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4BL5

Crystal structure of human GDP-L-fucose synthase with bound NADP and product GDP-L-fucose

Functional Information from GO Data
ChainGOidnamespacecontents
A0001913biological_processT cell mediated cytotoxicity
A0003824molecular_functioncatalytic activity
A0005515molecular_functionprotein binding
A0005829cellular_componentcytosol
A0007159biological_processleukocyte cell-cell adhesion
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
B0001913biological_processT cell mediated cytotoxicity
B0003824molecular_functioncatalytic activity
B0005515molecular_functionprotein binding
B0005829cellular_componentcytosol
B0007159biological_processleukocyte cell-cell adhesion
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
C0001913biological_processT cell mediated cytotoxicity
C0003824molecular_functioncatalytic activity
C0005515molecular_functionprotein binding
C0005829cellular_componentcytosol
C0007159biological_processleukocyte cell-cell adhesion
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
D0001913biological_processT cell mediated cytotoxicity
D0003824molecular_functioncatalytic activity
D0005515molecular_functionprotein binding
D0005829cellular_componentcytosol
D0007159biological_processleukocyte cell-cell adhesion
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
E0001913biological_processT cell mediated cytotoxicity
E0003824molecular_functioncatalytic activity
E0005515molecular_functionprotein binding
E0005829cellular_componentcytosol
E0007159biological_processleukocyte cell-cell adhesion
E0009055molecular_functionelectron transfer activity
E0009226biological_processnucleotide-sugar biosynthetic process
E0010595biological_processpositive regulation of endothelial cell migration
E0016491molecular_functionoxidoreductase activity
E0016853molecular_functionisomerase activity
E0019673biological_processGDP-mannose metabolic process
E0042351biological_process'de novo' GDP-L-fucose biosynthetic process
E0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
E0042802molecular_functionidentical protein binding
E0047918molecular_functionGDP-mannose 3,5-epimerase activity
E0050577molecular_functionGDP-L-fucose synthase activity
E0070062cellular_componentextracellular exosome
E1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
F0001913biological_processT cell mediated cytotoxicity
F0003824molecular_functioncatalytic activity
F0005515molecular_functionprotein binding
F0005829cellular_componentcytosol
F0007159biological_processleukocyte cell-cell adhesion
F0009055molecular_functionelectron transfer activity
F0009226biological_processnucleotide-sugar biosynthetic process
F0010595biological_processpositive regulation of endothelial cell migration
F0016491molecular_functionoxidoreductase activity
F0016853molecular_functionisomerase activity
F0019673biological_processGDP-mannose metabolic process
F0042351biological_process'de novo' GDP-L-fucose biosynthetic process
F0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
F0042802molecular_functionidentical protein binding
F0047918molecular_functionGDP-mannose 3,5-epimerase activity
F0050577molecular_functionGDP-L-fucose synthase activity
F0070062cellular_componentextracellular exosome
F1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
G0001913biological_processT cell mediated cytotoxicity
G0003824molecular_functioncatalytic activity
G0005515molecular_functionprotein binding
G0005829cellular_componentcytosol
G0007159biological_processleukocyte cell-cell adhesion
G0009055molecular_functionelectron transfer activity
G0009226biological_processnucleotide-sugar biosynthetic process
G0010595biological_processpositive regulation of endothelial cell migration
G0016491molecular_functionoxidoreductase activity
G0016853molecular_functionisomerase activity
G0019673biological_processGDP-mannose metabolic process
G0042351biological_process'de novo' GDP-L-fucose biosynthetic process
G0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
G0042802molecular_functionidentical protein binding
G0047918molecular_functionGDP-mannose 3,5-epimerase activity
G0050577molecular_functionGDP-L-fucose synthase activity
G0070062cellular_componentextracellular exosome
G1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
H0001913biological_processT cell mediated cytotoxicity
H0003824molecular_functioncatalytic activity
H0005515molecular_functionprotein binding
H0005829cellular_componentcytosol
H0007159biological_processleukocyte cell-cell adhesion
H0009055molecular_functionelectron transfer activity
H0009226biological_processnucleotide-sugar biosynthetic process
H0010595biological_processpositive regulation of endothelial cell migration
H0016491molecular_functionoxidoreductase activity
