SMTL ID : 3wqp.2 (1 other biounit)

Crystal structure of Rubisco T289D mutant from Thermococcus kodakarensis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-10-mer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.165, K.189, D.191, E.192 Chain H: N.111 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.191, A:E.192 MG.3: 7 residues within 4Å: Chain B: K.163, K.165, K.189, D.191, E.192 Chain G: N.111 Ligands: CAP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.191, B:E.192 MG.5: 7 residues within 4Å: Chain C: K.165, K.189, D.191, E.192, H.281 Chain F: N.111 Ligands: CAP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.191, C:E.192 MG.9: 7 residues within 4Å: Chain D: K.163, K.165, K.189, D.191, E.192 Chain J: N.111 Ligands: CAP.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.191, D:E.192 MG.13: 7 residues within 4Å: Chain E: K.163, K.165, K.189, D.191, E.192 Chain I: N.111 Ligands: CAP.14 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.191, E:E.192 MG.16: 6 residues within 4Å: Chain C: N.111 Chain F: K.165, K.189, D.191, E.192 Ligands: CAP.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.191, F:E.192 MG.18: 7 residues within 4Å: Chain B: N.111 Chain G: K.163, K.165, K.189, D.191, E.192 Ligands: CAP.19 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.191, G:E.192 MG.20: 7 residues within 4Å: Chain A: N.111 Chain H: K.165, K.189, D.191, E.192, H.281 Ligands: CAP.21 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.191, H:E.192 MG.24: 7 residues within 4Å: Chain E: N.111 Chain I: K.163, K.165, K.189, D.191, E.192 Ligands: CAP.25 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.191, I:E.192 MG.28: 7 residues within 4Å: Chain D: N.111 Chain J: K.163, K.165, K.189, D.191, E.192 Ligands: CAP.29 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.191, J:E.192

