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3PCB

STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYBENZOATE

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0005506molecular_functioniron ion binding
A0006725biological_processobsolete cellular aromatic compound metabolic process
A0008199molecular_functionferric iron binding
A0016491molecular_functionoxidoreductase activity
A0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
A0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
A0019439biological_processobsolete aromatic compound catabolic process
A0042952biological_processbeta-ketoadipate pathway
A0051213molecular_functiondioxygenase activity
B0003824molecular_functioncatalytic activity
B0005506molecular_functioniron ion binding
B0006725biological_processobsolete cellular aromatic compound metabolic process
B0008199molecular_functionferric iron binding
B0016491molecular_functionoxidoreductase activity
B0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
B0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
B0019439biological_processobsolete aromatic compound catabolic process
B0042952biological_processbeta-ketoadipate pathway
B0051213molecular_functiondioxygenase activity
C0003824molecular_functioncatalytic activity
C0005506molecular_functioniron ion binding
C0006725biological_processobsolete cellular aromatic compound metabolic process
C0008199molecular_functionferric iron binding
C0016491molecular_functionoxidoreductase activity
C0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
C0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
C0019439biological_processobsolete aromatic compound catabolic process
C0042952biological_processbeta-ketoadipate pathway
C0051213molecular_functiondioxygenase activity
D0003824molecular_functioncatalytic activity
D0005506molecular_functioniron ion binding
D0006725biological_processobsolete cellular aromatic compound metabolic process
D0008199molecular_functionferric iron binding
D0016491molecular_functionoxidoreductase activity
D0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
D0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
D0019439biological_processobsolete aromatic compound catabolic process
D0042952biological_processbeta-ketoadipate pathway
D0051213molecular_functiondioxygenase activity
E0003824molecular_functioncatalytic activity
E0005506molecular_functioniron ion binding
E0006725biological_processobsolete cellular aromatic compound metabolic process
E0008199molecular_functionferric iron binding
E0016491molecular_functionoxidoreductase activity
E0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
E0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
E0019439biological_processobsolete aromatic compound catabolic process
E0042952biological_processbeta-ketoadipate pathway
E0051213molecular_functiondioxygenase activity
F0003824molecular_functioncatalytic activity
F0005506molecular_functioniron ion binding
F0006725biological_processobsolete cellular aromatic compound metabolic process
F0008199molecular_functionferric iron binding
F0016491molecular_functionoxidoreductase activity
F0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
F0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
F0019439biological_processobsolete aromatic compound catabolic process
F0042952biological_processbeta-ketoadipate pathway
F0051213molecular_functiondioxygenase activity
M0003824molecular_functioncatalytic activity
M0005506molecular_functioniron ion binding
M0006725biological_processobsolete cellular aromatic compound metabolic process
M0008199molecular_functionferric iron binding
M0016491molecular_functionoxidoreductase activity
M0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
M0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
M0019439biological_processobsolete aromatic compound catabolic process
M0019619biological_process3,4-dihydroxybenzoate catabolic process
M0042952biological_processbeta-ketoadipate pathway
M0046872molecular_functionmetal ion binding
M0051213molecular_functiondioxygenase activity
N0003824molecular_functioncatalytic activity
N0005506molecular_functioniron ion binding
N0006725biological_processobsolete cellular aromatic compound metabolic process
N0008199molecular_functionferric iron binding
N0016491molecular_functionoxidoreductase activity
N0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
N0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
N0019439biological_processobsolete aromatic compound catabolic process
N0019619biological_process3,4-dihydroxybenzoate catabolic process
N0042952biological_processbeta-ketoadipate pathway
N0046872molecular_functionmetal ion binding
N0051213molecular_functiondioxygenase activity
O0003824molecular_functioncatalytic activity
O0005506molecular_functioniron ion binding
O0006725biological_processobsolete cellular aromatic compound metabolic process
O0008199molecular_functionferric iron binding
O0016491molecular_functionoxidoreductase activity
O0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
O0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
O0019439biological_processobsolete aromatic compound catabolic process
O0019619biological_process3,4-dihydroxybenzoate catabolic process
O0042952biological_processbeta-ketoadipate pathway
O0046872molecular_functionmetal ion binding
O0051213molecular_functiondioxygenase activity
P0003824molecular_functioncatalytic activity
P0005506molecular_functioniron ion binding
P0006725biological_processobsolete cellular aromatic compound metabolic process
P0008199molecular_functionferric iron binding
P0016491molecular_functionoxidoreductase activity
P0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
P0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
P0019439biological_processobsolete aromatic compound catabolic process
P0019619biological_process3,4-dihydroxybenzoate catabolic process
P0042952biological_processbeta-ketoadipate pathway
P0046872molecular_functionmetal ion binding
P0051213molecular_functiondioxygenase activity
Q0003824molecular_functioncatalytic activity
Q0005506molecular_functioniron ion binding
Q0006725biological_processobsolete cellular aromatic compound metabolic process
Q0008199molecular_functionferric iron binding
Q0016491molecular_functionoxidoreductase activity
Q0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
Q0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
Q0019439biological_processobsolete aromatic compound catabolic process
Q0019619biological_process3,4-dihydroxybenzoate catabolic process
Q0042952biological_processbeta-ketoadipate pathway
Q0046872molecular_functionmetal ion binding
Q0051213molecular_functiondioxygenase activity
R0003824molecular_functioncatalytic activity
R0005506molecular_functioniron ion binding
R0006725biological_processobsolete cellular aromatic compound metabolic process
R0008199molecular_functionferric iron binding
R0016491molecular_functionoxidoreductase activity
R0016702molecular_functionoxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
R0018578molecular_functionprotocatechuate 3,4-dioxygenase activity
R0019439biological_processobsolete aromatic compound catabolic process
R0019619biological_process3,4-dihydroxybenzoate catabolic process
R0042952biological_processbeta-ketoadipate pathway
R0046872molecular_functionmetal ion binding
R0051213molecular_functiondioxygenase activity
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FE M 600
ChainResidue
MTYR408
MTYR447
MHIS460
MHIS462
M3HB550

