3AXM | pdb_00003axm

Structure of rice Rubisco in complex with 6PG

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
O [auth H]d3axmh2 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
O [auth H]d3axmh1 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain Ribulose 1,5-bisphosphate carboxylase-oxygenase Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
M [auth G]d3axmg2 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
M [auth G]d3axmg1 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain Ribulose 1,5-bisphosphate carboxylase-oxygenase Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
K [auth F]d3axmf2 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
K [auth F]d3axmf1 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain Ribulose 1,5-bisphosphate carboxylase-oxygenase Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
I [auth E]d3axme2 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
I [auth E]d3axme1 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain Ribulose 1,5-bisphosphate carboxylase-oxygenase Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
G [auth D]d3axmd2 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
G [auth D]d3axmd1 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain Ribulose 1,5-bisphosphate carboxylase-oxygenase Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
E [auth C]d3axmc2 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
E [auth C]d3axmc1 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain Ribulose 1,5-bisphosphate carboxylase-oxygenase Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
C [auth B]d3axmb2 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
C [auth B]d3axmb1 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain Ribulose 1,5-bisphosphate carboxylase-oxygenase Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
Ad3axma2 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
Ad3axma1 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain Ribulose 1,5-bisphosphate carboxylase-oxygenase Ribulose 1,5-bisphosphate carboxylase-oxygenase (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
P [auth Z]d3axmz_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
N [auth Y]d3axmy_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
L [auth X]d3axmx_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
J [auth W]d3axmw_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
H [auth V]d3axmv_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
F [auth U]d3axmu_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
D [auth T]d3axmt_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)
B [auth S]d3axms_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Oryza sativa Japonica Group ) [TaxId: 39947 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
O [auth H]SCOP2B SuperfamilyRuBisCo, C-terminal domain 8043421 3000552 SCOP2B (2022-06-29)
O [auth H]SCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8043423 3001258 SCOP2B (2022-06-29)
M [auth G]SCOP2B SuperfamilyRuBisCo, C-terminal domain 8043421 3000552 SCOP2B (2022-06-29)
M [auth G]SCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8043423 3001258 SCOP2B (2022-06-29)
K [auth F]SCOP2B SuperfamilyRuBisCo, C-terminal domain 8043421 3000552 SCOP2B (2022-06-29)
K [auth F]SCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8043423 3001258 SCOP2B (2022-06-29)
I [auth E]SCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8043423 3001258 SCOP2B (2022-06-29)
I [auth E]SCOP2B SuperfamilyRuBisCo, C-terminal domain 8043421 3000552 SCOP2B (2022-06-29)
G [auth D]SCOP2B SuperfamilyRuBisCo, C-terminal domain 8043421 3000552 SCOP2B (2022-06-29)
G [auth D]SCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8043423 3001258 SCOP2B (2022-06-29)
E [auth C]SCOP2B SuperfamilyRuBisCo, C-terminal domain 8043421 3000552 SCOP2B (2022-06-29)
E [auth C]SCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8043423 3001258 SCOP2B (2022-06-29)
C [auth B]SCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8043423 3001258 SCOP2B (2022-06-29)
C [auth B]SCOP2B SuperfamilyRuBisCo, C-terminal domain 8043421 3000552 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRuBisCo, C-terminal domain 8043421 3000552 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8043423 3001258 SCOP2B (2022-06-29)
P [auth Z]SCOP2B SuperfamilyRuBisCO, small subunit 8043428 3001622 SCOP2B (2022-06-29)
N [auth Y]SCOP2B SuperfamilyRuBisCO, small subunit 8043428 3001622 SCOP2B (2022-06-29)
L [auth X]SCOP2B SuperfamilyRuBisCO, small subunit 8043428 3001622 SCOP2B (2022-06-29)
J [auth W]SCOP2B SuperfamilyRuBisCO, small subunit 8043428 3001622 SCOP2B (2022-06-29)
H [auth V]SCOP2B SuperfamilyRuBisCO, small subunit 8043428 3001622 SCOP2B (2022-06-29)
F [auth U]SCOP2B SuperfamilyRuBisCO, small subunit 8043428 3001622 SCOP2B (2022-06-29)
D [auth T]SCOP2B SuperfamilyRuBisCO, small subunit 8043428 3001622 SCOP2B (2022-06-29)
B [auth S]SCOP2B SuperfamilyRuBisCO, small subunit 8043428 3001622 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
