SMTL ID : 3kfe.1

Crystal structures of a group II chaperonin from Methanococcus maripaludis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.91, S.157, K.161, D.364 Ligands: ADP.2, SO4.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.91 MG.4: 6 residues within 4Å: Chain B: D.91, S.157, K.161, D.364 Ligands: ADP.5, SO4.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.91 MG.7: 6 residues within 4Å: Chain C: D.91, S.157, K.161, D.364 Ligands: ADP.8, SO4.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.91 MG.10: 6 residues within 4Å: Chain D: D.91, S.157, K.161, D.364 Ligands: ADP.11, SO4.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.91 MG.13: 6 residues within 4Å: Chain E: D.91, S.157, K.161, D.364 Ligands: ADP.14, SO4.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.91 MG.16: 6 residues within 4Å: Chain F: D.91, S.157, K.161, D.364 Ligands: ADP.17, SO4.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.91 MG.19: 6 residues within 4Å: Chain G: D.91, S.157, K.161, D.364 Ligands: ADP.20, SO4.21 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.91 MG.22: 6 residues within 4Å: Chain H: D.91, S.157, K.161, D.364 Ligands: ADP.23, SO4.24 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.91

8 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 20 residues within 4Å: Chain A: T.38, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.381, G.382, G.383, L.451, F.454, V.466, E.468 Ligands: MG.1, SO4.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.40, A:G.92, A:T.93, A:T.94, A:T.94, A:T.95, A:T.95, A:G.382, A:G.383, A:E.468 ADP.5: 22 residues within 4Å: Chain B: T.38, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.381, G.382, G.383, L.451, N.452, V.453, F.454, V.466, E.468 Ligands: MG.4, SO4.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.40, B:G.92, B:T.93, B:T.94, B:T.94, B:T.95, B:T.95, B:G.382, B:G.383, B:E.468 ADP.8: 20 residues within 4Å: Chain C: T.38, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.381, G.382, G.383, L.451, F.454, V.466, E.468 Ligands: MG.7, SO4.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.40, C:G.92, C:T.93, C:T.94, C:T.94, C:T.95, C:T.95, C:G.382, C:G.383, C:E.468 ADP.11: 19 residues within 4Å: Chain D: T.38, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.381, G.382, L.451, F.454, V.466, E.468 Ligands: MG.10, SO4.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.40, D:G.92, D:T.93, D:T.94, D:T.94, D:T.95, D:T.95, D:G.382, D:G.383, D:V.453, D:E.468 ADP.14: 20 residues within 4Å: Chain E: T.38, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.381, G.382, G.383, L.451, F.454, V.466, E.468 Ligands: MG.13, SO4.15 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.40, E:G.92, E:T.93, E:T.94, E:T.94, E:T.95, E:T.95, E:G.382, E:G.383, E:E.468 ADP.17: 19 residues within 4Å: Chain F: T.38, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.381, G.382, L.451, F.454, V.466, E.468 Ligands: MG.16, SO4.18 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.40, F:G.92, F:T.93, F:T.94, F:T.94, F:T.95, F:T.95, F:G.382, F:G.383, F:E.468 ADP.20: 19 residues within 4Å: Chain G: T.38, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.381, G.382, L.451, F.454, V.466, E.468 Ligands: MG.19, SO4.21 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.40, G:G.92, G:T.93, G:T.94, G:T.94, G:T.95, G:T.95, G:G.382, G:G.383, G:E.468 ADP.23: 20 residues within 4Å: Chain H: T.38, G.40, P.41, N.59, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.381, G.382, G.383, L.451, F.454, V.466, E.468 Ligands: MG.22, SO4.24 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:G.40, H:G.92, H:T.93, H:T.94, H:T.94, H:T.95, H:T.95, H:G.382, H:G.383, H:V.453, H:E.468

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 11 residues within 4Å: Chain A: N.59, D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.364 Ligands: MG.1, ADP.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.60, A:G.61, A:G.92, A:T.93, A:T.94, A:T.94, A:D.364 Salt bridges: A:K.161 SO4.6: 10 residues within 4Å: Chain B: D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.364 Ligands: MG.4, ADP.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.60, B:G.61, B:G.92, B:T.93, B:T.94, B:T.94, B:D.364 Salt bridges: B:K.161 SO4.9: 10 residues within 4Å: Chain C: D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.364 Ligands: MG.7, ADP.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.61, C:G.92, C:T.93, C:T.94, C:T.94, C:D.364 Salt bridges: C:K.161 SO4.12: 11 residues within 4Å: Chain D: N.59, D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.364 Ligands: MG.10, ADP.11 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.61, D:G.92, D:T.93, D:T.94, D:T.94, D:D.364 Salt bridges: D:K.161 SO4.15: 10 residues within 4Å: Chain E: D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.364 Ligands: MG.13, ADP.14 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.61, E:G.92, E:T.93, E:T.94, E:T.94, E:D.364 Salt bridges: E:K.161 SO4.18: 10 residues within 4Å: Chain F: D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.364 Ligands: MG.16, ADP.17 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.61, F:G.92, F:T.93, F:T.94, F:T.94, F:D.364 Salt bridges: F:K.161 SO4.21: 10 residues within 4Å: Chain G: D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.364 Ligands: MG.19, ADP.20 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:G.61, G:G.92, G:T.93, G:T.94, G:T.94, G:D.364 Salt bridges: G:K.161 SO4.24: 10 residues within 4Å: Chain H: D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.364 Ligands: MG.22, ADP.23 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:D.60, H:G.61, H:G.92, H:T.93, H:T.94, H:T.94, H:D.364 Salt bridges: H:K.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pereira, J.H. et al., Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J.Biol.Chem. (2010)

Release Date

2010-06-23

Peptides

Chaperonin: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Chaperonin

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