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FE N 600
ChainResidue
NTYR408
NTYR447
NHIS460
NHIS462
N3HB550

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FE O 600
ChainResidue
OTYR408
OTYR447
OHIS460
OHIS462
O3HB550

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FE P 600
ChainResidue
PTYR408
PTYR447
PHIS460
PHIS462
P3HB550

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FE Q 600
ChainResidue
QTYR408
QTYR447
QHIS460
QHIS462
Q3HB550

site_idAC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FE R 600
ChainResidue
RTYR408
RTYR447
RHIS460
RHIS462
R3HB550

site_idAC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE BME M 601
ChainResidue
MHIS361
MCYS429
MSER438
MHOH688

site_idAC8
Number of Residues10
DetailsBINDING SITE FOR RESIDUE 3HB M 550
ChainResidue
APRO15
AARG133
MTYR324
MTYR447
MTRP449
MARG457
MHIS462
MGLN477
MILE491
MFE600

site_idAC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE 3HB M 551
ChainResidue
MARG333
MHOH676

site_idACA
Number of Residues25
DetailsSITE "ACA" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS A AND M.
ChainResidue
ATHR12
MTYR408
MTYR447
MTRP449
MARG450
MARG457
MHIS460
MHIS462
MGLN477
MILE491
MFE600
AALA13
AHOH203
MHOH624
MHOH631
MHOH632
M3HB550
MHOH738
AGLY14
APRO15
ATYR16
AARG133
AGLY134
MTYR324
MTHR326

site_idACB
Number of Residues25
DetailsSITE "ACB" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS B AND N.
ChainResidue
BTHR12
BALA13
BGLY14
BPRO15
BTYR16
BARG133
BGLY134
NTYR324
NTHR326
NTYR408
NTYR447
NTRP449
NARG450
NARG457
NHIS460
NHIS462
NGLN477
NILE491
NFE600
BHOH242
NHOH630
NHOH637
NHOH638
N3HB550
NHOH756

site_idACC
Number of Residues25
DetailsSITE "ACC" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS C AND O.
ChainResidue
CTHR12
CALA13
CGLY14
CPRO15
CTYR16
CARG133
CGLY134
OTYR324
OTHR326
OTYR408
OTYR447
OTRP449
OARG450
OARG457
OHIS460
OHIS462
OGLN477
OILE491
OFE600
CHOH207
OHOH631
OHOH639
OHOH640
O3HB550
OHOH755

site_idACD
Number of Residues25
DetailsSITE "ACD" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS D AND P.
ChainResidue
PHOH748
DTHR12
DALA13
DGLY14
DPRO15
DTYR16
DARG133
DGLY134
PTYR324
PTHR326
PTYR408
PTYR447
PTRP449
PARG450
PARG457
PHIS460
PHIS462
PGLN477
PILE491
PFE600
DHOH714
PHOH633
PHOH641
PHOH642
P3HB550

