Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

2VDI

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0004497molecular_functionmonooxygenase activity
A0009507cellular_componentchloroplast
A0009853biological_processphotorespiration
A0015977biological_processcarbon fixation
A0015979biological_processphotosynthesis
A0016829molecular_functionlyase activity
A0016984molecular_functionribulose-bisphosphate carboxylase activity
A0019253biological_processreductive pentose-phosphate cycle
A0046872molecular_functionmetal ion binding
B0000287molecular_functionmagnesium ion binding
B0004497molecular_functionmonooxygenase activity
B0009507cellular_componentchloroplast
B0009853biological_processphotorespiration
B0015977biological_processcarbon fixation
B0015979biological_processphotosynthesis
B0016829molecular_functionlyase activity
B0016984molecular_functionribulose-bisphosphate carboxylase activity
B0019253biological_processreductive pentose-phosphate cycle
B0046872molecular_functionmetal ion binding
C0000287molecular_functionmagnesium ion binding
C0004497molecular_functionmonooxygenase activity
C0009507cellular_componentchloroplast
C0009853biological_processphotorespiration
C0015977biological_processcarbon fixation
C0015979biological_processphotosynthesis
C0016829molecular_functionlyase activity
C0016984molecular_functionribulose-bisphosphate carboxylase activity
C0019253biological_processreductive pentose-phosphate cycle
C0046872molecular_functionmetal ion binding
D0000287molecular_functionmagnesium ion binding
D0004497molecular_functionmonooxygenase activity
D0009507cellular_componentchloroplast
D0009853biological_processphotorespiration
D0015977biological_processcarbon fixation
D0015979biological_processphotosynthesis
D0016829molecular_functionlyase activity
D0016984molecular_functionribulose-bisphosphate carboxylase activity
D0019253biological_processreductive pentose-phosphate cycle
D0046872molecular_functionmetal ion binding
E0000287molecular_functionmagnesium ion binding
E0004497molecular_functionmonooxygenase activity
E0009507cellular_componentchloroplast
E0009853biological_processphotorespiration
E0015977biological_processcarbon fixation
E0015979biological_processphotosynthesis
E0016829molecular_functionlyase activity
E0016984molecular_functionribulose-bisphosphate carboxylase activity
E0019253biological_processreductive pentose-phosphate cycle
E0046872molecular_functionmetal ion binding
F0000287molecular_functionmagnesium ion binding
F0004497molecular_functionmonooxygenase activity
F0009507cellular_componentchloroplast
F0009853biological_processphotorespiration
F0015977biological_processcarbon fixation
F0015979biological_processphotosynthesis
F0016829molecular_functionlyase activity
F0016984molecular_functionribulose-bisphosphate carboxylase activity
F0019253biological_processreductive pentose-phosphate cycle
F0046872molecular_functionmetal ion binding
G0000287molecular_functionmagnesium ion binding
G0004497molecular_functionmonooxygenase activity
G0009507cellular_componentchloroplast
G0009853biological_processphotorespiration
G0015977biological_processcarbon fixation
G0015979biological_processphotosynthesis
G0016829molecular_functionlyase activity
G0016984molecular_functionribulose-bisphosphate carboxylase activity
G0019253biological_processreductive pentose-phosphate cycle
G0046872molecular_functionmetal ion binding
H0000287molecular_functionmagnesium ion binding
H0004497molecular_functionmonooxygenase activity
H0009507cellular_componentchloroplast
H0009853biological_processphotorespiration
H0015977biological_processcarbon fixation
H0015979biological_processphotosynthesis
H0016829molecular_functionlyase activity
H0016984molecular_functionribulose-bisphosphate carboxylase activity
H0019253biological_processreductive pentose-phosphate cycle
H0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A1476
ChainResidue
ALYS177
AKCX201
AASP203
AGLU204
ACAP1477

site_idAC2
Number of Residues27
DetailsBINDING SITE FOR RESIDUE CAP A1477
ChainResidue
AASP203
AGLU204
AHIS294
AARG295
AHIS327
ALYS334
ALEU335
ASER379
AGLY380
AGLY381
AGLY403
AGLY404
AMG1476
AHOH2124
AHOH2133
AHOH2150
AHOH2151
BGLU60
BTHR65
BTRP66
BASN123
BHOH2017
BHOH2037
ATHR173
ALYS175
ALYS177
AKCX201

