SMTL ID : 4rub.1

A CRYSTAL FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM NICOTIANA TABACUM IN THE ACTIVATED STATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: T.173, D.203, E.204, H.294 Chain G: N.123 Ligands: CAP.2, FMT.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 MG.4: 7 residues within 4Å: Chain C: T.173, D.203, E.204, H.294 Chain E: N.123 Ligands: CAP.5, FMT.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 MG.7: 7 residues within 4Å: Chain E: T.173, K.201, D.203, E.204, H.294 Ligands: CAP.8, FMT.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.203, E:E.204 MG.10: 7 residues within 4Å: Chain A: N.123 Chain G: K.201, D.203, E.204, H.294 Ligands: CAP.11, FMT.12 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.203, G:E.204 MG.13: 7 residues within 4Å: Chain I: T.173, D.203, E.204, H.294 Chain O: N.123 Ligands: CAP.14, FMT.15 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.203, I:E.204 MG.16: 7 residues within 4Å: Chain K: T.173, D.203, E.204, H.294 Chain M: N.123 Ligands: CAP.17, FMT.18 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.203, K:E.204 MG.19: 7 residues within 4Å: Chain M: T.173, K.201, D.203, E.204, H.294 Ligands: CAP.20, FMT.21 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.203, M:E.204 MG.22: 7 residues within 4Å: Chain I: N.123 Chain O: K.201, D.203, E.204, H.294 Ligands: CAP.23, FMT.24 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.203, O:E.204

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

CAP.2: 21 residues within 4Å: Chain A: T.173, K.175, K.177, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain G: E.60, T.65, W.66, N.123 Ligands: MG.1, FMT.3 18 PLIP interactions: 2 interactions with chain G, 16 interactions with chain A Hydrogen bonds: G:T.65, G:N.123, A:T.173, A:T.173, A:K.175, A:D.203, A:S.379, A:G.380, A:G.381, A:G.403, A:G.404 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.5: 21 residues within 4Å: Chain C: T.173, K.175, K.177, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain E: E.60, T.65, W.66, N.123 Ligands: MG.4, FMT.6 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:T.173, C:K.175, C:D.203, C:S.379, C:G.380, C:G.381, C:G.403, C:G.404, E:T.65, E:N.123 Salt bridges: C:K.175, C:K.175, C:K.177, C:R.295, C:H.327, C:K.334, C:K.334 CAP.8: 21 residues within 4Å: Chain C: E.60, T.65, W.66, N.123 Chain E: T.173, K.175, K.177, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MG.7, FMT.9 18 PLIP interactions: 15 interactions with chain E, 3 interactions with chain C Hydrogen bonds: E:T.173, E:K.175, E:D.203, E:H.294, E:G.380, E:G.381, E:G.403, E:G.404, C:T.65, C:T.65, C:N.123 Salt bridges: E:K.175, E:K.175, E:K.177, E:R.295, E:H.327, E:K.334, E:K.334 CAP.11: 22 residues within 4Å: Chain A: E.60, T.65, W.66, N.123 Chain G: T.173, K.175, K.177, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, Q.401, G.403, G.404 Ligands: MG.10, FMT.12 19 PLIP interactions: 16 interactions with chain G, 3 interactions with chain A Hydrogen bonds: G:T.173, G:T.173, G:K.175, G:D.203, G:S.379, G:G.380, G:G.381, G:G.403, G:G.404, A:T.65, A:T.65, A:N.123 Salt bridges: G:K.175, G:K.175, G:K.177, G:R.295, G:H.327, G:K.334, G:K.334 CAP.14: 21 residues within 4Å: Chain I: T.173, K.175, K.177, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain O: E.60, T.65, W.66, N.123 Ligands: MG.13, FMT.15 18 PLIP interactions: 15 interactions with chain I, 3 interactions with chain O Hydrogen bonds: I:T.173, I:K.175, I:D.203, I:S.379, I:G.380, I:G.381, I:G.403, I:G.404, O:T.65, O:T.65, O:N.123 Salt bridges: I:K.175, I:K.175, I:K.177, I:R.295, I:H.327, I:K.334, I:K.334 CAP.17: 21 residues within 4Å: Chain K: T.173, K.175, K.177, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain M: E.60, T.65, W.66, N.123 Ligands: MG.16, FMT.18 19 PLIP interactions: 3 interactions with chain M, 16 interactions with chain K Hydrogen bonds: M:T.65, M:T.65, M:N.123, K:T.173, K:T.173, K:K.175, K:D.203, K:S.379, K:G.380, K:G.381, K:G.403, K:G.404 Salt bridges: K:K.175, K:K.175, K:K.177, K:R.295, K:H.327, K:K.334, K:K.334 CAP.20: 21 residues within 4Å: Chain K: E.60, T.65, W.66, N.123 Chain M: T.173, K.175, K.177, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: MG.19, FMT.21 17 PLIP interactions: 14 interactions with chain M, 3 interactions with chain K Hydrogen bonds: M:K.175, M:D.203, M:H.294, M:G.380, M:G.381, M:G.403, M:G.404, K:T.65, K:T.65, K:N.123 Salt bridges: M:K.175, M:K.175, M:K.177, M:R.295, M:H.327, M:K.334, M:K.334 CAP.23: 22 residues within 4Å: Chain I: E.60, T.65, W.66, N.123 Chain O: T.173, K.175, K.177, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, Q.401, G.403, G.404 Ligands: MG.22, FMT.24 18 PLIP interactions: 3 interactions with chain I, 15 interactions with chain O Hydrogen bonds: I:T.65, I:T.65, I:N.123, O:T.173, O:K.175, O:D.203, O:S.379, O:G.380, O:G.381, O:G.403, O:G.404 Salt bridges: O:K.175, O:K.175, O:K.177, O:R.295, O:H.327, O:K.334, O:K.334

