SMTL ID : 4f0k.1

UNACTIVATED RUBISCO with MAGNESIUM AND CARBON DIOXIDE BOUND

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: H.302, Q.409 Ligands: CO2.2 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: H.302, Q.409 Ligands: CO2.8 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain E: H.302, Q.409 Ligands: CO2.14 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain G: H.302, Q.409 Ligands: CO2.20 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain I: H.302, Q.409 Ligands: CO2.26 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain K: H.302, Q.409 Ligands: CO2.32 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain M: H.302, Q.409 Ligands: CO2.38 No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain O: H.302, Q.409 Ligands: CO2.44 No protein-ligand interaction detected (PLIP)

8 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.2: 7 residues within 4Å: Chain A: T.182, K.210, D.212, E.213, S.387, Q.409 Ligands: MG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.182, A:S.387 CO2.8: 7 residues within 4Å: Chain C: T.182, K.210, D.212, E.213, S.387, Q.409 Ligands: MG.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.182, C:S.387 CO2.14: 7 residues within 4Å: Chain E: T.182, K.210, D.212, E.213, S.387, Q.409 Ligands: MG.13 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.182, E:S.387 CO2.20: 7 residues within 4Å: Chain G: T.182, K.210, D.212, E.213, S.387, Q.409 Ligands: MG.19 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:T.182, G:S.387 CO2.26: 7 residues within 4Å: Chain I: T.182, K.210, D.212, E.213, S.387, Q.409 Ligands: MG.25 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.387 CO2.32: 7 residues within 4Å: Chain K: T.182, K.210, D.212, E.213, S.387, Q.409 Ligands: MG.31 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.387 CO2.38: 7 residues within 4Å: Chain M: T.182, K.210, D.212, E.213, S.387, Q.409 Ligands: MG.37 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:S.387 CO2.44: 7 residues within 4Å: Chain O: T.182, K.210, D.212, E.213, S.387, Q.409 Ligands: MG.43 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:S.387

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Q.312, K.313, N.314, H.315 Chain K: Q.312, K.313, N.314, H.315 Ligands: GOL.33 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: R.170 Chain B: R.44, S.46 Chain E: L.228, F.229 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: A.239, A.240 Chain B: P.107, G.108, F.109, Y.128 Chain H: E.134 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain C: Q.312, K.313, N.314, H.315 Chain I: Q.312, K.313, N.314, H.315 Ligands: GOL.27 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain C: R.170 Chain D: R.44, S.46 Chain G: L.228, F.229 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain C: A.239, A.240 Chain D: P.107, G.108, F.109, Y.128 Chain F: E.134 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain E: Q.312, K.313, N.314, H.315 Chain M: Q.312, K.313, N.314, H.315 Ligands: GOL.39 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain C: L.228, F.229 Chain E: R.170 Chain F: R.44, S.46 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: E.134 Chain E: A.239, A.240 Chain F: P.107, G.108, F.109, Y.128 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain G: Q.312, K.313, N.314, H.315 Chain O: Q.312, K.313, N.314, H.315 Ligands: GOL.45 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain A: L.228, F.229 Chain G: R.170 Chain H: R.44, S.46 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain D: E.134 Chain G: A.239, A.240 Chain H: P.107, G.108, F.109, Y.128 Ligand excluded by PLIP GOL.27: 9 residues within 4Å: Chain C: Q.312, K.313, N.314, H.315 Chain I: Q.312, K.313, N.314, H.315 Ligands: GOL.9 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain I: R.170 Chain J: R.44, S.46 Chain M: L.228, F.229 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain I: A.239, A.240 Chain J: P.107, G.108, F.109, Y.128 Chain P: E.134 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain A: Q.312, K.313, N.314, H.315 Chain K: Q.312, K.313, N.314, H.315 Ligands: GOL.3 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain K: R.170 Chain L: R.44, S.46 Chain O: L.228, F.229 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain K: A.239, A.240 Chain L: P.107, G.108, F.109, Y.128 Chain N: E.134 Ligand excluded by PLIP GOL.39: 9 residues within 4Å: Chain E: Q.312, K.313, N.314, H.315 Chain M: Q.312, K.313, N.314, H.315 Ligands: GOL.15 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain K: L.228, F.229 Chain M: R.170 Chain N: R.44, S.46 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain J: E.134 Chain M: A.239, A.240 Chain N: P.107, G.108, F.109, Y.128 Ligand excluded by PLIP GOL.45: 9 residues within 4Å: Chain G: Q.312, K.313, N.314, H.315 Chain O: Q.312, K.313, N.314, H.315 Ligands: GOL.21 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain I: L.228, F.229 Chain O: R.170 Chain P: R.44, S.46 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain L: E.134 Chain O: A.239, A.240 Chain P: P.107, G.108, F.109, Y.128 Ligand excluded by PLIP

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 7 residues within 4Å: Chain B: Q.114 Chain D: Q.114 Chain F: Q.114 Chain H: Q.114 Ligands: CL.10, CL.16, CL.22 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain B: Q.114 Chain D: Q.114 Chain F: Q.114 Chain H: Q.114 Ligands: CL.4, CL.16, CL.22 Ligand excluded by PLIP CL.16: 7 residues within 4Å: Chain B: Q.114 Chain D: Q.114 Chain F: Q.114 Chain H: Q.114 Ligands: CL.4, CL.10, CL.22 Ligand excluded by PLIP CL.22: 7 residues within 4Å: Chain B: Q.114 Chain D: Q.114 Chain F: Q.114 Chain H: Q.114 Ligands: CL.4, CL.10, CL.16 Ligand excluded by PLIP CL.28: 7 residues within 4Å: Chain J: Q.114 Chain L: Q.114 Chain N: Q.114 Chain P: Q.114 Ligands: CL.34, CL.40, CL.46 Ligand excluded by PLIP CL.34: 7 residues within 4Å: Chain J: Q.114 Chain L: Q.114 Chain N: Q.114 Chain P: Q.114 Ligands: CL.28, CL.40, CL.46 Ligand excluded by PLIP CL.40: 7 residues within 4Å: Chain J: Q.114 Chain L: Q.114 Chain N: Q.114 Chain P: Q.114 Ligands: CL.28, CL.34, CL.46 Ligand excluded by PLIP CL.46: 7 residues within 4Å: Chain J: Q.114 Chain L: Q.114 Chain N: Q.114 Chain P: Q.114 Ligands: CL.28, CL.34, CL.40 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stec, B., Structural mechanism of RuBisCO activation by carbamylation of the active site lysine. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-11-14

Peptides

Ribulose bisphosphate carboxylase large chain: ACEGIKMO
Ribulose bisphosphate carboxylase small chain: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

M
A

O
A

B
B

D
B

F
B

H
B

J
B

L
B

N
B

P
B

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain

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