related domains] Small proteins Rubredoxin-like
1iro-1 [seq. related domains] Small proteins Rubredoxin-like
1qyp-1 [seq. related domains] Small proteins Rubredoxin-like
1fugb-4 [seq. related domains] Alpha and beta (a+b) S-adenosylmethionine synthetase. MAT inner domain
2dtb-1 [seq. related domains] Peptides Simple Helix
1cdlg-1 [seq. related domains] Peptides Simple helix
3mra-1 [seq. related domains] Peptides Simple helix
1a11-1 [seq. related domains] Peptides Simple helix
1oeg-1 [seq. related domains] Peptides Simple helix
1zec-1 [seq. related domains] Peptides Simple helix
1etgb-1 [seq. related domains] Peptides Simple helix
1odr-1 [seq. related domains] Peptides Simple helix
2nr1-1 [seq. related domains] Peptides Simple helix
1pei-1 [seq. related domains] Peptides Simple helix
2bbnb-1 [seq. related domains] Peptides Simple helix
2mag-1 [seq. related domains] Peptides Simple helix
2pta-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1wgtb-3 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1agg-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1mvj-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
4cpai-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1azk-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
2cco-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1chl-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1tabi-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1kal-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1omg-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1bi6h-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1mcti-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1omn-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1scy-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1ica-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1acw-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1lqq-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1bah-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1myn-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1gur-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1mmc-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1ayj-1 [seq. related domains] Small proteins Small inhibitors, toxins, lectins
1ter-1 [seq. related domains] Peptides Tertiapin
1hic-1 [seq. related domains] Small proteins Thrombin inhibitors
1dec-1 [seq. related domains] Small proteins Thrombin inhibitors
1aty-1 [seq. related domains] Peptides Transmembrane helical fragments
1spf-1 [seq. related domains] Peptides Transmembrane helical fragments
1bct-1 [seq. related domains] Peptides Transmembrane helical fragments
1peh-1 [seq. related domains] Peptides Transmembrane helical fragments
1btr-1 [seq. related domains] Peptides Transmembrane helical fragments
1btt-1 [seq. related domains] Peptides Transmembrane helical fragments
2pspb-2 [seq. related domains] Small proteins Trefoil
1vtp-1 [seq. related domains] Peptides Vacuolar targeting peptide from NA-PROPI (residues 29-54)
1tmf4-1 [seq. related domains] All beta Viral coat and capsid proteins
2bpa3-1 [seq. related domains] All beta Viral coat and capsid proteins
2mev2-1 [seq. related domains] All beta Viral coat and capsid proteins
1dhx-5 [seq. related domains] All beta Viral coat and capsid proteins
1dhx-1 [seq. related domains] All beta Viral coat and capsid proteins
1ajyb-3 [seq. related domains] Small proteins Zn2/Cys6 DNA-binding domain
1pyib-3 [seq. related domains] Small proteins Zn2/Cys6 DNA-binding domain
1tck-1 [seq. related domains] Small proteins mu-Conotoxin GIIIa
1edg-2 [seq. related domains] All alpha small domain attached to TIM barrel
1pona-1 [seq. related domains] Peptides two helices
1ponb-1 [seq. related domains] Peptides two helices
1novd-1 [seq. related domains] undefined undefined
1yuja-1 [seq. related domains] undefined undefined
1ae9b-2 [seq. related domains] undefined undefined
1bgk-1 [seq. related domains] undefined undefined
2ezea-1 [seq. related domains] undefined undefined
1mof-1 [seq. related domains] undefined undefined
1avfq-1 [seq. related domains] undefined undefined
1opp-1 [seq. related domains] undefined undefined
1dsk-1 [seq. related domains] undefined undefined
2glia-3 [seq. related domains] undefined undefined
1rmd-2 [seq. related domains] undefined undefined
1dorb-2 [seq. related domains] undefined undefined
1av1d-1 [seq. related domains] undefined undefined
1ayn4-1 [seq. related domains] undefined undefined
1pft-1 [seq. related domains] undefined undefined
1dsl-1 [seq. related domains] undefined undefined
1aqs-1 [seq. related domains] undefined undefined
1tsg-1 [seq. related domains] undefined undefined
1cuk-3 [seq. related domains] undefined undefined
1aiw-1 [seq. related domains] undefined undefined
1axh-1 [seq. related domains] undefined undefined
1vaob-4 [seq. related domains] undefined undefined
1hcw-1 [seq. related domains] undefined undefined
1fsv-1 [seq. related domains] undefined undefined
1div-1 [seq. related domains] undefined undefined
4hb1-1 [seq. related domains] undefined undefined
2bbg-1 [seq. related domains] undefined undefined
2brz-1 [seq. related domains] undefined undefined
1dar-3 [seq. related domains] undefined undefined
1zto-1 [seq. related domains] undefined undefined
1al0b-1 [seq. related domains] undefined undefined
1atic-1 [seq. related domains] undefined undefined
3leu-1 [seq. related domains] undefined undefined
2vgh-1 [seq. related domains] undefined undefined
1a1rd-1 [seq. related domains] undefined undefined
2erl-1 [seq. related domains] undefined undefined
1zfo-1 [seq. related domains] undefined undefined
1roo-1 [seq. related domains] undefined undefined
1prb-1 [seq. related domains] undefined undefined
1ztn-1 [seq. related domains] undefined undefined
1ery-1 [seq. related domains] undefined undefined
1jswc-3 [seq. related domains] undefined undefined
1fre-1 [seq. related domains] undefined undefined
1abz-1 [seq. related domains] undefined undefined
1apq-1 [seq. related domains] undefined undefined
2adx-1 [seq. related domains] undefined undefined
1aqt-2 [seq. related domains] undefined undefined
1aie-1 [seq. related domains] undefined undefined
1vpu-1 [seq. related domains] undefined undefined
1vii-1 [seq. related domains] undefined undefined
1apj-1 [seq. related domains] undefined undefined
1loi-1 [seq. related domains] undefined undefined
1qdp-1 [seq. related domains] undefined undefined
1ryt-2 [seq. related domains] undefined undefined
1alg-1 [seq. related domains] undefined undefined
1melb-2 [seq. related domains] undefined undefined
1ag7-1 [seq. related domains] undefined undefined
1dxgb-1 [seq. related domains] undefined undefined
1fge-1 [seq. related domains] undefined undefined
1p1p-1 [seq. related domains] undefined undefined
2ppsk-1 [seq. related domains] undefined undefined

Enter PDB code - optionally suffixing the code with the chain id.


3dee@compbio.dundee.ac.uk