SMTL ID : 1q3q.3 (2 other biounits)

Crystal structure of the chaperonin from Thermococcus strain KS-1 (two-point mutant complexed with AMP-PNP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.95, S.161, K.165 Ligands: ANP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.95 MG.3: 4 residues within 4Å: Chain B: D.95, S.161, K.165 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.95 MG.5: 4 residues within 4Å: Chain C: D.95, S.161, K.165 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.95 MG.7: 4 residues within 4Å: Chain D: D.95, S.161, K.165 Ligands: ANP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.95 MG.9: 4 residues within 4Å: Chain E: D.95, S.161, K.165 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.95 MG.11: 4 residues within 4Å: Chain F: D.95, S.161, K.165 Ligands: ANP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.95 MG.13: 4 residues within 4Å: Chain G: D.95, S.161, K.165 Ligands: ANP.14 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.95 MG.15: 4 residues within 4Å: Chain H: D.95, S.161, K.165 Ligands: ANP.16 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.95

8 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 23 residues within 4Å: Chain A: T.42, L.43, G.44, P.45, N.63, D.64, C.65, G.94, D.95, G.96, T.97, T.98, T.99, T.160, T.163, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.1 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.44, A:D.64, A:D.64, A:C.65, A:D.95, A:G.96, A:G.96, A:T.97, A:T.98, A:T.98, A:T.98, A:T.99, A:T.99, A:T.99, A:T.163, A:T.163, A:G.411, A:G.412, A:E.496 Water bridges: A:N.63, A:A.413, A:V.481, A:K.501, A:K.501 ANP.4: 22 residues within 4Å: Chain B: T.42, L.43, G.44, P.45, N.63, D.64, C.65, G.94, D.95, G.96, T.97, T.98, T.99, T.160, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.3 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.44, B:D.64, B:D.64, B:C.65, B:D.95, B:G.96, B:T.97, B:T.98, B:T.98, B:T.98, B:T.99, B:T.99, B:T.99, B:G.411, B:E.496 Water bridges: B:N.63, B:N.63, B:N.63, B:T.97, B:T.99, B:G.412, B:G.412, B:K.501 ANP.6: 23 residues within 4Å: Chain C: T.42, L.43, G.44, P.45, N.63, D.64, C.65, G.94, D.95, G.96, T.97, T.98, T.99, T.160, T.163, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.5 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:G.44, C:D.64, C:D.64, C:C.65, C:D.95, C:G.96, C:G.96, C:T.97, C:T.98, C:T.98, C:T.98, C:T.99, C:T.99, C:T.99, C:T.163, C:T.163, C:G.411, C:G.412, C:E.496 Water bridges: C:N.63, C:A.413, C:V.481, C:K.501, C:K.501 ANP.8: 22 residues within 4Å: Chain D: T.42, L.43, G.44, P.45, N.63, D.64, C.65, G.94, D.95, G.96, T.97, T.98, T.99, T.160, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.7 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:G.44, D:D.64, D:D.64, D:C.65, D:D.95, D:G.96, D:T.97, D:T.98, D:T.98, D:T.98, D:T.99, D:T.99, D:T.99, D:G.411, D:E.496 Water bridges: D:N.63, D:N.63, D:N.63, D:T.97, D:T.99, D:G.412, D:G.412, D:K.501 ANP.10: 23 residues within 4Å: Chain E: T.42, L.43, G.44, P.45, N.63, D.64, C.65, G.94, D.95, G.96, T.97, T.98, T.99, T.160, T.163, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.9 24 PLIP interactions: 24 interactions with chain E Hydrogen bonds: E:G.44, E:D.64, E:D.64, E:C.65, E:D.95, E:G.96, E:G.96, E:T.97, E:T.98, E:T.98, E:T.98, E:T.99, E:T.99, E:T.99, E:T.163, E:T.163, E:G.411, E:G.412, E:E.496 Water bridges: E:N.63, E:A.413, E:V.481, E:K.501, E:K.501 ANP.12: 22 residues within 4Å: Chain F: T.42, L.43, G.44, P.45, N.63, D.64, C.65, G.94, D.95, G.96, T.97, T.98, T.99, T.160, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.11 23 PLIP interactions: 23 interactions with chain F Hydrogen bonds: F:G.44, F:D.64, F:D.64, F:C.65, F:D.95, F:G.96, F:T.97, F:T.98, F:T.98, F:T.98, F:T.99, F:T.99, F:T.99, F:G.411, F:E.496 Water bridges: F:N.63, F:N.63, F:N.63, F:T.97, F:T.99, F:G.412, F:G.412, F:K.501 ANP.14: 23 residues within 4Å: Chain G: T.42, L.43, G.44, P.45, N.63, D.64, C.65, G.94, D.95, G.96, T.97, T.98, T.99, T.160, T.163, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.13 24 PLIP interactions: 24 interactions with chain G Hydrogen bonds: G:G.44, G:D.64, G:D.64, G:C.65, G:D.95, G:G.96, G:G.96, G:T.97, G:T.98, G:T.98, G:T.98, G:T.99, G:T.99, G:T.99, G:T.163, G:T.163, G:G.411, G:G.412, G:E.496 Water bridges: G:N.63, G:A.413, G:V.481, G:K.501, G:K.501 ANP.16: 22 residues within 4Å: Chain H: T.42, L.43, G.44, P.45, N.63, D.64, C.65, G.94, D.95, G.96, T.97, T.98, T.99, T.160, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.15 23 PLIP interactions: 23 interactions with chain H Hydrogen bonds: H:G.44, H:D.64, H:D.64, H:C.65, H:D.95, H:G.96, H:T.97, H:T.98, H:T.98, H:T.98, H:T.99, H:T.99, H:T.99, H:G.411, H:E.496 Water bridges: H:T.42, H:N.63, H:N.63, H:T.97, H:T.99, H:G.412, H:G.412, H:K.501

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shomura, Y. et al., Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms. J.Mol.Biol. (2004)

Release Date

2004-01-27

Peptides

Thermosome alpha subunit: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

E
C

F
D

G
C

H
D

Thermosome alpha subunit

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