3 Dee - Database of Protein Domain Definitions

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The current cluster is formed at a score of 1.009

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Classes% of representative set
undefined 39.71
Small proteins 2.94
Peptides 0.74
Alpha and beta (a/b) 3.68
Alpha and beta (a+b) 3.68
All beta 0.74
All alpha 48.53
Breakdown into folds% of cluster % of class
undefined
undefined from 3Dee 39.71 8.49
Small proteins
Crambin-like from SCOP 0.74 0.87
Glucocorticoid receptor-like (DNA-binding domain) from SCOP 0.74 0.87
Heat-stable enterotoxin B from 3Dee 0.74 0.87
Insulin-like from SCOP 0.74 0.87
Peptides
Transmembrane helical fragments from 3Dee 0.74 2.04
Alpha and beta (a/b)
ATP pyrophosphatases extra domain from 3Dee 0.74 0.36
Barstar (barnase inhibitor) from SCOP 0.74 0.36
DNA-binding winged domain from 3Dee 1.47 0.73
DNA/RNA polymerases Domain III from 3Dee 0.74 0.36
Alpha and beta (a+b)
Nucleotidyltransferases Domain II from 3Dee 0.74 0.52
Ribosome inactivating proteins (RIP) Domain II from 3Dee 1.47 1.04
The intermediate domain of GroEL from 3Dee 0.74 0.52
Urease, gamma-subunit from SCOP 0.74 0.52
All beta
Single-stranded left-handed beta-helix Domain II from 3Dee 0.74 0.45
All alpha
4-helical cytokines Short chain from 3Dee 0.74 0.49
Acyl-CoA binding protein from 3Dee 0.74 0.49
Anaphylotoxins (complement system) from SCOP 0.74 0.49
Annexin Domain from 3Dee 1.47 0.99
Anticodon-binding (C-terminal) domain of glutamyl-tRNA Domain II from 3Dee 0.74 0.49
Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin from SCOP 2.21 1.48
Citrate synthase Domain II from 3Dee 1.47 0.99
DNA polymerase beta, N-terminal (8 kD)-domain from 3Dee 0.74 0.49
DNA-binding 3-helical bundle from 3Dee 11.03 7.39
Diphtheria toxin repressor (DtxR) dimerization domain from 3Dee 0.74 0.49
Disulphide-bond formation facilitator (DSBA), insertion domain from SCOP 0.74 0.49
EF-hand from 3Dee 1.47 0.99
Endonuclease III from 3Dee 0.74 0.49
FIS protein from 3Dee 0.74 0.49
Four-helical up-and-down bundle from SCOP 0.74 0.49
Heme-linked catalases C-terminal domain from 3Dee 0.74 0.49
Hemocyanin, N-terminal domain from SCOP 1.47 0.99
Hexokinase all helical domain from 3Dee 0.74 0.49
Immunoglobulin-binding protein A, fragment B from 3Dee 0.74 0.49
Long alpha-hairpin from SCOP 2.21 1.48
Mu transposase, DNA-binding domain from 3Dee 0.74 0.49
Nucleotidyltransferases Domain III from 3Dee 0.74 0.49
Oligomers of long helices from 3Dee 2.21 1.48
ROP protein from 3Dee 0.74 0.49
Restriction endonucleases helical domain from 3Dee 0.74 0.49
Retroviral matrix proteins from SCOP 0.74 0.49
Spectrin repeat unit from 3Dee 0.74 0.49
Thermolysin-like metalloproteases, C-terminal domain from SCOP 0.74 0.49
Thymidine phosphorylase Domain I from 3Dee 0.74 0.49
Trp repressor from SCOP 0.74 0.49
Uteroglobin-like from SCOP 0.74 0.49
Winged DNA binding like from 3Dee 0.74 0.49
lambda repressor-like DNA-binding domains from SCOP 5.88 3.94
small domain attached to TIM barrel from 3Dee 0.74 0.49
the C-terminal domain of RNA polymerase alpha subunit from 3Dee 0.74 0.49

