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1RBL

STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM SYNECHOCOCCUS PCC6301

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0004497molecular_functionmonooxygenase activity
A0005515molecular_functionprotein binding
A0009853biological_processphotorespiration
A0015977biological_processcarbon fixation
A0015979biological_processphotosynthesis
A0016829molecular_functionlyase activity
A0016984molecular_functionribulose-bisphosphate carboxylase activity
A0019253biological_processreductive pentose-phosphate cycle
A0031470cellular_componentcarboxysome
A0046872molecular_functionmetal ion binding
B0000287molecular_functionmagnesium ion binding
B0004497molecular_functionmonooxygenase activity
B0005515molecular_functionprotein binding
B0009853biological_processphotorespiration
B0015977biological_processcarbon fixation
B0015979biological_processphotosynthesis
B0016829molecular_functionlyase activity
B0016984molecular_functionribulose-bisphosphate carboxylase activity
B0019253biological_processreductive pentose-phosphate cycle
B0031470cellular_componentcarboxysome
B0046872molecular_functionmetal ion binding
C0000287molecular_functionmagnesium ion binding
C0004497molecular_functionmonooxygenase activity
C0005515molecular_functionprotein binding
C0009853biological_processphotorespiration
C0015977biological_processcarbon fixation
C0015979biological_processphotosynthesis
C0016829molecular_functionlyase activity
C0016984molecular_functionribulose-bisphosphate carboxylase activity
C0019253biological_processreductive pentose-phosphate cycle
C0031470cellular_componentcarboxysome
C0046872molecular_functionmetal ion binding
D0000287molecular_functionmagnesium ion binding
D0004497molecular_functionmonooxygenase activity
D0005515molecular_functionprotein binding
D0009853biological_processphotorespiration
D0015977biological_processcarbon fixation
D0015979biological_processphotosynthesis
D0016829molecular_functionlyase activity
D0016984molecular_functionribulose-bisphosphate carboxylase activity
D0019253biological_processreductive pentose-phosphate cycle
D0031470cellular_componentcarboxysome
D0046872molecular_functionmetal ion binding
E0000287molecular_functionmagnesium ion binding
E0004497molecular_functionmonooxygenase activity
E0005515molecular_functionprotein binding
E0009853biological_processphotorespiration
E0015977biological_processcarbon fixation
E0015979biological_processphotosynthesis
E0016829molecular_functionlyase activity
E0016984molecular_functionribulose-bisphosphate carboxylase activity
E0019253biological_processreductive pentose-phosphate cycle
E0031470cellular_componentcarboxysome
E0046872molecular_functionmetal ion binding
F0000287molecular_functionmagnesium ion binding
F0004497molecular_functionmonooxygenase activity
F0005515molecular_functionprotein binding
F0009853biological_processphotorespiration
F0015977biological_processcarbon fixation
F0015979biological_processphotosynthesis
F0016829molecular_functionlyase activity
F0016984molecular_functionribulose-bisphosphate carboxylase activity
F0019253biological_processreductive pentose-phosphate cycle
F0031470cellular_componentcarboxysome
F0046872molecular_functionmetal ion binding
G0000287molecular_functionmagnesium ion binding
G0004497molecular_functionmonooxygenase activity
G0005515molecular_functionprotein binding
