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3PHB

Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG

Functional Information from GO Data
ChainGOidnamespacecontents
E0000255biological_processallantoin metabolic process
E0001882molecular_functionnucleoside binding
E0002060molecular_functionpurine nucleobase binding
E0003824molecular_functioncatalytic activity
E0004731molecular_functionpurine-nucleoside phosphorylase activity
E0005515molecular_functionprotein binding
E0005576cellular_componentextracellular region
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0006139biological_processnucleobase-containing compound metabolic process
E0006148biological_processinosine catabolic process
E0006149biological_processdeoxyinosine catabolic process
E0006157biological_processdeoxyadenosine catabolic process
E0006166biological_processpurine ribonucleoside salvage
E0006204biological_processIMP catabolic process
E0006738biological_processnicotinamide riboside catabolic process
E0006955biological_processimmune response
E0009116biological_processnucleoside metabolic process
E0009165biological_processnucleotide biosynthetic process
E0009410biological_processresponse to xenobiotic stimulus
E0016757molecular_functionglycosyltransferase activity
E0016763molecular_functionpentosyltransferase activity
E0032743biological_processpositive regulation of interleukin-2 production
E0034418biological_processurate biosynthetic process
E0034774cellular_componentsecretory granule lumen
E0042102biological_processpositive regulation of T cell proliferation
E0042301molecular_functionphosphate ion binding
E0042802molecular_functionidentical protein binding
E0043101biological_processpurine-containing compound salvage
E0046059biological_processdAMP catabolic process
E0046638biological_processpositive regulation of alpha-beta T cell differentiation
E0047975molecular_functionguanosine phosphorylase activity
E0070062cellular_componentextracellular exosome
E1904813cellular_componentficolin-1-rich granule lumen
Q0000255biological_processallantoin metabolic process
Q0001882molecular_functionnucleoside binding
Q0002060molecular_functionpurine nucleobase binding
Q0003824molecular_functioncatalytic activity
Q0004731molecular_functionpurine-nucleoside phosphorylase activity
Q0005515molecular_functionprotein binding
Q0005576cellular_componentextracellular region
Q0005737cellular_componentcytoplasm
Q0005829cellular_componentcytosol
Q0006139biological_processnucleobase-containing compound metabolic process
Q0006148biological_processinosine catabolic process
Q0006149biological_processdeoxyinosine catabolic process
Q0006157biological_processdeoxyadenosine catabolic process
Q0006166biological_processpurine ribonucleoside salvage
Q0006204biological_processIMP catabolic process
Q0006738biological_processnicotinamide riboside catabolic process
Q0006955biological_processimmune response
Q0009116biological_processnucleoside metabolic process
Q0009165biological_processnucleotide biosynthetic process
Q0009410biological_processresponse to xenobiotic stimulus
Q0016757molecular_functionglycosyltransferase activity
Q0016763molecular_functionpentosyltransferase activity
Q0032743biological_processpositive regulation of interleukin-2 production
Q0034418biological_processurate biosynthetic process
Q0034774cellular_componentsecretory granule lumen
Q0042102biological_processpositive regulation of T cell proliferation
Q0042301molecular_functionphosphate ion binding
Q0042802molecular_functionidentical protein binding
Q0043101biological_processpurine-containing compound salvage
Q0046059biological_processdAMP catabolic process
Q0046638biological_processpositive regulation of alpha-beta T cell differentiation
Q0047975molecular_functionguanosine phosphorylase activity
Q0070062cellular_componentextracellular exosome
Q1904813cellular_componentficolin-1-rich granule lumen
S0000255biological_processallantoin metabolic process
S0001882molecular_functionnucleoside binding
S0002060molecular_functionpurine nucleobase binding
S0003824molecular_functioncatalytic activity
S0004731molecular_functionpurine-nucleoside phosphorylase activity
S0005515molecular_functionprotein binding
S0005576cellular_componentextracellular region
S0005737cellular_componentcytoplasm
S0005829cellular_componentcytosol
S0006139biological_processnucleobase-containing compound metabolic process
S0006148biological_processinosine catabolic process
S0006149biological_processdeoxyinosine catabolic process
S0006157biological_processdeoxyadenosine catabolic process
S0006166biological_processpurine ribonucleoside salvage
S0006204biological_processIMP catabolic process
S0006738biological_processnicotinamide riboside catabolic process
S0006955biological_processimmune response
S0009116biological_processnucleoside metabolic process
S0009165biological_processnucleotide biosynthetic process
S0009410biological_processresponse to xenobiotic stimulus
S0016757molecular_functionglycosyltransferase activity
S0016763molecular_functionpentosyltransferase activity
S0032743biological_processpositive regulation of interleukin-2 production
S0034418biological_processurate biosynthetic process
S0034774cellular_componentsecretory granule lumen
S0042102biological_processpositive regulation of T cell proliferation
S0042301molecular_functionphosphate ion binding
S0042802molecular_functionidentical protein binding
S0043101biological_processpurine-containing compound salvage
S0046059biological_processdAMP catabolic process
S0046638biological_processpositive regulation of alpha-beta T cell differentiation
S0047975molecular_functionguanosine phosphorylase activity
S0070062cellular_componentextracellular exosome
S1904813cellular_componentficolin-1-rich granule lumen
T0000255biological_processallantoin metabolic process
