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1CVR

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

Functional Information from GO Data
ChainGOidnamespacecontents
A0006508biological_processproteolysis
A0008233molecular_functionpeptidase activity
A0008234molecular_functioncysteine-type peptidase activity
Functional Information from PDB Data
site_idAC1
Number of Residues16
DetailsBINDING SITE FOR RESIDUE H37 A 501
ChainResidue
AASP163
AGLN282
ATYR283
ATRP284
AMET288
AHOH640
AHOH724
AHOH772
ATHR191
APRO192
AGLY210
AHIS211
AGLY212
AHIS221
AVAL242
ACYS244

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 502
ChainResidue
AGLU161
AHIS166
AASP292
AHOH717
AHOH818
AHOH882

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 503
ChainResidue
AASP78
APHE249
AGLU258
AHOH632
AHOH672
AHOH690

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 504
ChainResidue
AVAL100
AASP103
ATYR105
AGLU107
AHOH716
AHOH819

site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE CA A 505
ChainResidue
AGLU293
AGLU296
AHIS302
AHOH619

site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE CA A 506
ChainResidue
AHIS221
AASP328
AHOH646
AHOH677

site_idAC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN A 507
ChainResidue
AGLU152
AHIS211
ATRP284
ALYS327
AHOH724
AHOH920

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CA A 508
ChainResidue
AGLU119
AASP387
AGLU405
AHOH712
AHOH922

site_idAC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 509
ChainResidue
AHIS130
AASN134
AHOH852
AHOH921

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"10523290","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1CVR","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues1
DetailsActive site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"23558682","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10523290","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1CVR","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues9
DetailsBinding site: {"evidences":[{"source":"PDB","id":"1CVR","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PDB","id":"1CVR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4IEF","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PDB","id":"4IEF","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues5
Detailsa catalytic site defined by CSA, PubMed 10523290
ChainResidueDetails
AGLY212
AGLU152
AHIS211
ACYS244
ACYS244

site_idMCSA1
Number of Residues4
DetailsM-CSA 806
ChainResidueDetails
AGLU152electrostatic stabiliser
AHIS211proton acceptor, proton donor
AGLY212electrostatic stabiliser
ACYS244electrostatic stabiliser

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PDB entries from 2025-07-09

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