SMTL ID : 3kdo.1

Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-10-mer

Ligands

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

CAP.1: 23 residues within 4Å: Chain A: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, L.390, G.391, G.392 Chain H: E.49, T.54, W.55, N.111 Ligands: MG.2 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain H Hydrogen bonds: A:K.163, A:D.191, A:G.369, A:Q.389, A:G.391, A:G.392, H:T.54, H:N.111 Water bridges: A:K.165, A:H.281, A:H.314, A:G.316, A:G.393, A:G.393 Salt bridges: A:K.163, A:K.163, A:K.165, A:R.282, A:H.314, A:K.322, A:K.322 CAP.3: 22 residues within 4Å: Chain B: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, L.390, G.391, G.392 Chain G: E.49, W.55, N.111 Ligands: MG.4 26 PLIP interactions: 25 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:K.163, B:G.369, B:Q.389, B:G.391, B:G.392, G:N.111 Water bridges: B:K.165, B:K.165, B:H.281, B:R.282, B:R.282, B:H.314, B:G.316, B:K.322, B:K.322, B:G.368, B:G.368, B:L.370, B:G.393 Salt bridges: B:K.163, B:K.163, B:K.165, B:R.282, B:H.314, B:K.322, B:K.322 CAP.5: 22 residues within 4Å: Chain C: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, L.390, G.391, G.392 Chain F: E.49, W.55, N.111 Ligands: MG.6 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:K.163, C:G.369, C:Q.389, C:G.391, C:G.392, F:N.111 Water bridges: C:K.165, C:K.165, C:H.281, C:R.282, C:R.282, C:R.282, C:H.314, C:K.322, C:S.367, C:G.368, C:L.370, C:L.370, C:G.393, F:W.55 Salt bridges: C:K.163, C:K.163, C:K.165, C:R.282, C:H.314, C:K.322, C:K.322 CAP.7: 23 residues within 4Å: Chain D: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, L.390, G.391, G.392 Chain J: E.49, T.54, W.55, N.111 Ligands: MG.8 28 PLIP interactions: 26 interactions with chain D, 2 interactions with chain J Hydrogen bonds: D:K.163, D:G.368, D:G.369, D:Q.389, D:G.391, D:G.392, J:T.54, J:N.111 Water bridges: D:K.165, D:K.165, D:K.165, D:H.281, D:R.282, D:H.285, D:H.314, D:K.322, D:S.367, D:S.367, D:L.370, D:L.370, D:G.393 Salt bridges: D:K.163, D:K.163, D:K.165, D:R.282, D:H.314, D:K.322, D:K.322 CAP.9: 19 residues within 4Å: Chain E: K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, G.391, G.392 Chain I: W.55, N.111 Ligands: MG.10 21 PLIP interactions: 20 interactions with chain E, 1 interactions with chain I Hydrogen bonds: E:K.163, E:S.367, E:G.369, E:Q.389, E:G.391, E:G.392, I:N.111 Water bridges: E:K.165, E:K.165, E:R.282, E:R.282, E:H.285, E:G.316, E:L.370 Salt bridges: E:K.163, E:K.163, E:K.165, E:R.282, E:H.314, E:K.322, E:K.322 CAP.11: 23 residues within 4Å: Chain C: E.49, T.54, W.55, N.111 Chain F: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, L.390, G.391, G.392 Ligands: MG.12 26 PLIP interactions: 24 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:K.163, F:G.369, F:Q.389, F:G.391, F:G.392, C:T.54, C:N.111 Water bridges: F:K.165, F:K.165, F:H.281, F:R.282, F:R.282, F:H.314, F:S.367, F:S.367, F:L.370, F:L.370, F:L.370, F:G.393 Salt bridges: F:K.163, F:K.163, F:K.165, F:R.282, F:H.314, F:K.322, F:K.322 CAP.13: 21 residues within 4Å: Chain B: E.49, W.55, N.111 Chain G: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, G.391, G.392 Ligands: MG.14 28 PLIP interactions: 26 interactions with chain G, 2 interactions with chain B Hydrogen bonds: G:K.163, G:G.369, G:Q.389, G:G.391, G:G.392, B:N.111 Water bridges: G:K.165, G:K.165, G:K.165, G:K.165, G:H.281, G:R.282, G:R.282, G:H.314, G:G.316, G:K.322, G:G.368, G:L.370, G:L.370, G:G.393, B:W.55 Salt bridges: G:K.163, G:K.163, G:K.165, G:R.282, G:H.314, G:K.322, G:K.322 CAP.15: 19 residues within 4Å: Chain A: W.55, N.111 Chain H: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, L.323, S.367, G.368, G.369, Q.389, G.391, G.392 Ligands: MG.16 19 PLIP interactions: 18 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:K.163, H:E.192, H:S.367, H:G.369, H:Q.389, H:G.391, H:G.392, A:N.111 Water bridges: H:K.165, H:L.370, H:L.370, H:G.393, H:G.393 Salt bridges: H:K.163, H:K.163, H:K.165, H:H.281, H:R.282, H:H.314 CAP.17: 23 residues within 4Å: Chain E: E.49, T.54, W.55, N.111 Chain I: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, L.390, G.391, G.392 Ligands: MG.18 26 PLIP interactions: 25 interactions with chain I, 1 interactions with chain E Hydrogen bonds: I:K.163, I:D.191, I:G.368, I:G.369, I:Q.389, I:G.391, I:G.392, E:N.111 Water bridges: I:H.281, I:R.282, I:R.282, I:H.285, I:H.314, I:S.367, I:S.367, I:G.368, I:L.370, I:L.370, I:G.393 Salt bridges: I:K.163, I:K.163, I:K.165, I:R.282, I:H.314, I:K.322, I:K.322 CAP.19: 22 residues within 4Å: Chain D: E.49, W.55, N.111 Chain J: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, L.390, G.391, G.392 Ligands: MG.20 20 PLIP interactions: 19 interactions with chain J, 1 interactions with chain D Hydrogen bonds: J:K.163, J:G.369, J:Q.389, J:G.391, J:G.392, D:N.111 Water bridges: J:H.281, J:R.282, J:R.282, J:H.285, J:H.314, J:G.316, J:K.322 Salt bridges: J:K.163, J:K.163, J:K.165, J:R.282, J:H.314, J:K.322, J:K.322