T0001882molecular_functionnucleoside binding
T0002060molecular_functionpurine nucleobase binding
T0003824molecular_functioncatalytic activity
T0004731molecular_functionpurine-nucleoside phosphorylase activity
T0005515molecular_functionprotein binding
T0005576cellular_componentextracellular region
T0005737cellular_componentcytoplasm
T0005829cellular_componentcytosol
T0006139biological_processnucleobase-containing compound metabolic process
T0006148biological_processinosine catabolic process
T0006149biological_processdeoxyinosine catabolic process
T0006157biological_processdeoxyadenosine catabolic process
T0006166biological_processpurine ribonucleoside salvage
T0006204biological_processIMP catabolic process
T0006738biological_processnicotinamide riboside catabolic process
T0006955biological_processimmune response
T0009116biological_processnucleoside metabolic process
T0009165biological_processnucleotide biosynthetic process
T0009410biological_processresponse to xenobiotic stimulus
T0016757molecular_functionglycosyltransferase activity
T0016763molecular_functionpentosyltransferase activity
T0032743biological_processpositive regulation of interleukin-2 production
T0034418biological_processurate biosynthetic process
T0034774cellular_componentsecretory granule lumen
T0042102biological_processpositive regulation of T cell proliferation
T0042301molecular_functionphosphate ion binding
T0042802molecular_functionidentical protein binding
T0043101biological_processpurine-containing compound salvage
T0046059biological_processdAMP catabolic process
T0046638biological_processpositive regulation of alpha-beta T cell differentiation
T0047975molecular_functionguanosine phosphorylase activity
T0070062cellular_componentextracellular exosome
T1904813cellular_componentficolin-1-rich granule lumen
U0000255biological_processallantoin metabolic process
U0001882molecular_functionnucleoside binding
U0002060molecular_functionpurine nucleobase binding
U0003824molecular_functioncatalytic activity
U0004731molecular_functionpurine-nucleoside phosphorylase activity
U0005515molecular_functionprotein binding
U0005576cellular_componentextracellular region
U0005737cellular_componentcytoplasm
U0005829cellular_componentcytosol
U0006139biological_processnucleobase-containing compound metabolic process
U0006148biological_processinosine catabolic process
U0006149biological_processdeoxyinosine catabolic process
U0006157biological_processdeoxyadenosine catabolic process
U0006166biological_processpurine ribonucleoside salvage
U0006204biological_processIMP catabolic process
U0006738biological_processnicotinamide riboside catabolic process
U0006955biological_processimmune response
U0009116biological_processnucleoside metabolic process
U0009165biological_processnucleotide biosynthetic process
U0009410biological_processresponse to xenobiotic stimulus
U0016757molecular_functionglycosyltransferase activity
U0016763molecular_functionpentosyltransferase activity
U0032743biological_processpositive regulation of interleukin-2 production
U0034418biological_processurate biosynthetic process
U0034774cellular_componentsecretory granule lumen
U0042102biological_processpositive regulation of T cell proliferation
U0042301molecular_functionphosphate ion binding
U0042802molecular_functionidentical protein binding
U0043101biological_processpurine-containing compound salvage
U0046059biological_processdAMP catabolic process
U0046638biological_processpositive regulation of alpha-beta T cell differentiation
U0047975molecular_functionguanosine phosphorylase activity
U0070062cellular_componentextracellular exosome
U1904813cellular_componentficolin-1-rich granule lumen
Y0000255biological_processallantoin metabolic process
Y0001882molecular_functionnucleoside binding
Y0002060molecular_functionpurine nucleobase binding
Y0003824molecular_functioncatalytic activity
Y0004731molecular_functionpurine-nucleoside phosphorylase activity
Y0005515molecular_functionprotein binding
Y0005576cellular_componentextracellular region
Y0005737cellular_componentcytoplasm
Y0005829cellular_componentcytosol
Y0006139biological_processnucleobase-containing compound metabolic process
Y0006148biological_processinosine catabolic process
Y0006149biological_processdeoxyinosine catabolic process
Y0006157biological_processdeoxyadenosine catabolic process
Y0006166biological_processpurine ribonucleoside salvage
Y0006204biological_processIMP catabolic process
Y0006738biological_processnicotinamide riboside catabolic process
Y0006955biological_processimmune response
Y0009116biological_processnucleoside metabolic process
Y0009165biological_processnucleotide biosynthetic process
Y0009410biological_processresponse to xenobiotic stimulus
Y0016757molecular_functionglycosyltransferase activity
Y0016763molecular_functionpentosyltransferase activity
Y0032743biological_processpositive regulation of interleukin-2 production
Y0034418biological_processurate biosynthetic process
Y0034774cellular_componentsecretory granule lumen
Y0042102biological_processpositive regulation of T cell proliferation
Y0042301molecular_functionphosphate ion binding
Y0042802molecular_functionidentical protein binding
Y0043101biological_processpurine-containing compound salvage
Y0046059biological_processdAMP catabolic process
Y0046638biological_processpositive regulation of alpha-beta T cell differentiation
Y0047975molecular_functionguanosine phosphorylase activity
Y0070062cellular_componentextracellular exosome
Y1904813cellular_componentficolin-1-rich granule lumen
Functional Information from PDB Data
site_idAC1
Number of Residues14
DetailsBINDING SITE FOR RESIDUE IM5 E 290
ChainResidue
ETYR88
ETHR242
EASN243
EHIS257
EVAL260
EPO4291
EALA116
EALA117
EGLY118
EPHE200
EGLU201
EVAL217
EGLY218
EMET219