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

CAP.2: 23 residues within 4Å: Chain A: K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.285, 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.1 23 PLIP interactions: 20 interactions with chain A, 3 interactions with chain H Hydrogen bonds: A:K.163, A:E.192, A:G.369, A:Q.389, A:Q.389, A:G.391, A:G.392, H:N.111 Water bridges: A:R.282, A:H.285, A:V.315, A:L.370, A:G.393, H:E.49, H:E.49 Salt bridges: A:K.163, A:K.163, A:K.165, A:R.282, A:H.285, A:H.314, A:K.322, A:K.322 CAP.4: 23 residues within 4Å: Chain B: V.161, K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.285, 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.3 26 PLIP interactions: 4 interactions with chain G, 22 interactions with chain B Hydrogen bonds: G:N.111, B:K.163, B:D.191, B:G.369, B:Q.389, B:G.391, B:G.392 Water bridges: G:E.49, G:E.49, G:T.54, B:H.281, B:H.285, B:H.314, B:G.316, B:S.367, B:L.370, B:L.370, 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.6: 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.5 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:K.163, C:D.191, C:S.367, C:G.369, C:Q.389, C:G.391, C:G.392, F:N.111 Water bridges: C:R.282, C:H.285, C:S.367, C:G.368, C:L.370, C:L.370, C:G.393, F:E.49, F:E.49 Salt bridges: C:K.163, C:K.163, C:K.165, C:R.282, C:H.314, C:K.322, C:K.322 CAP.10: 22 residues within 4Å: Chain D: 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.9 30 PLIP interactions: 28 interactions with chain D, 2 interactions with chain J Hydrogen bonds: D:K.163, D:E.192, 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:K.165, D:H.281, D:R.282, D:R.282, D:R.282, D:H.314, D:G.316, D:S.367, D:G.368, 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.14: 22 residues within 4Å: Chain E: 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 I: E.49, W.55, N.111 Ligands: MG.13 31 PLIP interactions: 29 interactions with chain E, 2 interactions with chain I Hydrogen bonds: E:K.163, E:G.369, E:Q.389, E:Q.389, E:G.391, E:G.392, I:N.111 Water bridges: E:K.165, E:K.165, E:K.165, E:K.165, E:H.281, E:R.282, E:R.282, E:H.285, E:H.314, E:G.316, E:K.322, E:S.367, E:G.368, E:G.368, E:L.370, E:G.393, I:W.55 Salt bridges: E:K.163, E:K.163, E:K.165, E:R.282, E:H.314, E:K.322, E:K.322 CAP.17: 23 residues within 4Å: Chain C: E.49, T.54, W.55, N.111 Chain F: K.163, K.165, K.189, D.191, E.192, H.281, R.282, H.285, H.314, K.322, L.323, S.367, G.368, G.369, Q.389, L.390, G.391, G.392 Ligands: MG.16 23 PLIP interactions: 20 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:K.163, F:E.192, F:G.369, F:Q.389, F:Q.389, F:G.391, F:G.392, C:N.111 Water bridges: F:R.282, F:H.285, F:V.315, F:L.370, F:G.393, C:E.49, C:E.49 Salt bridges: F:K.163, F:K.163, F:K.165, F:R.282, F:H.285, F:H.314, F:K.322, F:K.322 CAP.19: 23 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.285, 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: 22 interactions with chain G, 4 interactions with chain B Hydrogen bonds: G:K.163, G:D.191, G:G.369, G:Q.389, G:G.391, G:G.392, B:N.111 Water bridges: G:H.281, G:H.285, G:H.314, G:G.316, G:S.367, G:L.370, G:L.370, G:L.370, G:G.393, B:E.49, B:E.49, B:T.54 Salt bridges: G:K.163, G:K.163, G:K.165, G:R.282, G:H.314, G:K.322, G:K.322 CAP.21: 22 residues within 4Å: Chain A: E.49, W.55, N.111 Chain H: 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 24 PLIP interactions: 21 interactions with chain H, 3 interactions with chain A Hydrogen bonds: H:K.163, H:D.191, H:S.367, H:G.369, H:Q.389, H:G.391, H:G.392, A:N.111 Water bridges: H:R.282, H:H.285, H:S.367, H:G.368, H:L.370, H:L.370, H:G.393, A:E.49, A:E.49 Salt bridges: H:K.163, H:K.163, H:K.165, H:R.282, H:H.314, H:K.322, H:K.322 CAP.25: 22 residues within 4Å: Chain E: E.49, T.54, W.55, N.111 Chain I: 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.24 30 PLIP interactions: 28 interactions with chain I, 2 interactions with chain E Hydrogen bonds: I:K.163, I:E.192, I:G.369, I:Q.389, I:G.391, I:G.392, E:T.54, E:N.111 Water bridges: I:K.165, I:K.165, I:K.165, I:K.165, I:H.281, I:R.282, I:R.282, I:R.282, I:H.314, I:G.316, 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.29: 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.28 31 PLIP interactions: 2 interactions with chain D, 29 interactions with chain J Hydrogen bonds: D:N.111, J:K.163, J:G.369, J:Q.389, J:Q.389, J:G.391, J:G.392 Water bridges: D:W.55, J:K.165, J:K.165, J:K.165, J:K.165, J:H.281, J:R.282, J:R.282, J:H.285, J:H.314, J:G.316, J:K.322, J:S.367, J:G.368, J:G.368, J:L.370, J:G.393 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 7 residues within 4Å: Chain C: E.97, A.99, N.100, L.101, L.132, E.135, F.136 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.99, C:N.100, C:N.100 EDO.8: 3 residues within 4Å: Chain C: E.238, Y.266 Chain F: E.238 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain D: E.97, A.99, N.100, L.101, L.132, E.135, F.136 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.99, D:N.100, D:N.100 Water bridges: D:L.104 EDO.12: 4 residues within 4Å: Chain D: E.238, Y.266 Chain J: E.238, Y.266 No protein-ligand interaction detected (PLIP) EDO.15: 6 residues within 4Å: Chain E: E.97, A.99, N.100, L.132, E.135, F.136 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.97, E:A.99, E:L.132, E:E.135 EDO.22: 7 residues within 4Å: Chain H: E.97, A.99, N.100, L.101, L.132, E.135, F.136 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:A.99, H:N.100, H:N.100 EDO.23: 3 residues within 4Å: Chain A: E.238 Chain H: E.238, Y.266 No protein-ligand interaction detected (PLIP) EDO.26: 7 residues within 4Å: Chain I: E.97, A.99, N.100, L.101, L.132, E.135, F.136 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:A.99, I:N.100, I:N.100 Water bridges: I:L.104 EDO.27: 4 residues within 4Å: Chain E: E.238, Y.266 Chain I: E.238, Y.266 No protein-ligand interaction detected (PLIP) EDO.30: 6 residues within 4Å: Chain J: E.97, A.99, N.100, L.132, E.135, F.136 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:E.97, J:A.99, J:L.132, J:E.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiriyama, T. et al., Mutation design of thermophilic Rubisco based on the three-dimensional structure enhances its activity at ambient temperature. to be published

Release Date

2015-02-04

Peptides

Ribulose bisphosphate carboxylase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

F
F

G
G

H
H

I
I

J
J

Ribulose bisphosphate carboxylase

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