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.165, K.189, D.191, E.192 Chain H: N.111 Ligands: CAP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.191, A:E.192 MG.4: 7 residues within 4Å: Chain B: K.163, K.165, K.189, D.191, E.192 Chain G: N.111 Ligands: CAP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.191, B:E.192 MG.6: 6 residues within 4Å: Chain C: K.163, K.165, K.189, D.191, E.192 Ligands: CAP.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.191, C:D.191, C:E.192 MG.8: 7 residues within 4Å: Chain D: K.163, K.165, K.189, D.191, E.192 Chain J: N.111 Ligands: CAP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.191, D:E.192 MG.10: 7 residues within 4Å: Chain E: K.163, K.165, K.189, D.191, E.192 Chain I: N.111 Ligands: CAP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.191, E:E.192 MG.12: 8 residues within 4Å: Chain C: N.111 Chain F: K.163, K.165, K.189, D.191, E.192, H.281 Ligands: CAP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.191, F:E.192 MG.14: 7 residues within 4Å: Chain B: N.111 Chain G: K.163, K.189, D.191, E.192, H.281 Ligands: CAP.13 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.191, G:E.192 MG.16: 6 residues within 4Å: Chain H: K.163, K.165, K.189, D.191, E.192 Ligands: CAP.15 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.191, H:E.192 MG.18: 8 residues within 4Å: Chain E: N.111 Chain I: K.163, K.165, K.189, D.191, E.192, H.281 Ligands: CAP.17 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.191, I:E.192 MG.20: 6 residues within 4Å: Chain D: N.111 Chain J: K.163, K.189, D.191, E.192 Ligands: CAP.19 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.191, J:E.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishitani, Y. et al., Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile. J.Biol.Chem. (2010)

Release Date

2010-10-06

Peptides

Ribulose bisphosphate carboxylase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Ribulose bisphosphate carboxylase