site_idAC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 E 291
ChainResidue
EGLY32
ESER33
EHIS64
EARG84
EHIS86
EASN115
EALA116
ESER220
EIM5290
EHOH296

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PO4 E 292
ChainResidue
EMET1
EARG148
QPRO92
QGLN144
QHOH306

site_idAC4
Number of Residues16
DetailsBINDING SITE FOR RESIDUE IM5 Q 290
ChainResidue
EPHE159
QTYR88
QALA116
QALA117
QGLY118
QPHE200
QGLU201
QVAL217
QGLY218
QMET219
QTHR242
QASN243
QVAL245
QHIS257
QVAL260
QPO4291

site_idAC5
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 Q 291
ChainResidue
QGLY32
QSER33
QHIS64
QARG84
QHIS86
QASN115
QALA116
QSER220
QIM5290
QHOH301

site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PO4 Q 292
ChainResidue
QMET1
QARG148
YPRO92
YGLN144

site_idAC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PO4 S 290
ChainResidue
SPRO92
SGLN144
UARG148

site_idAC8
Number of Residues15
DetailsBINDING SITE FOR RESIDUE IM5 S 291
ChainResidue
SSER33
STYR88
SALA116
SGLY118
SPHE200
SGLU201
SVAL217
SGLY218
SMET219
STHR242
SASN243
SHIS257
SVAL260
SPO4292
UPHE159

site_idAC9
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 S 292
ChainResidue
SGLY32
SSER33
SHIS64
SARG84
SHIS86
SASN115
SALA116
SSER220
SIM5291
SHOH299

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PO4 T 290
ChainResidue
TMET1
TARG148
UPRO92
UGLN144

site_idBC2
Number of Residues17
DetailsBINDING SITE FOR RESIDUE IM5 T 291
ChainResidue
TGLU201
TVAL217
TGLY218
TMET219
TTHR242
TASN243
TVAL245
THIS257
TPO4292
SPHE159
THIS86
TTYR88
TALA116
TALA117
TGLY118
TVAL195
TPHE200

site_idBC3
Number of Residues9
DetailsBINDING SITE FOR RESIDUE PO4 T 292
ChainResidue
TGLY32
TSER33
THIS64
TARG84
THIS86
TASN115
TALA116
TSER220
TIM5291

site_idBC4
Number of Residues15
DetailsBINDING SITE FOR RESIDUE IM5 U 290
ChainResidue
TPHE159
UTYR88
UALA116
UALA117
UGLY118
UPHE200
UGLU201
UVAL217
UGLY218
UMET219
UTHR242
UASN243
UVAL245
UHIS257
UPO4291

site_idBC5
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 U 291
ChainResidue
UGLY32
USER33
UHIS64
UARG84
UHIS86
UASN115
UALA116
USER220
UIM5290
UHOH297