It is formed by merging the following clusters

Cluster 1

Descend tree into cluster 1

1aeif-3 [seq. related domains] All alpha Annexin Domain
1aeif-2 [seq. related domains] All alpha Annexin Domain
1gln-4 [seq. related domains] All alpha Anticodon-binding (C-terminal) domain of glutamyl-tRNA Domain II
1hssd-1 [seq. related domains] All alpha Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
1hyp-1 [seq. related domains] All alpha Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
1jtb-1 [seq. related domains] All alpha Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
1bnp-1 [seq. related domains] All alpha DNA polymerase beta, N-terminal (8 kD)-domain
1leb-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
2cgpc-2 [seq. related domains] All alpha DNA-binding 3-helical bundle
1hstb-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
1bib-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
2dtr-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
1awca-1 [seq. related domains] Alpha and beta (a/b) DNA-binding winged domain
3hsf-1 [seq. related domains] Alpha and beta (a/b) DNA-binding winged domain
1ktq-4 [seq. related domains] Alpha and beta (a/b) DNA/RNA polymerases Domain III
2mysa-4 [seq. related domains] All alpha EF-hand
1wdca-2 [seq. related domains] All alpha EF-hand
2abk-2 [seq. related domains] All alpha Endonuclease III
1hiws-1 [seq. related domains] All alpha Retroviral matrix proteins
1aonn-2 [seq. related domains] Alpha and beta (a+b) The intermediate domain of GroEL
1tpt-1 [seq. related domains] All alpha Thymidine phosphorylase Domain I
1jhga-1 [seq. related domains] All alpha Trp repressor
1a5oa-1 [seq. related domains] Alpha and beta (a+b) Urease, gamma-subunit
1utrb-1 [seq. related domains] All alpha Uteroglobin-like
1ecl-4 [seq. related domains] All alpha Winged DNA binding like
1jkw-1 [seq. related domains] undefined undefined
1ns1b-1 [seq. related domains] undefined undefined
1a0p-1 [seq. related domains] undefined undefined
1sfe-2 [seq. related domains] undefined undefined
1ezd-2 [seq. related domains] undefined undefined
1ignb-2 [seq. related domains] undefined undefined
1abv-1 [seq. related domains] undefined undefined
1gnd-2 [seq. related domains] undefined undefined
2ppsl-1 [seq. related domains] undefined undefined
2ezl-1 [seq. related domains] undefined undefined
1al04-1 [seq. related domains] undefined undefined
1iba-1 [seq. related domains] undefined undefined
1foy-1 [seq. related domains] undefined undefined
1gtpc-3 [seq. related domains] undefined undefined
2hfh-1 [seq. related domains] undefined undefined
1aisb-2 [seq. related domains] undefined undefined
1occu-1 [seq. related domains] undefined undefined
1if1b-1 [seq. related domains] undefined undefined
2fokb-3 [seq. related domains] undefined undefined
1bax-1 [seq. related domains] undefined undefined
1opc-1 [seq. related domains] undefined undefined
2fusb-1 [seq. related domains] undefined undefined
1ytfc-1 [seq. related domains] undefined undefined
1aoy-1 [seq. related domains] undefined undefined
1jkw-2 [seq. related domains] undefined undefined
1vhrb-1 [seq. related domains] undefined undefined
1pnbb-1 [seq. related domains] undefined undefined
1jsub-1 [seq. related domains] undefined undefined
1jsub-2 [seq. related domains] undefined undefined

Cluster 2

Descend tree into cluster 2

1vlk-1 [seq. related domains] All alpha 4-helical cytokines Short chain
2abd-1 [seq. related domains] All alpha Acyl-CoA binding protein
1cfaa-1 [seq. related domains] All alpha Anaphylotoxins (complement system)
1a19b-1 [seq. related domains] Alpha and beta (a/b) Barstar (barnase inhibitor)
1aj8b-2 [seq. related domains] All alpha Citrate synthase Domain II
3cts-2 [seq. related domains] All alpha Citrate synthase Domain II
1f36b-1 [seq. related domains] All alpha FIS protein
1lbid-3 [seq. related domains] All alpha Four-helical up-and-down bundle
8cata-3 [seq. related domains] All alpha Heme-linked catalases C-terminal domain
1nol-1 [seq. related domains] All alpha Hemocyanin, N-terminal domain
1hc2-1 [seq. related domains] All alpha Hemocyanin, N-terminal domain
1spzz-1 [seq. related domains] All alpha Immunoglobulin-binding protein A, fragment B
1ktq-2 [seq. related domains] All alpha Long alpha-hairpin
1grj-1 [seq. related domains] All alpha Long alpha-hairpin
1kfd-2 [seq. related domains] All alpha Long alpha-hairpin
1afd3-1 [seq. related domains] All alpha Oligomers of long helices
1gtoa-1 [seq. related domains] All alpha ROP protein
1pvib-1 [seq. related domains] All alpha Restriction endonucleases helical domain
2spcb-2 [seq. related domains] All alpha Spectrin repeat unit
1bhb-1 [seq. related domains] Peptides Transmembrane helical fragments
1beo-1 [seq. related domains] undefined undefined
1lre-1 [seq. related domains] undefined undefined
1tdtc-1 [seq. related domains] undefined undefined
2hp8-1 [seq. related domains] undefined undefined
1tbgh-1 [seq. related domains] undefined undefined
1aikn-1 [seq. related domains] undefined undefined
1sly-2 [seq. related domains] undefined undefined
1sknp-1 [seq. related domains] undefined undefined
1ajyb-2 [seq. related domains] undefined undefined
1afob-1 [seq. related domains] undefined undefined
1ab3-1 [seq. related domains] undefined undefined