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

FMT.3: 9 residues within 4Å: Chain A: T.173, K.201, D.202, D.203, E.204, H.294, H.327 Ligands: MG.1, CAP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.173, A:D.203, A:E.204 FMT.6: 9 residues within 4Å: Chain C: T.173, K.201, D.202, D.203, E.204, H.294, H.327 Ligands: MG.4, CAP.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.204, C:H.327 FMT.9: 9 residues within 4Å: Chain E: T.173, K.201, D.202, D.203, E.204, H.294, H.327 Ligands: MG.7, CAP.8 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.173, E:D.203, E:E.204, E:H.327 FMT.12: 9 residues within 4Å: Chain G: T.173, K.201, D.202, D.203, E.204, H.294, H.327 Ligands: MG.10, CAP.11 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:T.173, G:E.204, G:H.327 FMT.15: 9 residues within 4Å: Chain I: T.173, K.201, D.202, D.203, E.204, H.294, H.327 Ligands: MG.13, CAP.14 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.204 FMT.18: 9 residues within 4Å: Chain K: T.173, K.201, D.202, D.203, E.204, H.294, H.327 Ligands: MG.16, CAP.17 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:T.173, K:D.203, K:E.204, K:H.327 FMT.21: 9 residues within 4Å: Chain M: T.173, K.201, D.202, D.203, E.204, H.294, H.327 Ligands: MG.19, CAP.20 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:E.204, M:H.327 FMT.24: 9 residues within 4Å: Chain O: T.173, K.201, D.202, D.203, E.204, H.294, H.327 Ligands: MG.22, CAP.23 3 PLIP interactions: 3 interactions with chain O Hydrogen bonds: O:D.203, O:E.204, O:H.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suh, S.W. et al., A crystal form of ribulose-1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum in the activated state. J.Mol.Biol. (1987)

Release Date

1992-10-15

Peptides

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV): ACEGIKMO
RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV): BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
D

I
A

K
B

M
C

O
D

B
S

D
T

F
U

H
V

J
S

L
T

N
U

P
V

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)

RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (FORM IV)

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