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B1476
ChainResidue
BLYS177
BKCX201
BASP203
BGLU204
BCAP1477

site_idAC4
Number of Residues28
DetailsBINDING SITE FOR RESIDUE CAP B1477
ChainResidue
AGLU60
ATHR65
ATRP66
AASN123
AHOH2038
BTHR173
BLYS175
BLYS177
BKCX201
BASP203
BGLU204
BHIS294
BARG295
BHIS327
BLYS334
BLEU335
BSER379
BGLY380
BGLY381
BGLY403
BGLY404
BMG1476
BHOH2053
BHOH2091
BHOH2124
BHOH2150
BHOH2151
BHOH2152

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG C1476
ChainResidue
CLYS177
CKCX201
CASP203
CGLU204
CCAP1477

site_idAC6
Number of Residues28
DetailsBINDING SITE FOR RESIDUE CAP C1477
ChainResidue
CTHR173
CLYS175
CLYS177
CKCX201
CASP203
CGLU204
CHIS294
CARG295
CHIS327
CLYS334
CLEU335
CSER379
CGLY380
CGLY381
CGLY403
CGLY404
CMG1476
CHOH2055
CHOH2118
CHOH2126
CHOH2141
CHOH2142
CHOH2143
CHOH2144
DGLU60
DTHR65
DTRP66
DASN123

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG D1476
ChainResidue
DKCX201
DASP203
DGLU204
DCAP1477
DLYS177

site_idAC8
Number of Residues27
DetailsBINDING SITE FOR RESIDUE CAP D1477
ChainResidue
CGLU60
CTHR65
CTRP66
CASN123
DTHR173
DLYS175
DLYS177
DKCX201
DASP203
DGLU204
DHIS294
DARG295
DHIS327
DLYS334
DLEU335
DSER379
DGLY380
DGLY381
DGLY403
DGLY404
DMG1476
DHOH2129
DHOH2154
DHOH2155
DHOH2156
DHOH2157
DHOH2158

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG E1476
ChainResidue
ELYS177
EKCX201
EASP203
EGLU204
ECAP1477

site_idBC1
Number of Residues28
DetailsBINDING SITE FOR RESIDUE CAP E1477
ChainResidue
ETHR173
ELYS175
ELYS177
EKCX201
EASP203
EGLU204
EHIS294
EARG295
EHIS327
ELYS334
ELEU335
ESER379
EGLY380
EGLY381
EGLY403
EGLY404
EMG1476
EHOH2110
EHOH2138
EHOH2155
EHOH2156
EHOH2157
EHOH2158
FGLU60
FTHR65
FTRP66
FASN123
FHOH2015

site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG F1476
ChainResidue
FLYS177
FKCX201
FASP203
FGLU204
FCAP1477

site_idBC3
Number of Residues27
DetailsBINDING SITE FOR RESIDUE CAP F1477
ChainResidue
EGLU60
ETHR65
ETRP66
EASN123
EHOH2018
FTHR173
FLYS175
FLYS177
FKCX201
FASP203
FGLU204
FHIS294
FARG295
FHIS327
FLYS334
FLEU335
FSER379
FGLY380
FGLY381
FGLY403
FGLY404
FMG1476
FHOH2088
FHOH2090
FHOH2112
FHOH2113
FHOH2115

