SMTL ID : 3kfb.1

Crystal structure of a group II chaperonin from Methanococcus maripaludis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-16-mer

Ligands

16 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Covalent)

ANP.1: 27 residues within 4Å: Chain A: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.40, A:D.60, A:D.60, A:G.61, A:G.92, A:T.93, A:T.94, A:T.94, A:T.94, A:T.95, A:T.95, A:K.161, A:K.161, A:D.386, A:G.404, A:E.490, A:K.495 ANP.3: 27 residues within 4Å: Chain B: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.40, B:D.60, B:D.60, B:G.61, B:G.92, B:T.93, B:T.94, B:T.94, B:T.94, B:T.95, B:T.95, B:K.161, B:D.386, B:G.404, B:E.490, B:K.495 ANP.5: 27 residues within 4Å: Chain C: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.40, C:D.60, C:D.60, C:G.61, C:G.92, C:T.93, C:T.94, C:T.94, C:T.94, C:T.95, C:T.95, C:K.161, C:D.386, C:G.404, C:E.490, C:K.495 ANP.7: 27 residues within 4Å: Chain D: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.8 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:G.40, D:D.60, D:G.61, D:D.91, D:G.92, D:T.93, D:T.94, D:T.94, D:T.94, D:T.95, D:T.95, D:K.161, D:K.161, D:D.386, D:G.404, D:E.490, D:K.495 ANP.9: 27 residues within 4Å: Chain E: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.10 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:G.40, E:D.60, E:G.61, E:G.92, E:T.93, E:T.94, E:T.94, E:T.94, E:T.95, E:T.95, E:K.161, E:D.386, E:G.404, E:E.490, E:K.495 ANP.11: 27 residues within 4Å: Chain F: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.12 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:G.40, F:D.60, F:G.61, F:D.91, F:G.92, F:T.93, F:T.94, F:T.94, F:T.94, F:T.95, F:T.95, F:K.161, F:D.386, F:G.404, F:E.490, F:K.495 ANP.13: 27 residues within 4Å: Chain G: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.40, G:D.60, G:G.61, G:G.92, G:T.93, G:T.94, G:T.94, G:T.94, G:T.95, G:T.95, G:K.161, G:D.386, G:G.404, G:E.490, G:K.495 ANP.15: 27 residues within 4Å: Chain H: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.16 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:G.40, H:D.60, H:D.60, H:G.61, H:D.91, H:G.92, H:T.93, H:T.94, H:T.94, H:T.94, H:T.95, H:T.95, H:K.161, H:K.161, H:D.386, H:G.404, H:E.490, H:K.495 ANP.17: 27 residues within 4Å: Chain I: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:G.40, I:D.60, I:G.61, I:G.92, I:T.93, I:T.93, I:T.94, I:T.94, I:T.95, I:T.95, I:K.161, I:K.161, I:G.404, I:E.490, I:K.495 ANP.19: 27 residues within 4Å: Chain J: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.20 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:G.40, J:D.60, J:G.61, J:D.91, J:G.92, J:T.93, J:T.93, J:T.94, J:T.94, J:T.95, J:T.95, J:K.161, J:G.404, J:E.490, J:K.495 ANP.21: 27 residues within 4Å: Chain K: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.22 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.40, K:D.60, K:G.61, K:G.92, K:T.93, K:T.93, K:T.94, K:T.94, K:T.95, K:T.95, K:K.161, K:G.404, K:E.490, K:K.495 ANP.23: 27 residues within 4Å: Chain L: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.24 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:G.40, L:D.60, L:D.60, L:G.61, L:G.92, L:T.93, L:T.93, L:T.94, L:T.94, L:T.95, L:T.95, L:K.161, L:K.161, L:G.404, L:E.490, L:K.495 ANP.25: 27 residues within 4Å: Chain M: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.26 15 PLIP interactions: 15 interactions with chain M Hydrogen bonds: M:G.40, M:D.60, M:D.60, M:G.61, M:G.92, M:T.93, M:T.93, M:T.94, M:T.94, M:T.95, M:T.95, M:K.161, M:G.404, M:E.490, M:K.495 ANP.27: 27 residues within 4Å: Chain N: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.28 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:G.40, N:D.60, N:D.60, N:G.61, N:G.92, N:T.93, N:T.93, N:T.94, N:T.94, N:T.95, N:T.95, N:K.161, N:G.404, N:E.490, N:K.495 ANP.29: 27 residues within 4Å: Chain O: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.30 15 PLIP interactions: 15 interactions with chain O Hydrogen bonds: O:G.40, O:D.60, O:D.60, O:G.61, O:G.92, O:T.93, O:T.93, O:T.94, O:T.94, O:T.95, O:T.95, O:K.161, O:G.404, O:E.490, O:K.495 ANP.31: 27 residues within 4Å: Chain P: T.38, L.39, G.40, P.41, N.59, D.60, G.61, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, K.161, D.386, G.403, G.404, L.444, L.473, N.474, V.475, F.476, E.490, K.495 Ligands: MG.32 16 PLIP interactions: 16 interactions with chain P Hydrogen bonds: P:G.40, P:D.60, P:G.61, P:G.92, P:T.93, P:T.93, P:T.94, P:T.94, P:T.94, P:T.95, P:T.95, P:K.161, P:K.161, P:G.404, P:E.490, P:K.495

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.91, S.157, D.386 Ligands: ANP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.91, A:S.157 MG.4: 5 residues within 4Å: Chain B: D.91, S.157, K.161, D.386 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.91 MG.6: 4 residues within 4Å: Chain C: D.91, S.157, D.386 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.91 MG.8: 3 residues within 4Å: Chain D: D.91, S.157 Ligands: ANP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.91, D:S.157 MG.10: 4 residues within 4Å: Chain E: D.91, S.157, D.386 Ligands: ANP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.91 MG.12: 5 residues within 4Å: Chain F: D.91, S.157, K.161, D.386 Ligands: ANP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.91 MG.14: 4 residues within 4Å: Chain G: D.91, S.157, D.386 Ligands: ANP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.91 MG.16: 3 residues within 4Å: Chain H: D.91, S.157 Ligands: ANP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.91 MG.18: 4 residues within 4Å: Chain I: D.91, S.157, D.386 Ligands: ANP.17 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.91, I:S.157 MG.20: 5 residues within 4Å: Chain J: D.91, S.157, K.161, D.386 Ligands: ANP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.91 MG.22: 4 residues within 4Å: Chain K: D.91, S.157, D.386 Ligands: ANP.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.91 MG.24: 3 residues within 4Å: Chain L: D.91, S.157 Ligands: ANP.23 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.91, L:S.157 MG.26: 4 residues within 4Å: Chain M: D.91, S.157, D.386 Ligands: ANP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.91 MG.28: 5 residues within 4Å: Chain N: D.91, S.157, K.161, D.386 Ligands: ANP.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.91 MG.30: 4 residues within 4Å: Chain O: D.91, S.157, D.386 Ligands: ANP.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.91 MG.32: 3 residues within 4Å: Chain P: D.91, S.157 Ligands: ANP.31 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.91

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: ABCDEFGHIJKLMNOP

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
A

J
B

K
C

L
D

M
E

N
F

O
G

P
H

Chaperonin

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