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3NVD

Structure of YBBD in complex with pugnac

Replaces:  3CQM
Functional Information from GO Data
ChainGOidnamespacecontents
A0004553molecular_functionhydrolase activity, hydrolyzing O-glycosyl compounds
A0005975biological_processcarbohydrate metabolic process
B0004553molecular_functionhydrolase activity, hydrolyzing O-glycosyl compounds
B0005975biological_processcarbohydrate metabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues19
DetailsBINDING SITE FOR RESIDUE OAN A 646
ChainResidue
AILE90
AMET267
AASP318
AALA319
AASN321
AMET322
ANA643
AHOH896
AHOH999
BHOH871
BHOH1084
APHE92
AASP123
AVAL187
AARG191
ALYS221
AHIS222
ASER233
AHIS234

site_idAC2
Number of Residues11
DetailsBINDING SITE FOR RESIDUE PG4 A 647
ChainResidue
AASP34
AILE38
AILE394
ATYR399
APRO400
ATHR531
AILE532
ASER533
AHOH1257
AHOH1259
AHOH1286

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA A 643
ChainResidue
AHIS226
ASER233
AHIS270
AASP318
AMET322
AOAN646

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ACT A 644
ChainResidue
APRO274
AASP277
AASP278
ALYS299
ALYS425
AHOH1123

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT A 645
ChainResidue
AGLN272
AILE290
ALEU291
ALYS477
AARG478

site_idAC6
Number of Residues17
DetailsBINDING SITE FOR RESIDUE OAN B 646
ChainResidue
BARG57
BILE90
BPHE92
BASP123
BARG191
BLYS221
BHIS222
BSER233
BHIS234
BMET267
BASP318
BALA319
BASN321
BMET322
BMET348
BHOH707
BHOH867

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 643
ChainResidue
BHIS226
BSER233
BALA269
BHIS270
BASP318

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT B 644
ChainResidue
BASP230
BVAL231
BPRO238
BLEU239
BHOH1289

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ACT B 645
ChainResidue
BASN181
BHIS242
BARG246
BGLU251
BHOH955

Functional Information from PROSITE/UniProt
site_idPS00775
Number of Residues18
DetailsGLYCOSYL_HYDROL_F3 Glycosyl hydrolases family 3 active site. LLRqEmgfnGVIVTDalN
ChainResidueDetails
ALEU304-ASN321

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsActive site: {"description":"Proton donor/acceptor","evidences":[{"source":"PubMed","id":"20826810","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23177201","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2
DetailsActive site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"20826810","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23177201","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"20826810","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23177201","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsSite: {"description":"Important for catalytic activity","evidences":[{"source":"PubMed","id":"20826810","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

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PDB entries from 2025-11-12

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