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG G1476
ChainResidue
GLYS177
GKCX201
GASP203
GGLU204
GCAP1477

site_idBC5
Number of Residues28
DetailsBINDING SITE FOR RESIDUE CAP G1477
ChainResidue
GTHR173
GLYS175
GLYS177
GKCX201
GASP203
GGLU204
GHIS294
GARG295
GHIS327
GLYS334
GLEU335
GSER379
GGLY380
GGLY381
GGLY403
GGLY404
GMG1476
GHOH2066
GHOH2107
GHOH2137
GHOH2157
GHOH2158
GHOH2159
GHOH2160
HGLU60
HTHR65
HTRP66
HASN123

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG H1476
ChainResidue
HLYS177
HKCX201
HASP203
HGLU204
HCAP1477

site_idBC7
Number of Residues25
DetailsBINDING SITE FOR RESIDUE CAP H1477
ChainResidue
GGLU60
GTHR65
GTRP66
GASN123
GHOH2047
HTHR173
HLYS175
HLYS177
HKCX201
HASP203
HGLU204
HHIS294
HARG295
HHIS327
HLYS334
HLEU335
HSER379
HGLY380
HGLY381
HGLY403
HGLY404
HMG1476
HHOH2098
HHOH2145
HHOH2146

site_idBC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A1478
ChainResidue
ATYR24
ATHR68
AVAL69
AASP72
AEDO1479

site_idBC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A1479
ChainResidue
ALYS18
ATHR65
ATRP66
ATHR67
ATHR68
AEDO1478

site_idCC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO A1480
ChainResidue
AGLU52
AHOH2152
BPHE469

site_idCC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A1481
ChainResidue
AARG295
AHIS298
AASP473
AHOH2153

site_idCC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO H1478
ChainResidue
HTYR24
HTHR68
HVAL69
HASP72
HEDO1479
HHOH2016
HHOH2147
HHOH2148

site_idCC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE EDO H1479
ChainResidue
HLYS18
HTYR20
HTHR65
HTRP66
HTHR67
HTHR68
HEDO1478
HHOH2005
HHOH2148

site_idCC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO H1480
ChainResidue
GPHE469
GHOH2162
HGLU52

site_idCC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO H1481
ChainResidue
HLYS466
HPHE467
HGLU468
HPHE469
HHOH2149

site_idCC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO H1482
ChainResidue
HARG295
HPHE345
HASP473
HHOH2150

site_idCC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO G1478
ChainResidue
GTYR24
GGLY64
GTHR68
GVAL69
GASP72
GHOH2161

site_idCC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO G1479
ChainResidue
GVAL17
GLYS18
GTHR65
GTRP66
GTHR67
GTHR68
GHOH2016
GHOH2161

site_idDC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO G1480
ChainResidue
GLYS466
GPHE467
GGLU468
GPHE469
GHOH2162

site_idDC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO G1481
ChainResidue
GARG295
GSER328
GGLY329
GGLU336
GGLY337
GTHR342
GPHE345

site_idDC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO O1141
ChainResidue
ATYR226
ALYS227
AHOH2071
OLYS49
OGLU55
OHOH2022

site_idDC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO O1142
ChainResidue
OGLY37
OILE39
OPHE81
OGLY82
OCYS83

site_idDC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO F1478
ChainResidue
ELEU270
EHOH2099
FLEU270
FHOH2132

site_idDC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE EDO F1479
ChainResidue
EPRO176
FTHR63
FGLY64
FTHR65
FTHR67
FVAL69
FASP72
FHOH2007
FHOH2018
FHOH2022

site_idDC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO F1480
ChainResidue
FVAL17
FLYS18
FTHR65
FTRP66
FTHR67
FTHR68

site_idDC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO F1481
ChainResidue
EPHE469
FGLU52

site_idDC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO F1482
ChainResidue
FLYS466
FPHE467
FGLU468
FPHE469

site_idEC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO F1483
ChainResidue
FARG295
FSER328
FGLU336
FPHE345
FHOH2097

site_idEC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C1478
ChainResidue
CTYR24
CTHR68
CVAL69
CASP72

site_idEC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO C1479
ChainResidue
CLYS18
CTHR65
CTRP66
CTHR67
CTHR68