H0016853molecular_functionisomerase activity
H0019673biological_processGDP-mannose metabolic process
H0042351biological_process'de novo' GDP-L-fucose biosynthetic process
H0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
H0042802molecular_functionidentical protein binding
H0047918molecular_functionGDP-mannose 3,5-epimerase activity
H0050577molecular_functionGDP-L-fucose synthase activity
H0070062cellular_componentextracellular exosome
H1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
I0001913biological_processT cell mediated cytotoxicity
I0003824molecular_functioncatalytic activity
I0005515molecular_functionprotein binding
I0005829cellular_componentcytosol
I0007159biological_processleukocyte cell-cell adhesion
I0009055molecular_functionelectron transfer activity
I0009226biological_processnucleotide-sugar biosynthetic process
I0010595biological_processpositive regulation of endothelial cell migration
I0016491molecular_functionoxidoreductase activity
I0016853molecular_functionisomerase activity
I0019673biological_processGDP-mannose metabolic process
I0042351biological_process'de novo' GDP-L-fucose biosynthetic process
I0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
I0042802molecular_functionidentical protein binding
I0047918molecular_functionGDP-mannose 3,5-epimerase activity
I0050577molecular_functionGDP-L-fucose synthase activity
I0070062cellular_componentextracellular exosome
I1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
J0001913biological_processT cell mediated cytotoxicity
J0003824molecular_functioncatalytic activity
J0005515molecular_functionprotein binding
J0005829cellular_componentcytosol
J0007159biological_processleukocyte cell-cell adhesion
J0009055molecular_functionelectron transfer activity
J0009226biological_processnucleotide-sugar biosynthetic process
J0010595biological_processpositive regulation of endothelial cell migration
J0016491molecular_functionoxidoreductase activity
J0016853molecular_functionisomerase activity
J0019673biological_processGDP-mannose metabolic process
J0042351biological_process'de novo' GDP-L-fucose biosynthetic process
J0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
J0042802molecular_functionidentical protein binding
J0047918molecular_functionGDP-mannose 3,5-epimerase activity
J0050577molecular_functionGDP-L-fucose synthase activity
J0070062cellular_componentextracellular exosome
J1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
K0001913biological_processT cell mediated cytotoxicity
K0003824molecular_functioncatalytic activity
K0005515molecular_functionprotein binding
K0005829cellular_componentcytosol
K0007159biological_processleukocyte cell-cell adhesion
K0009055molecular_functionelectron transfer activity
K0009226biological_processnucleotide-sugar biosynthetic process
K0010595biological_processpositive regulation of endothelial cell migration
K0016491molecular_functionoxidoreductase activity
K0016853molecular_functionisomerase activity
K0019673biological_processGDP-mannose metabolic process
K0042351biological_process'de novo' GDP-L-fucose biosynthetic process
K0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
K0042802molecular_functionidentical protein binding
K0047918molecular_functionGDP-mannose 3,5-epimerase activity
K0050577molecular_functionGDP-L-fucose synthase activity
K0070062cellular_componentextracellular exosome
K1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
L0001913biological_processT cell mediated cytotoxicity
L0003824molecular_functioncatalytic activity
L0005515molecular_functionprotein binding
L0005829cellular_componentcytosol
L0007159biological_processleukocyte cell-cell adhesion
L0009055molecular_functionelectron transfer activity
L0009226biological_processnucleotide-sugar biosynthetic process
L0010595biological_processpositive regulation of endothelial cell migration
L0016491molecular_functionoxidoreductase activity
L0016853molecular_functionisomerase activity
L0019673biological_processGDP-mannose metabolic process
L0042351biological_process'de novo' GDP-L-fucose biosynthetic process
L0042356molecular_functionGDP-4-dehydro-D-rhamnose reductase activity
L0042802molecular_functionidentical protein binding
L0047918molecular_functionGDP-mannose 3,5-epimerase activity
L0050577molecular_functionGDP-L-fucose synthase activity
L0070062cellular_componentextracellular exosome
L1904906biological_processpositive regulation of endothelial cell-matrix adhesion via fibronectin
Functional Information from PDB Data
site_idAC1
Number of Residues24
DetailsBINDING SITE FOR RESIDUE NAP A 901
ChainResidue
AGLY14
AASP47
ALEU48
ALEU69
AALA71
AVAL73
ACYS112
ALEU113
ASER114
ATYR143
ALYS147
AGLY15
APRO170
ATHR171
AVAL173
AARG320
AGFB902
ASER16
AGLY17
ALEU18
AVAL19
ASER42
ASER43
AALA46

