SMTL ID : 1rbl.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.195, E.196, H.286 Chain C: N.115 Ligands: CAP.2, FMT.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.195, A:E.196 MG.4: 6 residues within 4Å: Chain A: N.115 Chain C: D.195, E.196, H.286 Ligands: CAP.5, FMT.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.195, C:E.196 MG.7: 6 residues within 4Å: Chain E: D.195, E.196, H.286 Chain G: N.115 Ligands: CAP.8, FMT.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.195, E:E.196 MG.10: 6 residues within 4Å: Chain E: N.115 Chain G: D.195, E.196, H.286 Ligands: CAP.11, FMT.12 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.195, G:E.196 MG.13: 6 residues within 4Å: Chain I: D.195, E.196, H.286 Chain K: N.115 Ligands: CAP.14, FMT.15 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.195, I:E.196 MG.16: 6 residues within 4Å: Chain I: N.115 Chain K: D.195, E.196, H.286 Ligands: CAP.17, FMT.18 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.195, K:E.196 MG.19: 6 residues within 4Å: Chain M: D.195, E.196, H.286 Chain O: N.115 Ligands: CAP.20, FMT.21 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.195, M:E.196 MG.22: 6 residues within 4Å: Chain M: N.115 Chain O: D.195, E.196, H.286 Ligands: CAP.23, FMT.24 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.195, O:E.196

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

CAP.2: 22 residues within 4Å: Chain A: T.165, K.167, K.169, D.195, E.196, H.286, R.287, H.319, K.326, L.327, S.371, G.372, G.373, F.394, G.395, G.396 Chain C: E.52, T.57, W.58, N.115 Ligands: MG.1, FMT.3 29 PLIP interactions: 26 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:T.165, A:K.167, A:E.196, A:S.371, A:G.373, A:G.395, A:G.396, C:T.57, C:T.57, C:N.115 Water bridges: A:T.165, A:T.165, A:H.286, A:R.287, A:R.287, A:H.319, A:G.321, A:G.321, A:S.371, A:G.372, A:G.372, A:G.397 Salt bridges: A:K.167, A:K.167, A:K.169, A:R.287, A:H.319, A:K.326, A:K.326 CAP.5: 22 residues within 4Å: Chain A: E.52, T.57, W.58, N.115 Chain C: T.165, K.167, K.169, D.195, E.196, H.286, R.287, H.319, K.326, L.327, S.371, G.372, G.373, F.394, G.395, G.396 Ligands: MG.4, FMT.6 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.165, C:T.165, C:K.167, C:E.196, C:S.371, C:G.373, C:G.395, C:G.396, A:T.57, A:N.115 Water bridges: C:K.169, C:K.169 Salt bridges: C:K.167, C:K.167, C:K.169, C:R.287, C:H.319, C:K.326, C:K.326 CAP.8: 22 residues within 4Å: Chain E: T.165, K.167, K.169, D.195, E.196, H.286, R.287, H.319, K.326, L.327, S.371, G.372, G.373, F.394, G.395, G.396 Chain G: E.52, T.57, W.58, N.115 Ligands: MG.7, FMT.9 17 PLIP interactions: 3 interactions with chain G, 14 interactions with chain E Hydrogen bonds: G:T.57, G:T.57, G:N.115, E:T.165, E:K.167, E:E.196, E:S.371, E:G.373, E:G.395, E:G.396 Salt bridges: E:K.167, E:K.167, E:K.169, E:R.287, E:H.319, E:K.326, E:K.326 CAP.11: 22 residues within 4Å: Chain E: E.52, T.57, W.58, N.115 Chain G: T.165, K.167, K.169, D.195, E.196, H.286, R.287, H.319, K.326, L.327, S.371, G.372, G.373, F.394, G.395, G.396 Ligands: MG.10, FMT.12 17 PLIP interactions: 15 interactions with chain G, 2 interactions with chain E Hydrogen bonds: G:T.165, G:T.165, G:K.167, G:E.196, G:S.371, G:G.373, G:G.395, G:G.396, E:T.57, E:N.115 Salt bridges: G:K.167, G:K.167, G:K.169, G:R.287, G:H.319, G:K.326, G:K.326 CAP.14: 22 residues within 4Å: Chain I: T.165, K.167, K.169, D.195, E.196, H.286, R.287, H.319, K.326, L.327, S.371, G.372, G.373, F.394, G.395, G.396 Chain K: E.52, T.57, W.58, N.115 Ligands: MG.13, FMT.15 17 PLIP interactions: 14 interactions with chain I, 3 interactions with chain K Hydrogen bonds: I:T.165, I:K.167, I:E.196, I:S.371, I:G.373, I:G.395, I:G.396, K:T.57, K:T.57, K:N.115 Salt bridges: I:K.167, I:K.167, I:K.169, I:R.287, I:H.319, I:K.326, I:K.326 CAP.17: 22 residues within 4Å: Chain I: E.52, T.57, W.58, N.115 Chain K: T.165, K.167, K.169, D.195, E.196, H.286, R.287, H.319, K.326, L.327, S.371, G.372, G.373, F.394, G.395, G.396 Ligands: MG.16, FMT.18 18 PLIP interactions: 3 interactions with chain I, 15 interactions with chain K Hydrogen bonds: I:T.57, I:T.57, I:N.115, K:T.165, K:T.165, K:K.167, K:E.196, K:S.371, K:G.373, K:G.395, K:G.396 Salt bridges: K:K.167, K:K.167, K:K.169, K:R.287, K:H.319, K:K.326, K:K.326 CAP.20: 22 residues within 4Å: Chain M: T.165, K.167, K.169, D.195, E.196, H.286, R.287, H.319, K.326, L.327, S.371, G.372, G.373, F.394, G.395, G.396 Chain O: E.52, T.57, W.58, N.115 Ligands: MG.19, FMT.21 17 PLIP interactions: 3 interactions with chain O, 14 interactions with chain M Hydrogen bonds: O:T.57, O:T.57, O:N.115, M:T.165, M:K.167, M:E.196, M:S.371, M:G.373, M:G.395, M:G.396 Salt bridges: M:K.167, M:K.167, M:K.169, M:R.287, M:H.319, M:K.326, M:K.326 CAP.23: 22 residues within 4Å: Chain M: E.52, T.57, W.58, N.115 Chain O: T.165, K.167, K.169, D.195, E.196, H.286, R.287, H.319, K.326, L.327, S.371, G.372, G.373, F.394, G.395, G.396 Ligands: MG.22, FMT.24 17 PLIP interactions: 15 interactions with chain O, 2 interactions with chain M Hydrogen bonds: O:T.165, O:T.165, O:K.167, O:E.196, O:S.371, O:G.373, O:G.395, O:G.396, M:T.57, M:N.115 Salt bridges: O:K.167, O:K.167, O:K.169, O:R.287, O:H.319, O:K.326, O:K.326