site_idACE
Number of Residues25
DetailsSITE "ACE" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS E AND Q.
ChainResidue
ETHR12
EALA13
EGLY14
EPRO15
ETYR16
EARG133
EGLY134
QTYR324
QTHR326
QTYR408
QTYR447
QTRP449
QARG450
QARG457
QHIS460
QHIS462
QGLN477
QILE491
QFE600
EHOH207
QHOH987
QHOH1002
QHOH1003
Q3HB550
QHOH1177

site_idACF
Number of Residues25
DetailsSITE "ACF" IS THE ACTIVE SITE OF THE PROTOMER CONSISTING OF CHAINS F AND R.
ChainResidue
FTHR12
FALA13
FGLY14
FPRO15
FTYR16
FARG133
FGLY134
RTYR324
RTHR326
RTYR408
RTYR447
RTRP449
RARG450
RARG457
RHIS460
RHIS462
RGLN477
RILE491
RFE600
FHOH1186
RHOH1223
RHOH1238
RHOH1239
R3HB550
RHOH1413

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE BME N 601
ChainResidue
NHIS361
NCYS429
NLEU430
NSER438

site_idBC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE 3HB N 550
ChainResidue
BPRO15
BARG133
NTYR324
NTYR447
NTRP449
NARG457
NHIS462
NGLN477
NILE491
NFE600

site_idBC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE 3HB N 551
ChainResidue
NARG333
NHOH687

site_idBC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE BME O 601
ChainResidue
OHIS361
OCYS429
OSER438
OHOH699

site_idBC5
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 3HB O 550
ChainResidue
CGLY14
CPRO15
CARG133
OTYR324
OTYR447
OTRP449
OARG457
OHIS462
OGLN477
OILE491
OFE600

site_idBC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE 3HB O 551
ChainResidue
OARG333
OHOH688

site_idBC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE BME P 601
ChainResidue
PHIS361
PCYS429
PLEU430
PSER438
PHOH698

site_idBC8
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 3HB P 550
ChainResidue
DGLY14
DPRO15
DARG133
PTYR324
PTYR447
PTRP449
PARG457
PHIS462
PGLN477
PILE491
PFE600

site_idBC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE 3HB P 551
ChainResidue
PARG333
PHOH687
RPRO322

site_idCC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE BME Q 601
ChainResidue
QHIS361
QCYS429
QLEU430
QSER438
QHOH1091

site_idCC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE 3HB Q 550
ChainResidue
EPRO15
EARG133
QTYR324
QTYR447
QTRP449
QARG457
QHIS462
QGLN477
QILE491
QFE600

site_idCC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE 3HB Q 551
ChainResidue
QARG333
QHOH1074

site_idCC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE BME R 601
ChainResidue
RHIS361
RCYS429
RLEU430
RSER438
RHOH1327

site_idCC5
Number of Residues10
DetailsBINDING SITE FOR RESIDUE 3HB R 550
ChainResidue
FPRO15
FARG133
RTYR324
RTYR447
RTRP449
RARG457
RHIS462
RGLN477
RILE491
RFE600

site_idCC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE 3HB R 551
ChainResidue
RARG333
RHOH1310

site_idVEA
Number of Residues29
DetailsSITE "VEA" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS A AND M.
ChainResidue
ATYR79
AVAL114
AASN115
AASN116
AALA117
AALA118
AMET122
AHIS125
AASN127
AARG142
AVAL157
MASP304
MARG307
MILE339
MPRO340
MGLN341
MSER342
MILE343
MSER344
MGLU345
AHOH219
AHOH222
MHOH636
AHOH231
MHOH642
AHOH234
MHOH657
AHOH247
MHOH714

site_idVEB
Number of Residues29
DetailsSITE "VEB" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS B AND N.
ChainResidue
BTYR79
BVAL114
BASN115
BASN116
BALA117
BALA118
BMET122
BHIS125
BASN127
BARG142
BVAL157
NASP304
NARG307
NILE339
NPRO340
NGLN341
NSER342
NILE343
NSER344
NGLU345
BHOH282
BHOH290
NHOH643
BHOH308
NHOH651
BHOH317
NHOH666
BHOH359
NHOH727

