SMTL ID : 5nv3.1

Structure of Rubisco from Rhodobacter sphaeroides in complex with CABP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-oligomer

Ligands

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

CAP.1: 21 residues within 4Å: Chain A: T.163, K.165, K.167, K.191, E.194, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, G.392, G.393 Chain I: E.50, T.55, W.56, N.113 Ligands: MG.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain I Hydrogen bonds: A:T.163, A:K.165, A:S.368, A:G.370, A:G.392, A:G.393, I:E.50, I:T.55, I:N.113 Salt bridges: A:K.165, A:K.165, A:K.167, A:H.283, A:R.284, A:H.316, A:K.323, A:K.323 CAP.3: 21 residues within 4Å: Chain C: T.163, K.165, K.167, K.191, E.194, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, G.392, G.393 Chain K: E.50, T.55, W.56, N.113 Ligands: MG.4 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain K Hydrogen bonds: C:T.163, C:K.165, C:S.368, C:G.370, C:G.392, C:G.393, K:E.50, K:T.55, K:N.113 Salt bridges: C:K.165, C:K.165, C:K.167, C:H.283, C:R.284, C:H.316, C:K.323, C:K.323 CAP.5: 21 residues within 4Å: Chain E: T.163, K.165, K.167, K.191, E.194, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, G.392, G.393 Chain M: E.50, T.55, W.56, N.113 Ligands: MG.6 17 PLIP interactions: 14 interactions with chain E, 3 interactions with chain M Hydrogen bonds: E:T.163, E:K.165, E:S.368, E:G.370, E:G.392, E:G.393, M:E.50, M:T.55, M:N.113 Salt bridges: E:K.165, E:K.165, E:K.167, E:H.283, E:R.284, E:H.316, E:K.323, E:K.323 CAP.7: 21 residues within 4Å: Chain G: T.163, K.165, K.167, K.191, E.194, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, G.392, G.393 Chain O: E.50, T.55, W.56, N.113 Ligands: MG.8 17 PLIP interactions: 3 interactions with chain O, 14 interactions with chain G Hydrogen bonds: O:E.50, O:T.55, O:N.113, G:T.163, G:K.165, G:S.368, G:G.370, G:G.392, G:G.393 Salt bridges: G:K.165, G:K.165, G:K.167, G:H.283, G:R.284, G:H.316, G:K.323, G:K.323 CAP.9: 21 residues within 4Å: Chain A: E.50, T.55, W.56, N.113 Chain I: T.163, K.165, K.167, K.191, E.194, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, G.392, G.393 Ligands: MG.10 20 PLIP interactions: 17 interactions with chain I, 3 interactions with chain A Hydrogen bonds: I:T.163, I:T.163, I:K.165, I:R.284, I:S.368, I:S.368, I:G.370, I:G.392, I:G.393, A:T.55, A:T.55, A:N.113 Salt bridges: I:K.165, I:K.165, I:K.167, I:H.283, I:R.284, I:H.316, I:K.323, I:K.323 CAP.11: 21 residues within 4Å: Chain C: E.50, T.55, W.56, N.113 Chain K: T.163, K.165, K.167, K.191, E.194, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, G.392, G.393 Ligands: MG.12 20 PLIP interactions: 17 interactions with chain K, 3 interactions with chain C Hydrogen bonds: K:T.163, K:T.163, K:K.165, K:R.284, K:S.368, K:S.368, K:G.370, K:G.392, K:G.393, C:T.55, C:T.55, C:N.113 Salt bridges: K:K.165, K:K.165, K:K.167, K:H.283, K:R.284, K:H.316, K:K.323, K:K.323 CAP.13: 21 residues within 4Å: Chain E: E.50, T.55, W.56, N.113 Chain M: T.163, K.165, K.167, K.191, E.194, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, G.392, G.393 Ligands: MG.14 20 PLIP interactions: 17 interactions with chain M, 3 interactions with chain E Hydrogen bonds: M:T.163, M:T.163, M:K.165, M:R.284, M:S.368, M:S.368, M:G.370, M:G.392, M:G.393, E:T.55, E:T.55, E:N.113 Salt bridges: M:K.165, M:K.165, M:K.167, M:H.283, M:R.284, M:H.316, M:K.323, M:K.323 CAP.15: 21 residues within 4Å: Chain G: E.50, T.55, W.56, N.113 Chain O: T.163, K.165, K.167, K.191, E.194, H.283, R.284, H.287, H.316, K.323, L.324, S.368, G.369, G.370, G.392, G.393 Ligands: MG.16 20 PLIP interactions: 3 interactions with chain G, 17 interactions with chain O Hydrogen bonds: G:T.55, G:T.55, G:N.113, O:T.163, O:T.163, O:K.165, O:R.284, O:S.368, O:S.368, O:G.370, O:G.392, O:G.393 Salt bridges: O:K.165, O:K.165, O:K.167, O:H.283, O:R.284, O:H.316, O:K.323, O:K.323

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: T.163, K.167, K.191, D.193, E.194, H.283 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.193, A:E.194 MG.4: 7 residues within 4Å: Chain C: T.163, K.167, K.191, D.193, E.194, H.283 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.193, C:E.194 MG.6: 7 residues within 4Å: Chain E: T.163, K.167, K.191, D.193, E.194, H.283 Ligands: CAP.5 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.193, E:E.194 MG.8: 7 residues within 4Å: Chain G: T.163, K.167, K.191, D.193, E.194, H.283 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.193, G:E.194 MG.10: 7 residues within 4Å: Chain I: T.163, K.167, K.191, D.193, E.194, H.283 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.193, I:E.194 MG.12: 7 residues within 4Å: Chain K: T.163, K.167, K.191, D.193, E.194, H.283 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.193, K:E.194 MG.14: 7 residues within 4Å: Chain M: T.163, K.167, K.191, D.193, E.194, H.283 Ligands: CAP.13 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.193, M:E.194 MG.16: 7 residues within 4Å: Chain O: T.163, K.167, K.191, D.193, E.194, H.283 Ligands: CAP.15 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.193, O:E.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhat, J.Y. et al., Mechanism of Enzyme Repair by the AAA(+) Chaperone Rubisco Activase. Mol. Cell (2017)

Release Date

2017-07-26

Peptides

Ribulose bisphosphate carboxylase large chain: ACEGIKMO
Ribulose bisphosphate carboxylase small chain 1: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
D

I
E

K
F

M
G

O
H

B
I

D
J

F
K

H
L

J
M

L
N

N
O

P
P

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain 1