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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-16-mer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.95, K.165 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) 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: 3 residues within 4Å: Chain E: D.95, K.165 Ligands: ANP.10 No protein-ligand interaction detected (PLIP) 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 MG.17: 3 residues within 4Å: Chain I: D.95, K.165 Ligands: ANP.18 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain J: D.95, S.161, K.165 Ligands: ANP.20 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.95 MG.21: 4 residues within 4Å: Chain K: D.95, S.161, K.165 Ligands: ANP.22 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.95 MG.23: 4 residues within 4Å: Chain L: D.95, S.161, K.165 Ligands: ANP.24 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.95 MG.25: 3 residues within 4Å: Chain M: D.95, K.165 Ligands: ANP.26 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain N: D.95, S.161, K.165 Ligands: ANP.28 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.95 MG.29: 4 residues within 4Å: Chain O: D.95, S.161, K.165 Ligands: ANP.30 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.95 MG.31: 4 residues within 4Å: Chain P: D.95, S.161, K.165 Ligands: ANP.32 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.95

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

ANP.2: 24 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, F.482, I.494, E.496 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.44, A:D.64, A:C.65, 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:G.411, A:G.412, A:E.496 Water bridges: A:T.42, A:T.42, A:N.63, A:T.99, A:K.501, A:K.501 ANP.4: 24 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, T.163, K.165, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.44, B:C.65, B:G.94, 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:G.412, B:G.412, B:E.496, B:K.501 Salt bridges: B:K.165 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: 24 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, F.482, I.494, E.496 Ligands: MG.9 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:G.44, E:D.64, E:C.65, 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:G.411, E:G.412, E:E.496 Water bridges: E:T.42, E:T.42, E:N.63, E:T.99, E:K.501, E:K.501 ANP.12: 24 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, T.163, K.165, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.11 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:G.44, F:C.65, F:G.94, 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:G.412, F:G.412, F:E.496, F:K.501 Salt bridges: F:K.165 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 ANP.18: 24 residues within 4Å: Chain I: 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, F.482, I.494, E.496 Ligands: MG.17 20 PLIP interactions: 20 interactions with chain I Hydrogen bonds: I:G.44, I:D.64, I:C.65, I:G.96, I:T.97, I:T.98, I:T.98, I:T.98, I:T.99, I:T.99, I:T.99, I:G.411, I:G.412, I:E.496 Water bridges: I:T.42, I:T.42, I:N.63, I:T.99, I:K.501, I:K.501 ANP.20: 24 residues within 4Å: Chain J: 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, K.165, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.19 19 PLIP interactions: 19 interactions with chain J Hydrogen bonds: J:G.44, J:C.65, J:G.94, J:G.96, J:T.97, J:T.98, J:T.98, J:T.98, J:T.99, J:T.99, J:T.99, J:G.411, J:E.496 Water bridges: J:N.63, J:G.412, J:G.412, J:E.496, J:K.501 Salt bridges: J:K.165 ANP.22: 23 residues within 4Å: Chain K: 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.21 24 PLIP interactions: 24 interactions with chain K Hydrogen bonds: K:G.44, K:D.64, K:D.64, K:C.65, K:D.95, K:G.96, K:G.96, K:T.97, K:T.98, K:T.98, K:T.98, K:T.99, K:T.99, K:T.99, K:T.163, K:T.163, K:G.411, K:G.412, K:E.496 Water bridges: K:N.63, K:A.413, K:V.481, K:K.501, K:K.501 ANP.24: 22 residues within 4Å: Chain L: 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.23 23 PLIP interactions: 23 interactions with chain L Hydrogen bonds: L:G.44, L:D.64, L:D.64, L:C.65, L:D.95, L:G.96, L:T.97, L:T.98, L:T.98, L:T.98, L:T.99, L:T.99, L:T.99, L:G.411, L:E.496 Water bridges: L:N.63, L:N.63, L:N.63, L:T.97, L:T.99, L:G.412, L:G.412, L:K.501 ANP.26: 24 residues within 4Å: Chain M: 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, F.482, I.494, E.496 Ligands: MG.25 20 PLIP interactions: 20 interactions with chain M Hydrogen bonds: M:G.44, M:D.64, M:C.65, M:G.96, M:T.97, M:T.98, M:T.98, M:T.98, M:T.99, M:T.99, M:T.99, M:G.411, M:G.412, M:E.496 Water bridges: M:T.42, M:T.42, M:N.63, M:T.99, M:K.501, M:K.501 ANP.28: 24 residues within 4Å: Chain N: 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, K.165, A.410, G.411, I.447, L.451, I.479, I.494, E.496 Ligands: MG.27 19 PLIP interactions: 19 interactions with chain N Hydrogen bonds: N:G.44, N:C.65, N:G.94, N:G.96, N:T.97, N:T.98, N:T.98, N:T.98, N:T.99, N:T.99, N:T.99, N:G.411, N:E.496 Water bridges: N:N.63, N:G.412, N:G.412, N:E.496, N:K.501 Salt bridges: N:K.165 ANP.30: 23 residues within 4Å: Chain O: 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.29 24 PLIP interactions: 24 interactions with chain O Hydrogen bonds: O:G.44, O:D.64, O:D.64, O:C.65, O:D.95, O:G.96, O:G.96, O:T.97, O:T.98, O:T.98, O:T.98, O:T.99, O:T.99, O:T.99, O:T.163, O:T.163, O:G.411, O:G.412, O:E.496 Water bridges: O:N.63, O:A.413, O:V.481, O:K.501, O:K.501 ANP.32: 22 residues within 4Å: Chain P: 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.31 23 PLIP interactions: 23 interactions with chain P Hydrogen bonds: P:G.44, P:D.64, P:D.64, P:C.65, P:D.95, P:G.96, P:T.97, P:T.98, P:T.98, P:T.98, P:T.99, P:T.99, P:T.99, P:G.411, P:E.496 Water bridges: P:N.63, P:N.63, P:N.63, P:T.97, P:T.99, P:G.412, P:G.412, P:K.501

Links

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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: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

M
A

N
B

O
C

P
D

Thermosome alpha subunit

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