G0009853biological_processphotorespiration
G0015977biological_processcarbon fixation
G0015979biological_processphotosynthesis
G0016829molecular_functionlyase activity
G0016984molecular_functionribulose-bisphosphate carboxylase activity
G0019253biological_processreductive pentose-phosphate cycle
G0031470cellular_componentcarboxysome
G0046872molecular_functionmetal ion binding
H0000287molecular_functionmagnesium ion binding
H0004497molecular_functionmonooxygenase activity
H0005515molecular_functionprotein binding
H0009853biological_processphotorespiration
H0015977biological_processcarbon fixation
H0015979biological_processphotosynthesis
H0016829molecular_functionlyase activity
H0016984molecular_functionribulose-bisphosphate carboxylase activity
H0019253biological_processreductive pentose-phosphate cycle
H0031470cellular_componentcarboxysome
H0046872molecular_functionmetal ion binding
I0009853biological_processphotorespiration
I0015977biological_processcarbon fixation
I0015979biological_processphotosynthesis
I0016984molecular_functionribulose-bisphosphate carboxylase activity
I0019253biological_processreductive pentose-phosphate cycle
I0031470cellular_componentcarboxysome
J0009853biological_processphotorespiration
J0015977biological_processcarbon fixation
J0015979biological_processphotosynthesis
J0016984molecular_functionribulose-bisphosphate carboxylase activity
J0019253biological_processreductive pentose-phosphate cycle
J0031470cellular_componentcarboxysome
K0009853biological_processphotorespiration
K0015977biological_processcarbon fixation
K0015979biological_processphotosynthesis
K0016984molecular_functionribulose-bisphosphate carboxylase activity
K0019253biological_processreductive pentose-phosphate cycle
K0031470cellular_componentcarboxysome
L0009853biological_processphotorespiration
L0015977biological_processcarbon fixation
L0015979biological_processphotosynthesis
L0016984molecular_functionribulose-bisphosphate carboxylase activity
L0019253biological_processreductive pentose-phosphate cycle
L0031470cellular_componentcarboxysome
M0009853biological_processphotorespiration
M0015977biological_processcarbon fixation
M0015979biological_processphotosynthesis
M0016984molecular_functionribulose-bisphosphate carboxylase activity
M0019253biological_processreductive pentose-phosphate cycle
M0031470cellular_componentcarboxysome
N0009853biological_processphotorespiration
N0015977biological_processcarbon fixation
N0015979biological_processphotosynthesis
N0016984molecular_functionribulose-bisphosphate carboxylase activity
N0019253biological_processreductive pentose-phosphate cycle
N0031470cellular_componentcarboxysome
O0009853biological_processphotorespiration
O0015977biological_processcarbon fixation
O0015979biological_processphotosynthesis
O0016984molecular_functionribulose-bisphosphate carboxylase activity
O0019253biological_processreductive pentose-phosphate cycle
O0031470cellular_componentcarboxysome
P0009853biological_processphotorespiration
P0015977biological_processcarbon fixation
P0015979biological_processphotosynthesis
P0016984molecular_functionribulose-bisphosphate carboxylase activity
P0019253biological_processreductive pentose-phosphate cycle
P0031470cellular_componentcarboxysome
Functional Information from PDB Data
site_id1P
Number of Residues4
DetailsTHE BINDING SITE OF THE FIRST PHOSPHATE GROUP OF THE CAP
ChainResidue
MPHE65
AGLY404
AGLY381
AGLY403