site_idEC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO K1141
ChainResidue
KGLY37
KTRP38
KILE39
KGLY82

site_idEC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B1478
ChainResidue
BTYR24
BTHR68
BVAL69
BASP72
BEDO1479
BHOH2153

site_idEC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B1479
ChainResidue
BLYS18
BTHR65
BTRP66
BTHR67
BTHR68
BEDO1478
BHOH2008

site_idEC7
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO B1480
ChainResidue
BGLU52
BALA129

site_idEC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B1481
ChainResidue
AHOH2152
BLYS466
BGLU468
BPHE469

site_idEC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO J1141
ChainResidue
HTYR226
HLYS227
HALA230
JLYS49
JGLU55
JASP69
JHOH2019
JHOH2023

site_idFC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C1480
ChainResidue
CLEU270
CHOH2145
CHOH2146
DLEU270

site_idFC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO G1482
ChainResidue
GLEU270
GGLY273
GPHE274
HLEU270
HTHR271

site_idFC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A1482
ChainResidue
ALEU270
AGLY273
APHE274
AHOH2154
BLEU270
BTHR271

site_idFC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO D1478
ChainResidue
DLYS18
DTHR65
DTRP66
DTHR67
DTHR68

site_idFC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO D1479
ChainResidue
CPHE469
DGLU52
DHOH2005

site_idFC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO D1480
ChainResidue
DLYS466
DGLU468
DPHE469

site_idFC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO E1478
ChainResidue
ETYR24
EGLY64
EVAL69
EASP72
EEDO1479

site_idFC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO E1479
ChainResidue
ELYS18
ETHR65
ETRP66
ETHR67
ETHR68
EEDO1478

site_idFC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO E1480
ChainResidue
EGLU52

site_idGC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO E1481
ChainResidue
ELYS466
EGLU468
EPHE469
EHOH2159

site_idGC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO E1482
ChainResidue
EGLU336
EGLY337
EGLU338
EASP473

site_idGC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO N1141
ChainResidue
NILE39
NGLY82
NCYS83

site_idGC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO L1141
ChainResidue
LGLY37
LTRP38
LILE39
LGLY82

site_idGC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO J1142
ChainResidue
JGLY37
JGLY82
JCYS83
JHOH2036

Functional Information from PROSITE/UniProt
site_idPS00157
Number of Residues9
DetailsRUBISCO_LARGE Ribulose bisphosphate carboxylase large chain active site. GlDFtKdDE
ChainResidueDetails
AGLY196-GLU204

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsMOD_RES: N-methylmethionine => ECO:0000269|PubMed:11641402
ChainResidueDetails
IMME1
EHIS294
FLYS175
FHIS294
GLYS175
GHIS294
HLYS175
HHIS294
JMME1
KMME1
LMME1
MMME1
NMME1
OMME1
PMME1
ELYS175

site_idSWS_FT_FI2
Number of Residues8
DetailsBINDING: in homodimeric partner
ChainResidueDetails
AASN123
BASN123
CASN123
DASN123
EASN123
FASN123
GASN123
HASN123

site_idSWS_FT_FI3
Number of Residues40
DetailsBINDING:
ChainResidueDetails
ATHR173
BSER379
CTHR173
CLYS177
CARG295
CHIS327
CSER379
DTHR173
DLYS177
DARG295
DHIS327
ALYS177
DSER379
ETHR173
ELYS177
EARG295
EHIS327
ESER379
FTHR173
FLYS177
FARG295
FHIS327
AARG295
FSER379
GTHR173
GLYS177
GARG295
GHIS327
GSER379
HTHR173
HLYS177
HARG295
HHIS327
AHIS327
HSER379
ASER379
BTHR173
BLYS177
BARG295
BHIS327