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PO4 Y 290
ChainResidue
EPRO92
EGLN144
YMET1
YARG148
YHOH303

site_idBC7
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PO4 Y 291
ChainResidue
EARG207
YARG133

site_idBC8
Number of Residues18
DetailsBINDING SITE FOR RESIDUE IM5 Y 292
ChainResidue
QPHE159
YHIS86
YTYR88
YALA116
YALA117
YGLY118
YVAL195
YPHE200
YGLU201
YVAL217
YGLY218
YMET219
YTHR242
YASN243
YVAL245
YHIS257
YVAL260
YPO4293

site_idBC9
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 Y 293
ChainResidue
YGLY32
YSER33
YHIS64
YARG84
YHIS86
YASN115
YALA116
YSER220
YIM5292
YHOH296

Functional Information from PROSITE/UniProt
site_idPS01240
Number of Residues42
DetailsPNP_MTAP_2 Purine and other phosphorylases family 2 signature. VmmqGrfHmYegypLwkvTfpVrVfhllGvdt.LVvtNAaGGL
ChainResidueDetails
EVAL79-LEU120

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:23438750, ECO:0000305|PubMed:14706628, ECO:0000305|PubMed:1763067, ECO:0007744|PDB:1RCT, ECO:0007744|PDB:1ULA, ECO:0007744|PDB:1ULB, ECO:0007744|PDB:4EAR, ECO:0007744|PDB:4EB8, ECO:0007744|PDB:4GKA
ChainResidueDetails
ESER33
QSER33
SSER33
TSER33
USER33
YSER33

site_idSWS_FT_FI2
Number of Residues6
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P55859
ChainResidueDetails
EHIS64
QHIS64
SHIS64
THIS64
UHIS64
YHIS64

site_idSWS_FT_FI3
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:23438750, ECO:0000305|PubMed:14706628, ECO:0000305|PubMed:1763067, ECO:0007744|PDB:1RCT, ECO:0007744|PDB:1ULA, ECO:0007744|PDB:1ULB, ECO:0007744|PDB:1V3Q, ECO:0007744|PDB:4EAR, ECO:0007744|PDB:4EB8, ECO:0007744|PDB:4GKA
ChainResidueDetails
EARG84
QARG84
SARG84
TARG84
UARG84
YARG84

site_idSWS_FT_FI4
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:14706628, ECO:0000269|PubMed:23438750, ECO:0007744|PDB:1RCT, ECO:0007744|PDB:4EAR, ECO:0007744|PDB:4EB8
ChainResidueDetails
ETYR88
QTYR88
STYR88
TTYR88
UTYR88
YTYR88

site_idSWS_FT_FI5
Number of Residues24
DetailsBINDING: BINDING => ECO:0000269|PubMed:14706628, ECO:0000269|PubMed:23438750, ECO:0000305|PubMed:1763067, ECO:0007744|PDB:1RCT, ECO:0007744|PDB:1ULB, ECO:0007744|PDB:4EAR, ECO:0007744|PDB:4EB8, ECO:0007744|PDB:4GKA
ChainResidueDetails
EALA116
SGLU201
SSER220
SASN243
TALA116
TGLU201
TSER220
TASN243
UALA116
UGLU201
USER220
EGLU201
UASN243
YALA116
YGLU201
YSER220
YASN243
ESER220
EASN243
QALA116
QGLU201
QSER220
QASN243
SALA116

site_idSWS_FT_FI6
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:14706628, ECO:0007744|PDB:1RCT
ChainResidueDetails
EMET219
UHIS257
YMET219
YHIS257
EHIS257
QMET219
QHIS257
SMET219
SHIS257
TMET219
THIS257
UMET219

site_idSWS_FT_FI7
Number of Residues6
DetailsSITE: Important for substrate specificity => ECO:0000269|PubMed:9305964
ChainResidueDetails
EASN243
QASN243
SASN243
TASN243
UASN243
YASN243

site_idSWS_FT_FI8
Number of Residues6
DetailsMOD_RES: N-acetylmethionine => ECO:0000269|Ref.8, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:22223895
ChainResidueDetails
EMET1
QMET1
SMET1
TMET1
UMET1
YMET1

site_idSWS_FT_FI9
Number of Residues6
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163
ChainResidueDetails
ESER251
QSER251
SSER251
TSER251
USER251
YSER251

