SMTL ID : 5koz.2 (1 other biounit)

Structure function studies of R. palustris RubisCO (K192C mutant; CABP-bound)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x CAP: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE(Non-covalent)

CAP.1: 25 residues within 4Å: Chain A: I.185, K.187, K.189, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, T.412, A.413, G.414, G.415 Chain B: E.69, T.74, N.132 Ligands: MG.2, CO3.3 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.187, A:E.215, A:H.312, A:S.389, A:S.389, A:G.391, A:G.414, A:G.415, B:T.74, B:N.132 Water bridges: A:K.189, A:K.189, A:K.189, A:K.189, A:R.309, A:R.309, A:H.342, A:S.389, A:S.389, A:G.390, A:G.416 Salt bridges: A:K.187, A:K.187, A:K.189, A:R.309, A:H.342, A:K.350, A:K.350 CAP.4: 25 residues within 4Å: Chain A: E.69, T.74, N.132 Chain B: I.185, K.187, K.189, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, T.412, A.413, G.414, G.415 Ligands: MG.5, CO3.6 25 PLIP interactions: 22 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.187, B:H.312, B:S.389, B:G.391, B:G.414, B:G.415, A:T.74, A:T.74, A:N.132 Water bridges: B:K.189, B:K.189, B:R.309, B:R.309, B:S.389, B:M.392, B:M.392, B:M.392, B:G.416 Salt bridges: B:K.187, B:K.187, B:K.189, B:R.309, B:H.342, B:K.350, B:K.350 CAP.7: 24 residues within 4Å: Chain C: I.185, K.187, K.189, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415 Chain D: E.69, T.74, N.132 Ligands: MG.8, CO3.9 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.187, C:H.308, C:H.312, C:S.389, C:G.391, C:G.414, C:G.415, D:T.74, D:T.74, D:N.132 Water bridges: C:R.309, C:R.309, C:H.342, C:G.344, C:G.344, C:K.350, C:K.350, C:M.392, C:G.416, C:G.416 Salt bridges: C:K.187, C:K.187, C:K.189, C:R.309, C:H.342, C:K.350, C:K.350 CAP.10: 24 residues within 4Å: Chain C: E.69, T.74, N.132 Chain D: I.185, K.187, K.189, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415 Ligands: MG.11, CO3.12 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.187, D:H.308, D:H.312, D:S.389, D:G.391, D:G.414, D:G.415, C:T.74, C:N.132 Water bridges: D:R.309, D:R.309, D:G.344, D:S.389, D:G.416 Salt bridges: D:K.187, D:K.187, D:K.189, D:R.309, D:H.342, D:K.350, D:K.350 CAP.13: 23 residues within 4Å: Chain E: I.185, K.187, K.189, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, A.413, G.414, G.415 Chain F: E.69, T.74, N.132 Ligands: MG.14, CO3.15 27 PLIP interactions: 23 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:K.187, E:D.214, E:H.308, E:H.312, E:S.389, E:S.389, E:G.391, E:T.412, E:G.414, E:G.415, F:T.74, F:T.74, F:N.132 Water bridges: E:K.189, E:K.189, E:K.189, E:S.389, E:G.416, E:G.416, F:E.69 Salt bridges: E:K.187, E:K.187, E:K.189, E:R.309, E:H.342, E:K.350, E:K.350 CAP.16: 24 residues within 4Å: Chain E: E.69, T.74, N.132 Chain F: I.185, K.187, K.189, D.214, E.215, H.308, R.309, H.312, H.342, G.344, K.350, M.351, S.389, G.390, G.391, M.392, A.413, G.414, G.415 Ligands: MG.17, CO3.18 26 PLIP interactions: 23 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:K.187, F:E.215, F:H.312, F:S.389, F:S.389, F:G.391, F:G.414, F:G.415, E:T.74, E:T.74, E:N.132 Water bridges: F:K.189, F:R.309, F:R.309, F:R.309, F:K.350, F:S.389, F:M.392, F:G.416 Salt bridges: F:K.187, F:K.187, F:K.189, F:R.309, F:H.342, F:K.350, F:K.350

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: I.185, K.187, K.189, D.214, E.215 Chain B: N.132 Ligands: CAP.1, CO3.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.214, A:E.215 MG.5: 8 residues within 4Å: Chain A: N.132 Chain B: I.185, K.187, K.189, D.214, E.215 Ligands: CAP.4, CO3.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.214, B:E.215 MG.8: 9 residues within 4Å: Chain C: I.185, K.187, K.189, D.214, E.215, H.308 Chain D: N.132 Ligands: CAP.7, CO3.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.214, C:E.215 MG.11: 9 residues within 4Å: Chain C: N.132 Chain D: I.185, K.187, K.189, D.214, E.215, H.308 Ligands: CAP.10, CO3.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.214, D:E.215 MG.14: 9 residues within 4Å: Chain E: I.185, K.187, K.189, D.214, E.215, H.308 Chain F: N.132 Ligands: CAP.13, CO3.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.214, E:E.215 MG.17: 9 residues within 4Å: Chain E: N.132 Chain F: I.185, K.187, K.189, D.214, E.215, H.308 Ligands: CAP.16, CO3.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.214, F:E.215

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.3: 12 residues within 4Å: Chain A: I.185, C.212, N.213, D.214, E.215, L.282, H.308, H.342, S.389, T.412 Ligands: CAP.1, MG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.213, A:S.389 Water bridges: A:H.306 CO3.6: 13 residues within 4Å: Chain B: I.185, C.212, N.213, D.214, E.215, L.282, H.306, H.308, H.342, S.389, T.412 Ligands: CAP.4, MG.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.213, B:E.215, B:S.389 CO3.9: 11 residues within 4Å: Chain C: I.185, C.212, N.213, D.214, E.215, L.282, H.308, H.342, S.389 Ligands: CAP.7, MG.8 No protein-ligand interaction detected (PLIP) CO3.12: 12 residues within 4Å: Chain D: I.185, C.212, N.213, D.214, E.215, L.282, H.306, H.308, H.342, S.389 Ligands: CAP.10, MG.11 1 PLIP interactions: 1 interactions with chain D Water bridges: D:H.306 CO3.15: 12 residues within 4Å: Chain E: I.185, C.212, N.213, D.214, E.215, L.282, H.308, H.342, S.389, T.412 Ligands: CAP.13, MG.14 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.213, E:E.215, E:H.308 CO3.18: 12 residues within 4Å: Chain F: I.185, C.212, N.213, D.214, E.215, L.282, H.306, H.308, H.342, S.389 Ligands: CAP.16, MG.17 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.389 Water bridges: F:H.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arbing, M.A. et al., Structure function studies of R. palustris RubisCO. To Be Published

Release Date

2017-07-05

Peptides

Ribulose bisphosphate carboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

Ribulose bisphosphate carboxylase

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