site_id1P2
Number of Residues4
Details
ChainResidue
IPHE65
BGLY404
BGLY381
BGLY403

site_id1P3
Number of Residues4
Details
ChainResidue
NPHE65
CGLY404
CGLY381
CGLY403

site_id1P4
Number of Residues4
Details
ChainResidue
JPHE65
DGLY404
DGLY381
DGLY403

site_id1P5
Number of Residues4
Details
ChainResidue
OPHE65
EGLY404
EGLY381
EGLY403

site_id1P6
Number of Residues4
Details
ChainResidue
KPHE65
FGLY404
FGLY381
FGLY403

site_id1P7
Number of Residues4
Details
ChainResidue
PPHE65
GGLY404
GGLY381
GGLY403

site_id1P8
Number of Residues4
Details
ChainResidue
LPHE65
HGLY404
HGLY381
HGLY403

site_id2P
Number of Residues2
DetailsTHE BINDING SITE OF THE 2ND PHOSPHATE OF CAP
ChainResidue
AARG295
AHIS327

site_id2P2
Number of Residues2
Details
ChainResidue
BARG295
BHIS327

site_id2P3
Number of Residues2
Details
ChainResidue
CARG295
CHIS327

site_id2P4
Number of Residues2
Details
ChainResidue
DARG295
DHIS327

site_id2P5
Number of Residues2
Details
ChainResidue
EARG295
EHIS327

site_id2P6
Number of Residues2
Details
ChainResidue
FARG295
FHIS327

site_id2P7
Number of Residues2
Details
ChainResidue
GARG295
GHIS327

site_id2P8
Number of Residues2
Details
ChainResidue
HHIS327
HARG295

site_idAC1
Number of Residues23
DetailsBINDING SITE FOR RESIDUE CAP A 476
ChainResidue
ATHR173
ALYS175
ALYS177
AHIS294
AARG295
AHIS327
ALYS334
ALEU335
ASER379
AGLY380
AGLY381
AGLY403
AGLY404
BTHR65
BTRP66
BASN123
AHOH514
AHOH515
AHOH520
AHOH521
AHOH569
AHOH570
AHOH571

site_idAC2
Number of Residues18
DetailsBINDING SITE FOR RESIDUE CAP B 476
ChainResidue
ATHR65
ATRP66
AASN123
BTHR173
BLYS175
BLYS177
BHIS294
BARG295
BHIS327
BLYS334
BLEU335
BSER379
BGLY380
BGLY381
BGLY403
BGLY404
AHOH502
AHOH503

site_idAC3
Number of Residues16
DetailsBINDING SITE FOR RESIDUE CAP C 476
ChainResidue
CTHR173
CLYS175
CLYS177
CHIS294
CARG295
CHIS327
CLYS334
CLEU335
CSER379
CGLY380
CGLY381
CGLY403
CGLY404
DTHR65
DTRP66
DASN123

site_idAC4
Number of Residues16
DetailsBINDING SITE FOR RESIDUE CAP D 476
ChainResidue
CTHR65
CTRP66
CASN123
DTHR173
DLYS175
DLYS177
DHIS294
DARG295
DHIS327
DLYS334
DLEU335
DSER379
DGLY380
DGLY381
DGLY403
DGLY404

site_idAC5
Number of Residues16
DetailsBINDING SITE FOR RESIDUE CAP H 476
ChainResidue
GTHR65
GTRP66
GASN123
HTHR173
HLYS175
HLYS177
HHIS294
HARG295
HHIS327
HLYS334
HLEU335
HSER379
HGLY380
HGLY381
HGLY403
HGLY404

site_idAC6
Number of Residues16
DetailsBINDING SITE FOR RESIDUE CAP G 476
ChainResidue
GTHR173
GLYS175
GLYS177
GHIS294
GARG295
GHIS327
GLYS334
GLEU335
GSER379
GGLY380
GGLY381
GGLY403
GGLY404
HTHR65
HTRP66
HASN123

site_idAC7
Number of Residues16
DetailsBINDING SITE FOR RESIDUE CAP F 476
ChainResidue
ETHR65
ETRP66
EASN123
FTHR173
FLYS175
FLYS177
FHIS294
FARG295
FHIS327
FLYS334
FLEU335
FSER379
FGLY380
FGLY381
FGLY403
FGLY404

site_idAC8
Number of Residues16
DetailsBINDING SITE FOR RESIDUE CAP E 476
ChainResidue
ETHR173
ELYS175
ELYS177
EHIS294
EARG295
EHIS327
ELYS334
ELEU335
ESER379
EGLY380
EGLY381
EGLY403
EGLY404
FTHR65
FTRP66
FASN123

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT A 478
ChainResidue
ALYS201
AASP202
AASP203
AGLU204
AHIS294
AHIS327

site_idAD1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT D 478
ChainResidue
DLYS201
DASP202
DASP203
DGLU204
DHIS294
DHIS327

site_idAD2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT E 478
ChainResidue
ELYS201
EASP202
EASP203
EGLU204
EHIS294
EHIS327

site_idAD3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT F 478
ChainResidue
FLYS201
FASP202
FASP203
FGLU204
FHIS294
FHIS327

site_idAD4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT H 478
ChainResidue
HLYS201
HASP202
HASP203
HGLU204
HHIS294
HHIS327

site_idAD5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT G 478
ChainResidue
GLYS201
GASP202
GASP203
GGLU204
GHIS294
GHIS327

site_idAD6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT C 478
ChainResidue
CLYS201
CASP202
CASP203
CGLU204
CHIS294
CHIS327

