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1XD3

Crystal structure of UCHL3-UbVME complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0004843molecular_functioncysteine-type deubiquitinase activity
A0005515molecular_functionprotein binding
A0005654cellular_componentnucleoplasm
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006508biological_processproteolysis
A0006511biological_processubiquitin-dependent protein catabolic process
A0008233molecular_functionpeptidase activity
A0008234molecular_functioncysteine-type peptidase activity
A0016567biological_processprotein ubiquitination
A0016579biological_processprotein deubiquitination
A0019784molecular_functiondeNEDDylase activity
A0030163biological_processprotein catabolic process
A0043130molecular_functionubiquitin binding
A0043687biological_processpost-translational protein modification
C0004843molecular_functioncysteine-type deubiquitinase activity
C0005515molecular_functionprotein binding
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006508biological_processproteolysis
C0006511biological_processubiquitin-dependent protein catabolic process
C0008233molecular_functionpeptidase activity
C0008234molecular_functioncysteine-type peptidase activity
C0016567biological_processprotein ubiquitination
C0016579biological_processprotein deubiquitination
C0019784molecular_functiondeNEDDylase activity
C0030163biological_processprotein catabolic process
C0043130molecular_functionubiquitin binding
C0043687biological_processpost-translational protein modification
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG C 2001
ChainResidue
AHOH2246
CASP163
CHOH2129
CHOH2193
CHOH2366

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG C 2002
ChainResidue
CHOH2194
CHOH2281
AHOH2123
AHOH2191
AHOH2227
CHOH2150

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG C 2003
ChainResidue
CHIS179
CHOH2184
CHOH2185
CHOH2191
CHOH2270
CHOH2374

site_idAC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE MG C 2004
ChainResidue
CMG2005
CHOH2065
CHOH2072
CHOH2169
CHOH2190
CHOH2249
CHOH2397
CHOH2425

site_idAC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MG C 2005
ChainResidue
CGLN78
CASP79
CMG2004
CHOH2169
CHOH2181
CHOH2190
CHOH2249

site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG A 2006
ChainResidue
ALYS108
AASP109
AHOH2346
BHOH1243

site_idAC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG C 2007
ChainResidue
CGLU149
CHOH2069
CHOH2078
CHOH2433

site_idAC8
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MG C 2008
ChainResidue
CASP79
CTHR81
CTYR181

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 2009
ChainResidue
AHOH2264
AHOH2305
DHOH2344
DHOH2347
DHOH2354

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG A 2010
ChainResidue
ALYS21
AGLY24
ALEU25
AGLU114

site_idBC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GVE B 1176
ChainResidue
AILE58
AGLN89
AASN93
ACYS95
AVAL166
ALEU168
AHIS169
BGLY75

site_idBC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GVE D 2276
ChainResidue
CGLN89
CASN93
CCYS95
CVAL166
CLEU168
CHIS169
CHOH2432
DGLY75

Functional Information from PROSITE/UniProt
site_idPS00140
Number of Residues17
DetailsUCH_1 Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. QtisNACGtigLIHAIA
ChainResidueDetails
AGLN89-ALA105

site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
BLYS27-ASP52

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Nucleophile => ECO:0000269|PubMed:19154770, ECO:0000269|PubMed:20380862, ECO:0000269|PubMed:9790970
ChainResidueDetails
ACYS95
CCYS95

site_idSWS_FT_FI2
Number of Residues2
DetailsACT_SITE: Proton donor => ECO:0000250|UniProtKB:P09936
ChainResidueDetails
AHIS169
CHIS169

site_idSWS_FT_FI3
Number of Residues2
DetailsSITE: Important for enzyme activity => ECO:0000250|UniProtKB:P09936
ChainResidueDetails
AASP184
CASP184

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569
ChainResidueDetails
ASER130
CSER130

Catalytic Information from CSA
site_idCSA1
Number of Residues4
DetailsAnnotated By Reference To The Literature 1uch
ChainResidueDetails
ACYS95
AHIS169
AASP184
AGLN89

site_idCSA2
Number of Residues4
DetailsAnnotated By Reference To The Literature 1uch
ChainResidueDetails
CCYS95
CHIS169
CASP184
CGLN89

site_idMCSA1
Number of Residues4
DetailsM-CSA 597
ChainResidueDetails
AGLN89electrostatic stabiliser
ACYS95covalent catalysis, proton shuttle (general acid/base)
AHIS169proton shuttle (general acid/base)
AASP184electrostatic stabiliser

site_idMCSA2
Number of Residues4
DetailsM-CSA 597
ChainResidueDetails
CGLN89electrostatic stabiliser
CCYS95covalent catalysis, proton shuttle (general acid/base)
CHIS169proton shuttle (general acid/base)
CASP184electrostatic stabiliser

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PDB entries from 2024-09-18

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