site_idAC2
Number of Residues19
DetailsBINDING SITE FOR RESIDUE GFB A 902
ChainResidue
AGLY74
AGLY75
ALEU76
ACYS116
AASN140
ATYR143
AASN172
AGLY185
AHIS186
AVAL187
ALYS194
ATRP208
APRO213
AARG215
AILE252
ASER276
AASP277
ALYS282
ANAP901

site_idAC3
Number of Residues23
DetailsBINDING SITE FOR RESIDUE NAP B 901
ChainResidue
BGLY14
BSER16
BGLY17
BLEU18
BVAL19
BSER43
BALA46
BASP47
BLEU48
BLEU69
BALA70
BALA71
BVAL73
BCYS112
BLEU113
BSER114
BTYR143
BLYS147
BTHR171
BVAL173
BHIS186
BARG320
BGFB902

site_idAC4
Number of Residues23
DetailsBINDING SITE FOR RESIDUE GFB B 902
ChainResidue
BGLY74
BGLY75
BLEU76
BASN79
BCYS116
BASN140
BTYR143
BASN172
BGLY185
BHIS186
BVAL187
BLEU191
BLYS194
BVAL207
BTRP208
BGLY209
BPRO213
BARG215
BILE252
BSER276
BASP277
BLYS282
BNAP901

site_idAC5
Number of Residues23
DetailsBINDING SITE FOR RESIDUE NAP C 901
ChainResidue
CALA70
CALA71
CVAL73
CCYS112
CLEU113
CSER114
CTYR143
CLYS147
CTHR171
CVAL173
CHIS186
CARG320
CGFB902
CGLY14
CSER16
CGLY17
CLEU18
CVAL19
CSER43
CALA46
CASP47
CLEU48
CLEU69

site_idAC6
Number of Residues23
DetailsBINDING SITE FOR RESIDUE GFB C 902
ChainResidue
CGLY74
CGLY75
CLEU76
CPHE77
CASN79
CSER114
CCYS116
CASN140
CTYR143
CASN172
CGLY185
CHIS186
CVAL187
CLYS194
CVAL207
CTRP208
CARG215
CILE252
CSER276
CASP277
CLYS282
CNAP901
CHOH2006

site_idAC7
Number of Residues25
DetailsBINDING SITE FOR RESIDUE NAP D 901
ChainResidue
DGLY14
DGLY15
DSER16
DGLY17
DLEU18
DVAL19
DSER43
DALA46
DASP47
DLEU48
DLEU69
DALA70
DALA71
DVAL73
DCYS112
DLEU113
DSER114
DTYR143
DLYS147
DPRO170
DTHR171
DVAL173
DHIS186
DARG320
DGFB902

site_idAC8
Number of Residues19
DetailsBINDING SITE FOR RESIDUE GFB D 902
ChainResidue
DGLY74
DGLY75
DLEU76
DSER114
DCYS116
DASN140
DTYR143
DASN172
DGLY185
DHIS186
DVAL187
DLYS194
DTRP208
DARG215
DILE252
DSER276
DASP277
DLYS282
DNAP901

