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4B8Z

Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, rhombohedral crystal form

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0005515molecular_functionprotein binding
A0005829cellular_componentcytosol
A0007159biological_processleukocyte cell-cell adhesion
A0008152biological_processmetabolic process
A0009055molecular_functionelectron transfer activity
A0009226biological_processnucleotide-sugar biosynthetic process
A0010595biological_processpositive regulation of endothelial cell migration
A0016491molecular_functionoxidoreductase activity
A0016853molecular_functionisomerase activity
A0019673biological_processGDP-mannose metabolic process
A0042351biological_process'de novo' GDP-L-fucose biosynthetic process
A0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
A0042802molecular_functionidentical protein binding
A0047918molecular_functionGDP-mannose 3,5-epimerase activity
A0050577molecular_functionGDP-L-fucose synthase activity
A0070062cellular_componentextracellular exosome
A1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
B0003824molecular_functioncatalytic activity
B0005515molecular_functionprotein binding
B0005829cellular_componentcytosol
B0007159biological_processleukocyte cell-cell adhesion
B0008152biological_processmetabolic process
B0009055molecular_functionelectron transfer activity
B0009226biological_processnucleotide-sugar biosynthetic process
B0010595biological_processpositive regulation of endothelial cell migration
B0016491molecular_functionoxidoreductase activity
B0016853molecular_functionisomerase activity
B0019673biological_processGDP-mannose metabolic process
B0042351biological_process'de novo' GDP-L-fucose biosynthetic process
B0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
B0042802molecular_functionidentical protein binding
B0047918molecular_functionGDP-mannose 3,5-epimerase activity
B0050577molecular_functionGDP-L-fucose synthase activity
B0070062cellular_componentextracellular exosome
B1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
C0003824molecular_functioncatalytic activity
C0005515molecular_functionprotein binding
C0005829cellular_componentcytosol
C0007159biological_processleukocyte cell-cell adhesion
C0008152biological_processmetabolic process
C0009055molecular_functionelectron transfer activity
C0009226biological_processnucleotide-sugar biosynthetic process
C0010595biological_processpositive regulation of endothelial cell migration
C0016491molecular_functionoxidoreductase activity
C0016853molecular_functionisomerase activity
C0019673biological_processGDP-mannose metabolic process
C0042351biological_process'de novo' GDP-L-fucose biosynthetic process
C0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
C0042802molecular_functionidentical protein binding
C0047918molecular_functionGDP-mannose 3,5-epimerase activity
C0050577molecular_functionGDP-L-fucose synthase activity
C0070062cellular_componentextracellular exosome
C1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
D0003824molecular_functioncatalytic activity
D0005515molecular_functionprotein binding
D0005829cellular_componentcytosol
D0007159biological_processleukocyte cell-cell adhesion
D0008152biological_processmetabolic process
D0009055molecular_functionelectron transfer activity
D0009226biological_processnucleotide-sugar biosynthetic process
D0010595biological_processpositive regulation of endothelial cell migration
D0016491molecular_functionoxidoreductase activity
D0016853molecular_functionisomerase activity
D0019673biological_processGDP-mannose metabolic process
D0042351biological_process'de novo' GDP-L-fucose biosynthetic process
D0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
D0042802molecular_functionidentical protein binding
D0047918molecular_functionGDP-mannose 3,5-epimerase activity
D0050577molecular_functionGDP-L-fucose synthase activity
D0070062cellular_componentextracellular exosome
D1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
Functional Information from PDB Data
site_idAC1
Number of Residues23
DetailsBINDING SITE FOR RESIDUE NAP A 900
ChainResidue
AGLY14
ALEU48
ALEU69
AALA71
AVAL73
AMET93
ACYS112
ALEU113
ASER114
ATYR143
ALYS147
ASER16
APRO170
ATHR171
AASN172
AVAL173
AGLY17
ALEU18
AVAL19
ASER42
ASER43
AALA46
AASP47