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 9 residues within 4Å: Chain A: T.165, K.193, D.194, D.195, E.196, H.286, H.319 Ligands: MG.1, CAP.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.194, A:E.196 FMT.6: 9 residues within 4Å: Chain C: T.165, K.193, D.194, D.195, E.196, H.286, H.319 Ligands: MG.4, CAP.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.165, C:D.194, C:E.196 FMT.9: 9 residues within 4Å: Chain E: T.165, K.193, D.194, D.195, E.196, H.286, H.319 Ligands: MG.7, CAP.8 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.194, E:E.196 FMT.12: 9 residues within 4Å: Chain G: T.165, K.193, D.194, D.195, E.196, H.286, H.319 Ligands: MG.10, CAP.11 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:T.165, G:D.194, G:E.196 FMT.15: 9 residues within 4Å: Chain I: T.165, K.193, D.194, D.195, E.196, H.286, H.319 Ligands: MG.13, CAP.14 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.194, I:E.196 FMT.18: 9 residues within 4Å: Chain K: T.165, K.193, D.194, D.195, E.196, H.286, H.319 Ligands: MG.16, CAP.17 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:T.165, K:D.194, K:E.196 FMT.21: 9 residues within 4Å: Chain M: T.165, K.193, D.194, D.195, E.196, H.286, H.319 Ligands: MG.19, CAP.20 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:D.194, M:E.196 FMT.24: 9 residues within 4Å: Chain O: T.165, K.193, D.194, D.195, E.196, H.286, H.319 Ligands: MG.22, CAP.23 3 PLIP interactions: 3 interactions with chain O Hydrogen bonds: O:T.165, O:D.194, O:E.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newman, J. et al., Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301. Acta Crystallogr.,Sect.D (1993)

Release Date

1994-06-22

Peptides

RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN): ACEGIKMO
RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN): 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
M

D
I

F
N

H
J

J
O

L
K

N
P

P
L

RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)

RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)