O [auth H]e3axmH3 A: Fusion glycoprotein F2X: Fusion glycoprotein F2H: Fusion glycoprotein F2T: Beta-barrel_RNDF:ECOD (20:10:01)
M [auth G]e3axmG3 A: Fusion glycoprotein F2X: Fusion glycoprotein F2H: Fusion glycoprotein F2T: Beta-barrel_RNDF:ECOD (20:10:01)
K [auth F]e3axmF3 A: Fusion glycoprotein F2X: Fusion glycoprotein F2H: Fusion glycoprotein F2T: Beta-barrel_RNDF:ECOD (20:10:01)
I [auth E]e3axmE3 A: Fusion glycoprotein F2X: Fusion glycoprotein F2H: Fusion glycoprotein F2T: Beta-barrel_RNDF:ECOD (20:10:01)
G [auth D]e3axmD3 A: Fusion glycoprotein F2X: Fusion glycoprotein F2H: Fusion glycoprotein F2T: Beta-barrel_RNDF:ECOD (20:10:01)
E [auth C]e3axmC3 A: Fusion glycoprotein F2X: Fusion glycoprotein F2H: Fusion glycoprotein F2T: Beta-barrel_RNDF:ECOD (20:10:01)
C [auth B]e3axmB3 A: Fusion glycoprotein F2X: Fusion glycoprotein F2H: Fusion glycoprotein F2T: Beta-barrel_RNDF:ECOD (20:10:01)
Ae3axmA3 A: Fusion glycoprotein F2X: Fusion glycoprotein F2H: Fusion glycoprotein F2T: Beta-barrel_RNDF:ECOD (20:10:01)
P [auth Z]e3axmZ2 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Peptidase_M49F:ECOD (20:10:01)
N [auth Y]e3axmY2 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Peptidase_M49F:ECOD (20:10:01)
L [auth X]e3axmX2 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Peptidase_M49F:ECOD (20:10:01)
J [auth W]e3axmW2 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Peptidase_M49F:ECOD (20:10:01)
H [auth V]e3axmV2 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Peptidase_M49F:ECOD (20:10:01)
F [auth U]e3axmU2 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Peptidase_M49F:ECOD (20:10:01)
D [auth T]e3axmT2 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Peptidase_M49F:ECOD (20:10:01)
B [auth S]e3axmS2 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Peptidase_M49F:ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
O [auth H]3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
O [auth H]3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
M [auth G]3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
M [auth G]3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
K [auth F]3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
K [auth F]3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
I [auth E]3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
I [auth E]3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
G [auth D]3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
G [auth D]3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
E [auth C]3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
E [auth C]3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
C [auth B]3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
C [auth B]3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
A3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
A3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
P [auth Z]3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
N [auth Y]3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
L [auth X]3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
J [auth W]3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
H [auth V]3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
F [auth U]3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
D [auth T]3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
B [auth S]3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF02788Ribulose bisphosphate carboxylase large chain, N-terminal domain (RuBisCO_large_N)Ribulose bisphosphate carboxylase large chain, N-terminal domainThe N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold. Domain
PF00016Ribulose bisphosphate carboxylase large chain, catalytic domain (RuBisCO_large)Ribulose bisphosphate carboxylase large chain, catalytic domainThe C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold. Domain
PF00101Ribulose bisphosphate carboxylase, small chain (RuBisCO_small)Ribulose bisphosphate carboxylase, small chainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Ribulose bisphosphate carboxylase large chain
Ribulose bisphosphate carboxylase small chain, chloroplastic

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR020888Ribulose bisphosphate carboxylase large subunit, type IFamily
IPR036376Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamilyHomologous Superfamily
IPR020878Ribulose bisphosphate carboxylase, large chain, active siteActive Site
IPR000685Ribulose bisphosphate carboxylase, large subunit, C-terminalDomain
IPR033966RuBisCOFamily
IPR017443Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminalDomain
IPR036422RuBisCO large subunit, N-terminal domain superfamilyHomologous Superfamily
IPR024680Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminalDomain
IPR036385Ribulose bisphosphate carboxylase, small subunit superfamilyHomologous Superfamily
IPR024681Ribulose bisphosphate carboxylase, small subunitFamily
IPR000894Ribulose bisphosphate carboxylase small subunit, domainDomain