site_idAC9
Number of Residues24
DetailsBINDING SITE FOR RESIDUE NAP E 901
ChainResidue
EGLY14
ESER16
EGLY17
ELEU18
EVAL19
ESER43
EALA46
EASP47
ELEU48
ELEU69
EALA70
EALA71
EVAL73
EMET93
ECYS112
ELEU113
ETYR143
ELYS147
EPRO170
ETHR171
EVAL173
EHIS186
EARG320
EGFB902

site_idBC1
Number of Residues18
DetailsBINDING SITE FOR RESIDUE GFB E 902
ChainResidue
EGLY74
EGLY75
ELEU76
ECYS116
EASN140
ETYR143
EASN172
EGLY185
EHIS186
EVAL187
ELYS194
ETRP208
EARG215
ESER276
EASP277
ELYS282
ENAP901
EHOH2002

site_idBC2
Number of Residues24
DetailsBINDING SITE FOR RESIDUE NAP F 901
ChainResidue
FGLY14
FSER16
FGLY17
FLEU18
FVAL19
FSER43
FALA46
FASP47
FLEU48
FTHR49
FLEU69
FALA70
FALA71
FVAL73
FCYS112
FLEU113
FSER114
FTYR143
FLYS147
FTHR171
FVAL173
FHIS186
FARG320
FGFB902

site_idBC3
Number of Residues21
DetailsBINDING SITE FOR RESIDUE GFB F 902
ChainResidue
FGLY74
FGLY75
FLEU76
FASN79
FSER114
FCYS116
FASN140
FTYR143
FASN172
FGLY185
FHIS186
FVAL187
FLYS194
FTRP208
FGLY209
FARG215
FILE252
FSER276
FASP277
FLYS282
FNAP901

site_idBC4
Number of Residues25
DetailsBINDING SITE FOR RESIDUE NAP G 901
ChainResidue
GGLY14
GGLY15
GSER16
GGLY17
GLEU18
GVAL19
GSER42
GSER43
GALA46
GASP47
GLEU48
GLEU69
GALA70
GALA71
GVAL73
GCYS112
GLEU113
GSER114
GTYR143
GLYS147
GTHR171
GVAL173
GHIS186
GARG320
GGFB902

site_idBC5
Number of Residues24
DetailsBINDING SITE FOR RESIDUE GFB G 902
ChainResidue
GGLY74
GGLY75
GLEU76
GASN79
GSER114
GCYS116
GASN140
GTYR143
GASN172
GGLY185
GHIS186
GVAL187
GLEU191
GLYS194
GVAL207
GTRP208
GGLY209
GPRO213
GARG215
GILE252
GSER276
GASP277
GLYS282
GNAP901

site_idBC6
Number of Residues23
DetailsBINDING SITE FOR RESIDUE NAP H 901
ChainResidue
HGLY14
HSER16
HGLY17
HLEU18
HVAL19
HSER43
HALA46
HASP47
HLEU48
HTHR49
HLEU69
HALA71
HVAL73
HCYS112
HLEU113
HTYR143
HLYS147
HPRO170
HTHR171
HVAL173
HHIS186
HARG320
HGFB902

site_idBC7
Number of Residues24
DetailsBINDING SITE FOR RESIDUE GFB H 902
ChainResidue
HGLY74
HGLY75
HLEU76
HPHE77
HASN79
HCYS116
HASN140
HTYR143
HASN172
HGLY185
HHIS186
HVAL187
HLEU191
HLYS194
HVAL207
HTRP208
HGLY209
HPRO213
HARG215
HILE252
HSER276
HASP277
HLYS282
HNAP901