site_idAD7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FMT B 478
ChainResidue
BLYS201
BASP202
BASP203
BGLU204
BHIS294
BHIS327

site_idAD8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG A 477
ChainResidue
AASP203
AGLU204

site_idAD9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG B 477
ChainResidue
BASP203
BGLU204

site_idAE1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG C 477
ChainResidue
CASP203
CGLU204

site_idAE2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG D 477
ChainResidue
DASP203
DGLU204

site_idAE3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG E 477
ChainResidue
EASP203
EGLU204

site_idAE4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG F 477
ChainResidue
FASP203
FGLU204

site_idAE5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG G 477
ChainResidue
GASP203
GGLU204

site_idAE6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE MG H 477
ChainResidue
HASP203
HGLU204

site_idCA2
Number of Residues4
Details
ChainResidue
BMG477
BLYS201
BHIS294
BSER379

site_idCA3
Number of Residues4
Details
ChainResidue
CMG477
CLYS201
CHIS294
CSER379

site_idCA4
Number of Residues4
Details
ChainResidue
DMG477
DLYS201
DHIS294
DSER379

site_idCA5
Number of Residues4
Details
ChainResidue
EMG477
ELYS201
EHIS294
ESER379

site_idCA6
Number of Residues4
Details
ChainResidue
FMG477
FLYS201
FHIS294
FSER379

site_idCA7
Number of Residues4
Details
ChainResidue
GMG477
GLYS201
GHIS294
GSER379

site_idCA8
Number of Residues4
Details
ChainResidue
HMG477
HLYS201
HHIS294
HSER379

site_idCAB
Number of Residues4
DetailsOTHER RESIDUES INVOLVED IN BINDING THE CAP
ChainResidue
AMG477
ALYS201
AHIS294
ASER379

site_idMG
Number of Residues3
DetailsTHE MAGNESIUM BINDING SITE
ChainResidue
ALYS201
AASP203
AGLU204

site_idMG2
Number of Residues3
Details
ChainResidue
BLYS201
BASP203
BGLU204

site_idMG3
Number of Residues3
Details
ChainResidue
CLYS201
CASP203
CGLU204

site_idMG4
Number of Residues3
Details
ChainResidue
DLYS201
DASP203
DGLU204

site_idMG5
Number of Residues3
Details
ChainResidue
ELYS201
EASP203
EGLU204

site_idMG6
Number of Residues3
Details
ChainResidue
FLYS201
FASP203
FGLU204

site_idMG7
Number of Residues3
Details
ChainResidue
GLYS201
GASP203
GGLU204

site_idMG8
Number of Residues3
Details
ChainResidue
HLYS201
HASP203
HGLU204

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 Residues16
DetailsACT_SITE: Proton acceptor
ChainResidueDetails
ALYS175
EHIS294
FLYS175
FHIS294
GLYS175
GHIS294
HLYS175
HHIS294
AHIS294
BLYS175
BHIS294
CLYS175
CHIS294
DLYS175
DHIS294
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:8245022
ChainResidueDetails
ALYS201
BLYS201
CLYS201
DLYS201
ELYS201
FLYS201
GLYS201
HLYS201

site_idSWS_FT_FI5
Number of Residues16
DetailsBINDING: BINDING => ECO:0000269|PubMed:8245022
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: N6-carboxylysine => ECO:0000269|PubMed:16593333
ChainResidueDetails
ALYS201
BLYS201
CLYS201
DLYS201
ELYS201
FLYS201
GLYS201
HLYS201

Catalytic Information from CSA
site_idCSA1
Number of Residues6
Detailsa catalytic site defined by CSA, PubMed 8245022, 7922027, 8648644
ChainResidueDetails
ALYS175
ALYS201
ALYS177
AHIS294
AASP203
AHIS327

site_idCSA2
Number of Residues6
Detailsa catalytic site defined by CSA, PubMed 8245022, 7922027, 8648644
ChainResidueDetails
BLYS175
BLYS201
BLYS177
BHIS294
BASP203
BHIS327

site_idCSA3
Number of Residues6
Detailsa catalytic site defined by CSA, PubMed 8245022, 7922027, 8648644
ChainResidueDetails
CLYS175
CLYS201
CLYS177
CHIS294
CASP203
CHIS327