site_idVEC
Number of Residues29
DetailsSITE "VEC" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS C AND O.
ChainResidue
CTYR79
CVAL114
CASN115
CASN116
CALA117
CALA118
CMET122
CHIS125
CASN127
CARG142
CVAL157
OASP304
OARG307
OILE339
OPRO340
OGLN341
OSER342
OILE343
OSER344
OGLU345
CHOH220
CHOH223
OHOH644
CHOH231
OHOH652
CHOH234
OHOH668
CHOH246
CHOH267

site_idVED
Number of Residues29
DetailsSITE "VED" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS D AND P.
ChainResidue
DTYR79
DVAL114
DASN115
DASN116
DALA117
DALA118
DMET122
DHIS125
DASN127
DARG142
DVAL157
PASP304
PARG307
PILE339
PPRO340
PGLN341
PSER342
PILE343
PSER344
PGLU345
DHOH754
PHOH639
DHOH773
DHOH780
PHOH652
DHOH789
PHOH668
DHOH831
PHOH723

site_idVEE
Number of Residues29
DetailsSITE "VEE" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS E AND Q.
ChainResidue
ETYR79
EVAL114
EASN115
EASN116
EALA117
EALA118
EMET122
EHIS125
EASN127
EARG142
EVAL157
QASP304
QARG307
QILE339
QPRO340
QGLN341
QSER342
QILE343
QSER344
QGLU345
EHOH222
QHOH998
EHOH229
EHOH234
QHOH1023
EHOH237
QHOH1049
EHOH249
QHOH1135

site_idVEF
Number of Residues29
DetailsSITE "VEF" IS THE VESTIGIAL SITE OF THE PROTOMER CONSISTING OF CHAINS F AND R.
ChainResidue
FTYR79
FVAL114
FASN115
FASN116
FALA117
FALA118
FMET122
FHIS125
FASN127
FARG142
FVAL157
RASP304
RARG307
RILE339
RPRO340
RGLN341
RSER342
RILE343
RSER344
RGLU345
FHOH1226
FHOH1234
RHOH1245
FHOH1252
RHOH1259
FHOH1261
RHOH1285
FHOH1303
RHOH1371

Functional Information from PROSITE/UniProt
site_idPS00083
Number of Residues29
DetailsINTRADIOL_DIOXYGENAS Intradiol ring-cleavage dioxygenases signature. VaGrVvdqyGkpVpntlVEMwqanagGrY
ChainResidueDetails
MVAL380-TYR408
ALEU51-TYR79

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues24
DetailsBINDING: BINDING => ECO:0000269|PubMed:7990141
ChainResidueDetails
MARG409
OPRO448
OILE461
OPHE463
PARG409
PPRO448
PILE461
PPHE463
QARG409
QPRO448
QILE461
MPRO448
QPHE463
RARG409
RPRO448
RILE461
RPHE463
MILE461
MPHE463
NARG409
NPRO448
NILE461
NPHE463
OARG409

Catalytic Information from CSA
site_idMCSA1
Number of Residues5
DetailsM-CSA 936
ChainResidueDetails
MARG409metal ligand
MPRO448metal ligand, proton shuttle (general acid/base)
MPRO458electrostatic stabiliser
MILE461metal ligand
MPHE463metal ligand

site_idMCSA2
Number of Residues5
DetailsM-CSA 936
ChainResidueDetails
NARG409metal ligand
NPRO448metal ligand, proton shuttle (general acid/base)
NPRO458electrostatic stabiliser
NILE461metal ligand
NPHE463metal ligand

site_idMCSA3
Number of Residues5
DetailsM-CSA 936
ChainResidueDetails
OARG409metal ligand
OPRO448metal ligand, proton shuttle (general acid/base)
OPRO458electrostatic stabiliser
OILE461metal ligand
OPHE463metal ligand

site_idMCSA4
Number of Residues5
DetailsM-CSA 936
ChainResidueDetails
PARG409metal ligand
PPRO448metal ligand, proton shuttle (general acid/base)
PPRO458electrostatic stabiliser
PILE461metal ligand
PPHE463metal ligand

site_idMCSA5
Number of Residues5
DetailsM-CSA 936
ChainResidueDetails
QARG409metal ligand
QPRO448metal ligand, proton shuttle (general acid/base)
QPRO458electrostatic stabiliser
QILE461metal ligand
QPHE463metal ligand

site_idMCSA6
Number of Residues5
DetailsM-CSA 936
ChainResidueDetails
RARG409metal ligand
RPRO448metal ligand, proton shuttle (general acid/base)
RPRO458electrostatic stabiliser
RILE461metal ligand
RPHE463metal ligand

218853

PDB entries from 2024-04-24

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