site_idBC8
Number of Residues27
DetailsBINDING SITE FOR RESIDUE NAP I 901
ChainResidue
IGLY14
IGLY15
ISER16
IGLY17
ILEU18
IVAL19
ISER42
ISER43
IALA46
IASP47
ILEU48
ILEU69
IALA70
IALA71
IVAL73
IMET93
ICYS112
ILEU113
ISER114
ITYR143
ILYS147
IPRO170
ITHR171
IVAL173
IHIS186
IARG320
IGFB902

site_idBC9
Number of Residues22
DetailsBINDING SITE FOR RESIDUE GFB I 902
ChainResidue
IGLY74
IGLY75
ILEU76
ICYS116
IASN140
ITYR143
IASN172
IGLY185
IHIS186
IVAL187
ILEU191
ILYS194
IVAL207
ITRP208
IGLY209
IPRO213
IARG215
IILE252
ISER276
IASP277
ILYS282
INAP901

site_idCC1
Number of Residues26
DetailsBINDING SITE FOR RESIDUE NAP J 901
ChainResidue
JGLY14
JGLY15
JSER16
JGLY17
JLEU18
JVAL19
JSER42
JSER43
JALA46
JASP47
JLEU48
JLEU69
JALA70
JALA71
JVAL73
JCYS112
JLEU113
JSER114
JTYR143
JLYS147
JPRO170
JTHR171
JVAL173
JHIS186
JARG320
JGFB902

site_idCC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE GFB J 902
ChainResidue
JGLY74
JGLY75
JLEU76
JPHE77
JASN79
JCYS116
JASN140
JTYR143
JASN172
JGLY185
JHIS186
JVAL187
JLYS194
JTRP208
JARG215
JILE252
JSER276
JASP277
JLYS282
JNAP901

site_idCC3
Number of Residues26
DetailsBINDING SITE FOR RESIDUE NAP K 901
ChainResidue
KGLY14
KGLY15
KSER16
KGLY17
KLEU18
KVAL19
KSER42
KSER43
KALA46
KASP47
KLEU48
KLEU69
KALA70
KALA71
KVAL73
KMET93
KCYS112
KLEU113
KSER114
KTYR143
KLYS147
KPRO170
KTHR171
KVAL173
KHIS186
KARG320

site_idCC4
Number of Residues21
DetailsBINDING SITE FOR RESIDUE GFB K 902
ChainResidue
KGLY74
KGLY75
KLEU76
KASN79
KCYS116
KASN140
KTYR143
KASN172
KGLY185
KHIS186
KVAL187
KLEU191
KLYS194
KVAL207
KTRP208
KPRO213
KARG215
KILE252
KSER276
KASP277
KLYS282

site_idCC5
Number of Residues26
DetailsBINDING SITE FOR RESIDUE NAP L 901
ChainResidue
LGLY14
LSER16
LGLY17
LLEU18
LVAL19
LSER42
LSER43
LALA46
LASP47
LLEU48
LLEU69
LALA70
LALA71
LVAL73
LMET93
LCYS112
LLEU113
LSER114
LTYR143
LPRO170
LTHR171
LVAL173
LHIS186
LARG320
LGFB902
LHOH2003

site_idCC6
Number of Residues18
DetailsBINDING SITE FOR RESIDUE GFB L 902
ChainResidue
LGLY74
LGLY75
LLEU76
LCYS116
LASN140
LTYR143
LASN172
LGLY185
LHIS186
LVAL187
LLYS194
LTRP208
LGLY209
LARG215
LSER276
LASP277
LLYS282
LNAP901

site_idCC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO F 1321
ChainResidue
FTHR49
FTHR51
FHIS92
FASN96

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsActive site: {"description":"Proton donor/acceptor","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues120
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23774504","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of human GDP-L-fucose synthase with bound NADP.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of human GDP-L-fucose synthase with bound NADP.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues48
DetailsBinding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"APR-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of human GDP-L-fucose synthase with bound NADP.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues24
DetailsSite: {"description":"Important for catalytic activity","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues12
DetailsSite: {"description":"Lowers pKa of active site Tyr","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

238582

PDB entries from 2025-07-09

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