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING: via carbamate group => ECO:0000269|PubMed:11641402, ECO:0000269|PubMed:11866526
ChainResidueDetails
AKCX201
BKCX201
CKCX201
DKCX201
EKCX201
FKCX201
GKCX201
HKCX201

site_idSWS_FT_FI5
Number of Residues16
DetailsBINDING: BINDING => ECO:0000269|PubMed:11641402, ECO:0000269|PubMed:11866526
ChainResidueDetails
AASP203
EGLU204
FASP203
FGLU204
GASP203
GGLU204
HASP203
HGLU204
AGLU204
BASP203
BGLU204
CASP203
CGLU204
DASP203
DGLU204
EASP203

site_idSWS_FT_FI6
Number of Residues8
DetailsSITE: Transition state stabilizer
ChainResidueDetails
ALYS334
BLYS334
CLYS334
DLYS334
ELYS334
FLYS334
GLYS334
HLYS334

site_idSWS_FT_FI7
Number of Residues8
DetailsMOD_RES: N-acetylproline => ECO:0000269|PubMed:16668742
ChainResidueDetails
APRO3
BPRO3
CPRO3
DPRO3
EPRO3
FPRO3
GPRO3
HPRO3

site_idSWS_FT_FI8
Number of Residues16
DetailsMOD_RES: 4-hydroxyproline => ECO:0000269|PubMed:11641402, ECO:0000269|PubMed:11866526
ChainResidueDetails
AHYP104
EHYP151
FHYP104
FHYP151
GHYP104
GHYP151
HHYP104
HHYP151
AHYP151
BHYP104
BHYP151
CHYP104
CHYP151
DHYP104
DHYP151
EHYP104

site_idSWS_FT_FI9
Number of Residues8
DetailsMOD_RES: N6-carboxylysine => ECO:0000269|PubMed:11641402, ECO:0000269|PubMed:11866526, ECO:0000269|PubMed:6302265
ChainResidueDetails
AKCX201
BKCX201
CKCX201
DKCX201
EKCX201
FKCX201
GKCX201
HKCX201

site_idSWS_FT_FI10
Number of Residues16
DetailsMOD_RES: S-methylcysteine => ECO:0000269|PubMed:11641402, ECO:0000269|PubMed:11866526
ChainResidueDetails
ASMC256
ESMC369
FSMC256
FSMC369
GSMC256
GSMC369
HSMC256
HSMC369
ASMC369
BSMC256
BSMC369
CSMC256
CSMC369
DSMC256
DSMC369
ESMC256

Catalytic Information from CSA
site_idCSA1
Number of Residues5
DetailsAnnotated By Reference To The Literature 1rbl
ChainResidueDetails
ALYS175
AHIS294
ALYS177
AASP203
AHIS327

site_idCSA2
Number of Residues5
DetailsAnnotated By Reference To The Literature 1rbl
ChainResidueDetails
BLYS175
BHIS294
BLYS177
BASP203
BHIS327

site_idCSA3
Number of Residues5
DetailsAnnotated By Reference To The Literature 1rbl
ChainResidueDetails
CLYS175
CHIS294
CLYS177
CASP203
CHIS327

site_idCSA4
Number of Residues5
DetailsAnnotated By Reference To The Literature 1rbl
ChainResidueDetails
DLYS175
DHIS294
DLYS177
DASP203
DHIS327

site_idCSA5
Number of Residues5
DetailsAnnotated By Reference To The Literature 1rbl
ChainResidueDetails
ELYS175
EHIS294
ELYS177
EASP203
EHIS327

site_idCSA6
Number of Residues5
DetailsAnnotated By Reference To The Literature 1rbl
ChainResidueDetails
FLYS175
FHIS294
FLYS177
FASP203
FHIS327

site_idCSA7
Number of Residues5
DetailsAnnotated By Reference To The Literature 1rbl
ChainResidueDetails
GLYS175
GHIS294
GLYS177
GASP203
GHIS327

site_idCSA8
Number of Residues5
DetailsAnnotated By Reference To The Literature 1rbl
ChainResidueDetails
HLYS175
HHIS294
HLYS177
HASP203
HHIS327

223532

PDB entries from 2024-08-07

PDB statisticsPDBj update infoContact PDBjnumon