Cluster 3

Descend tree into cluster 3

1qtqa-3 [seq. related domains] Alpha and beta (a/b) ATP pyrophosphatases extra domain
1ab1-1 [seq. related domains] Small proteins Crambin-like
1a5j-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
1ret-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
1akha-2 [seq. related domains] All alpha DNA-binding 3-helical bundle
1vnd-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
1hdp-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
1pdnc-2 [seq. related domains] All alpha DNA-binding 3-helical bundle
1hcra-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
2lfb-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
1akha-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
1pdnc-1 [seq. related domains] All alpha DNA-binding 3-helical bundle
2dtr-2 [seq. related domains] All alpha Diphtheria toxin repressor (DtxR) dimerization domain
1acvb-2 [seq. related domains] All alpha Disulphide-bond formation facilitator (DSBA), insertion domain
2nlla-1 [seq. related domains] Small proteins Glucocorticoid receptor-like (DNA-binding domain)
1ehs-1 [seq. related domains] Small proteins Heat-stable enterotoxin B
2yhx-1 [seq. related domains] All alpha Hexokinase all helical domain
1sju-1 [seq. related domains] Small proteins Insulin-like
1tnt-1 [seq. related domains] All alpha Mu transposase, DNA-binding domain
2bpgb-3 [seq. related domains] Alpha and beta (a+b) Nucleotidyltransferases Domain II
1bpza-1 [seq. related domains] All alpha Nucleotidyltransferases Domain III
1d66b-2 [seq. related domains] All alpha Oligomers of long helices
1pyib-2 [seq. related domains] All alpha Oligomers of long helices
1ifu-2 [seq. related domains] Alpha and beta (a+b) Ribosome inactivating proteins (RIP) Domain II
1bryz-2 [seq. related domains] Alpha and beta (a+b) Ribosome inactivating proteins (RIP) Domain II
1lxa-2 [seq. related domains] All beta Single-stranded left-handed beta-helix Domain II
1trlb-1 [seq. related domains] All alpha Thermolysin-like metalloproteases, C-terminal domain
1lmb4-1 [seq. related domains] All alpha lambda repressor-like DNA-binding domains
2r63-1 [seq. related domains] All alpha lambda repressor-like DNA-binding domains
1au7b-1 [seq. related domains] All alpha lambda repressor-like DNA-binding domains
1uxd-1 [seq. related domains] All alpha lambda repressor-like DNA-binding domains
1adr-1 [seq. related domains] All alpha lambda repressor-like DNA-binding domains
2puga-1 [seq. related domains] All alpha lambda repressor-like DNA-binding domains
1lbgd-5 [seq. related domains] All alpha lambda repressor-like DNA-binding domains
1ner-1 [seq. related domains] All alpha lambda repressor-like DNA-binding domains
1cec-2 [seq. related domains] All alpha small domain attached to TIM barrel
1coo-1 [seq. related domains] All alpha the C-terminal domain of RNA polymerase alpha subunit
1vib-1 [seq. related domains] undefined undefined
1taq-2 [seq. related domains] undefined undefined
1jud-2 [seq. related domains] undefined undefined
1wjdb-1 [seq. related domains] undefined undefined
1exnb-2 [seq. related domains] undefined undefined
2ezi-1 [seq. related domains] undefined undefined
1nkl-1 [seq. related domains] undefined undefined
1sly-4 [seq. related domains] undefined undefined
1cuk-2 [seq. related domains] undefined undefined
1aum-1 [seq. related domains] undefined undefined
1huib-1 [seq. related domains] undefined undefined
1tc3c-1 [seq. related domains] undefined undefined
1af7-1 [seq. related domains] undefined undefined
2fusb-3 [seq. related domains] undefined undefined

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

3dee@compbio.dundee.ac.uk