Catalytic Information from CSA
site_idMCSA1
Number of Residues10
DetailsM-CSA 17
ChainResidueDetails
ESER33hydrogen bond donor
EHIS257electrostatic stabiliser, hydrogen bond acceptor
EHIS64electrostatic stabiliser
EHIS86electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
ETYR88electrostatic stabiliser, hydrogen bond donor
EGLU89activator, electrostatic stabiliser, hydrogen bond acceptor
EALA116electrostatic stabiliser, hydrogen bond donor
EMET219electrostatic stabiliser, hydrogen bond donor
ESER220electrostatic stabiliser, hydrogen bond donor
EASN243electrostatic stabiliser, hydrogen bond donor, polar interaction

site_idMCSA2
Number of Residues10
DetailsM-CSA 17
ChainResidueDetails
QSER33hydrogen bond donor
QHIS257electrostatic stabiliser, hydrogen bond acceptor
QHIS64electrostatic stabiliser
QHIS86electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
QTYR88electrostatic stabiliser, hydrogen bond donor
QGLU89activator, electrostatic stabiliser, hydrogen bond acceptor
QALA116electrostatic stabiliser, hydrogen bond donor
QMET219electrostatic stabiliser, hydrogen bond donor
QSER220electrostatic stabiliser, hydrogen bond donor
QASN243electrostatic stabiliser, hydrogen bond donor, polar interaction

site_idMCSA3
Number of Residues10
DetailsM-CSA 17
ChainResidueDetails
SSER33hydrogen bond donor
SHIS257electrostatic stabiliser, hydrogen bond acceptor
SHIS64electrostatic stabiliser
SHIS86electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
STYR88electrostatic stabiliser, hydrogen bond donor
SGLU89activator, electrostatic stabiliser, hydrogen bond acceptor
SALA116electrostatic stabiliser, hydrogen bond donor
SMET219electrostatic stabiliser, hydrogen bond donor
SSER220electrostatic stabiliser, hydrogen bond donor
SASN243electrostatic stabiliser, hydrogen bond donor, polar interaction

site_idMCSA4
Number of Residues10
DetailsM-CSA 17
ChainResidueDetails
TSER33hydrogen bond donor
THIS257electrostatic stabiliser, hydrogen bond acceptor
THIS64electrostatic stabiliser
THIS86electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
TTYR88electrostatic stabiliser, hydrogen bond donor
TGLU89activator, electrostatic stabiliser, hydrogen bond acceptor
TALA116electrostatic stabiliser, hydrogen bond donor
TMET219electrostatic stabiliser, hydrogen bond donor
TSER220electrostatic stabiliser, hydrogen bond donor
TASN243electrostatic stabiliser, hydrogen bond donor, polar interaction

site_idMCSA5
Number of Residues10
DetailsM-CSA 17
ChainResidueDetails
USER33hydrogen bond donor
UHIS257electrostatic stabiliser, hydrogen bond acceptor
UHIS64electrostatic stabiliser
UHIS86electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
UTYR88electrostatic stabiliser, hydrogen bond donor
UGLU89activator, electrostatic stabiliser, hydrogen bond acceptor
UALA116electrostatic stabiliser, hydrogen bond donor
UMET219electrostatic stabiliser, hydrogen bond donor
USER220electrostatic stabiliser, hydrogen bond donor
UASN243electrostatic stabiliser, hydrogen bond donor, polar interaction

site_idMCSA6
Number of Residues10
DetailsM-CSA 17
ChainResidueDetails
YSER33hydrogen bond donor
YHIS257electrostatic stabiliser, hydrogen bond acceptor
YHIS64electrostatic stabiliser
YHIS86electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
YTYR88electrostatic stabiliser, hydrogen bond donor
YGLU89activator, electrostatic stabiliser, hydrogen bond acceptor
YALA116electrostatic stabiliser, hydrogen bond donor
YMET219electrostatic stabiliser, hydrogen bond donor
YSER220electrostatic stabiliser, hydrogen bond donor
YASN243electrostatic stabiliser, hydrogen bond donor, polar interaction

227111

PDB entries from 2024-11-06

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