site_idCSA4
Number of Residues6
Detailsa catalytic site defined by CSA, PubMed 8245022, 7922027, 8648644
ChainResidueDetails
DLYS175
DLYS201
DLYS177
DHIS294
DASP203
DHIS327

site_idCSA5
Number of Residues6
Detailsa catalytic site defined by CSA, PubMed 8245022, 7922027, 8648644
ChainResidueDetails
ELYS175
ELYS201
ELYS177
EHIS294
EASP203
EHIS327

site_idCSA6
Number of Residues6
Detailsa catalytic site defined by CSA, PubMed 8245022, 7922027, 8648644
ChainResidueDetails
FLYS175
FLYS201
FLYS177
FHIS294
FASP203
FHIS327

site_idCSA7
Number of Residues6
Detailsa catalytic site defined by CSA, PubMed 8245022, 7922027, 8648644
ChainResidueDetails
GLYS175
GLYS201
GLYS177
GHIS294
GASP203
GHIS327

site_idCSA8
Number of Residues6
Detailsa catalytic site defined by CSA, PubMed 8245022, 7922027, 8648644
ChainResidueDetails
HLYS175
HLYS201
HLYS177
HHIS294
HASP203
HHIS327

site_idMCSA1
Number of Residues6
DetailsM-CSA 907
ChainResidueDetails
ALYS175electrostatic stabiliser, metal ligand, proton donor
ALYS201metal ligand, nucleophile, proton donor
AASP203metal ligand
AGLU204metal ligand
AHIS294proton acceptor
ALYS334electrostatic stabiliser

site_idMCSA2
Number of Residues6
DetailsM-CSA 907
ChainResidueDetails
BLYS175electrostatic stabiliser, metal ligand, proton donor
BLYS201metal ligand, nucleophile, proton donor
BASP203metal ligand
BGLU204metal ligand
BHIS294proton acceptor
BLYS334electrostatic stabiliser

site_idMCSA3
Number of Residues6
DetailsM-CSA 907
ChainResidueDetails
CLYS175electrostatic stabiliser, metal ligand, proton donor
CLYS201metal ligand, nucleophile, proton donor
CASP203metal ligand
CGLU204metal ligand
CHIS294proton acceptor
CLYS334electrostatic stabiliser

site_idMCSA4
Number of Residues6
DetailsM-CSA 907
ChainResidueDetails
DLYS175electrostatic stabiliser, metal ligand, proton donor
DLYS201metal ligand, nucleophile, proton donor
DASP203metal ligand
DGLU204metal ligand
DHIS294proton acceptor
DLYS334electrostatic stabiliser

site_idMCSA5
Number of Residues6
DetailsM-CSA 907
ChainResidueDetails
ELYS175electrostatic stabiliser, metal ligand, proton donor
ELYS201metal ligand, nucleophile, proton donor
EASP203metal ligand
EGLU204metal ligand
EHIS294proton acceptor
ELYS334electrostatic stabiliser

site_idMCSA6
Number of Residues6
DetailsM-CSA 907
ChainResidueDetails
FLYS175electrostatic stabiliser, metal ligand, proton donor
FLYS201metal ligand, nucleophile, proton donor
FASP203metal ligand
FGLU204metal ligand
FHIS294proton acceptor
FLYS334electrostatic stabiliser

site_idMCSA7
Number of Residues6
DetailsM-CSA 907
ChainResidueDetails
GLYS175electrostatic stabiliser, metal ligand, proton donor
GLYS201metal ligand, nucleophile, proton donor
GASP203metal ligand
GGLU204metal ligand
GHIS294proton acceptor
GLYS334electrostatic stabiliser

site_idMCSA8
Number of Residues6
DetailsM-CSA 907
ChainResidueDetails
HLYS175electrostatic stabiliser, metal ligand, proton donor
HLYS201metal ligand, nucleophile, proton donor
HASP203metal ligand
HGLU204metal ligand
HHIS294proton acceptor
HLYS334electrostatic stabiliser

224004

PDB entries from 2024-08-21

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