site_idAC2
Number of Residues17
DetailsBINDING SITE FOR RESIDUE GDP A 901
ChainResidue
AGLY75
ALEU76
AASN172
AGLY185
AHIS186
AVAL187
AGLY190
ALYS194
ATRP208
AGLY209
APRO213
AARG215
AILE252
ASER276
AASP277
ALYS282
AHOH2003

site_idAC3
Number of Residues26
DetailsBINDING SITE FOR RESIDUE NAP B 900
ChainResidue
BGLY14
BSER16
BGLY17
BLEU18
BVAL19
BSER42
BSER43
BALA46
BASP47
BLEU48
BLEU69
BALA70
BALA71
BVAL73
BMET93
BCYS112
BLEU113
BSER114
BTYR143
BLYS147
BPRO170
BTHR171
BVAL173
BHIS186
BARG320
BHOH2001

site_idAC4
Number of Residues16
DetailsBINDING SITE FOR RESIDUE GDP B 901
ChainResidue
BGLY75
BLEU76
BPHE77
BASN172
BGLY185
BHIS186
BVAL187
BLYS194
BTRP208
BGLY209
BPRO213
BARG215
BILE252
BSER276
BASP277
BLYS282

site_idAC5
Number of Residues26
DetailsBINDING SITE FOR RESIDUE NAP C 900
ChainResidue
CSER114
CTYR143
CLYS147
CPRO170
CTHR171
CVAL173
CHIS186
CARG320
CHOH2001
CGLY14
CSER16
CGLY17
CLEU18
CVAL19
CSER42
CSER43
CALA46
CASP47
CLEU48
CLEU69
CALA70
CALA71
CVAL73
CMET93
CCYS112
CLEU113

site_idAC6
Number of Residues15
DetailsBINDING SITE FOR RESIDUE GDP C 901
ChainResidue
CGLY75
CLEU76
CPHE77
CASN172
CGLY185
CHIS186
CVAL187
CLYS194
CTRP208
CGLY209
CPRO213
CARG215
CSER276
CASP277
CLYS282

site_idAC7
Number of Residues26
DetailsBINDING SITE FOR RESIDUE NAP D 900
ChainResidue
DGLY14
DSER16
DGLY17
DLEU18
DVAL19
DSER42
DSER43
DALA46
DASP47
DLEU48
DLEU69
DALA70
DALA71
DVAL73
DMET93
DCYS112
DLEU113
DSER114
DTYR143
DLYS147
DPRO170
DTHR171
DASN172
DVAL173
DHIS186
DARG320

site_idAC8
Number of Residues14
DetailsBINDING SITE FOR RESIDUE GDP D 901
ChainResidue
DGLY75
DLEU76
DPHE77
DASN172
DGLY185
DHIS186
DVAL187
DLYS194
DTRP208
DPRO213
DARG215
DSER276
DASP277
DLYS282

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE: Proton donor/acceptor => ECO:0000250
ChainResidueDetails
ATYR143
BTYR143
CTYR143
DTYR143

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:23774504, ECO:0000269|Ref.9
ChainResidueDetails
AGLY14
DGLY14
DLYS147
DPRO170
ALYS147
APRO170
BGLY14
BLYS147
BPRO170
CGLY14
CLYS147
CPRO170

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|Ref.9
ChainResidueDetails
AHIS186
BHIS186
CHIS186
DHIS186

site_idSWS_FT_FI4
Number of Residues16
DetailsBINDING: BINDING => ECO:0000305|Ref.9
ChainResidueDetails
ALYS194
CTRP208
CARG215
CASP277
DLYS194
DTRP208
DARG215
DASP277
ATRP208
AARG215
AASP277
BLYS194
BTRP208
BARG215
BASP277
CLYS194

site_idSWS_FT_FI5
Number of Residues8
DetailsSITE: Important for catalytic activity => ECO:0000250
ChainResidueDetails
ASER114
ACYS116
BSER114
BCYS116
CSER114
CCYS116
DSER114
DCYS116

site_idSWS_FT_FI6
Number of Residues4
DetailsSITE: Lowers pKa of active site Tyr => ECO:0000250
ChainResidueDetails
ALYS147
BLYS147
CLYS147
DLYS147

218853

PDB entries from 2024-04-24

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