SMTL ID : 5w74.1

Crystal Structure of the Group II Chaperonin from Methanococcus Maripaludis D386ADeltaLid Mutant in the Open, ADP-Bound State

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

homo-16-mer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: L.39, G.40, P.41, D.91, G.92, T.94, T.95, G.160, G.403, G.404, G.405, L.444, L.473, N.474, V.475, M.483, V.488, E.490, K.495 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.40, A:G.92, A:T.94, A:T.95, A:T.95, A:T.95, A:T.95, A:G.404, A:G.405, A:N.474, A:V.475, A:E.490, A:K.495, A:K.495 ADP.3: 15 residues within 4Å: Chain B: L.39, G.40, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.403, G.404, V.488, E.490, K.495 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.40, B:G.92, B:T.93, B:T.94, B:T.94, B:T.94, B:T.95, B:T.95, B:T.95, B:T.95, B:G.404, B:G.405, B:E.490, B:K.495 ADP.5: 21 residues within 4Å: Chain C: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, L.473, F.476, V.488, E.490, K.495 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.40, C:G.92, C:T.93, C:T.94, C:T.94, C:T.94, C:T.95, C:T.95, C:T.95, C:T.95, C:T.95, C:G.404, C:G.405, C:E.490, C:K.495 ADP.7: 20 residues within 4Å: Chain D: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, F.476, V.488, E.490, K.495 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.40, D:G.92, D:T.93, D:T.94, D:T.94, D:T.94, D:T.95, D:T.95, D:T.95, D:T.95, D:T.95, D:G.404, D:G.405, D:E.490, D:K.495 ADP.9: 21 residues within 4Å: Chain E: L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.403, G.404, G.405, L.444, L.473, N.474, F.476, V.488, E.490, K.495 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:T.38, E:G.40, E:G.92, E:T.93, E:T.94, E:T.94, E:T.95, E:T.95, E:T.95, E:T.95, E:G.404, E:G.405, E:N.474, E:V.475, E:E.490, E:K.495, E:K.495 ADP.11: 21 residues within 4Å: Chain F: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, L.473, F.476, V.488, E.490, K.495 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.40, F:G.92, F:T.93, F:T.94, F:T.94, F:T.94, F:T.95, F:T.95, F:T.95, F:T.95, F:T.95, F:G.404, F:G.405, F:E.490, F:K.495 ADP.13: 21 residues within 4Å: Chain G: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, L.473, F.476, V.488, E.490, K.495 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:T.38, G:G.40, G:G.92, G:T.93, G:T.94, G:T.94, G:T.95, G:T.95, G:T.95, G:T.95, G:G.404, G:G.405, G:E.490, G:K.495 ADP.15: 21 residues within 4Å: Chain H: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, L.473, F.476, V.488, E.490, K.495 Ligands: MG.16 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.40, H:G.92, H:T.93, H:T.94, H:T.94, H:T.94, H:T.95, H:T.95, H:T.95, H:T.95, H:T.95, H:G.404, H:G.405, H:E.490, H:K.495 ADP.17: 20 residues within 4Å: Chain I: L.39, G.40, P.41, D.91, G.92, T.94, T.95, G.160, G.403, G.404, G.405, L.444, L.473, N.474, V.475, M.483, V.488, E.490, K.495 Ligands: MG.18 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:G.40, I:G.92, I:T.95, I:T.95, I:T.95, I:G.404, I:G.405, I:N.474, I:V.475, I:E.490, I:K.495, I:K.495 ADP.19: 15 residues within 4Å: Chain J: L.39, G.40, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.403, G.404, V.488, E.490, K.495 Ligands: MG.20 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:G.40, J:G.92, J:T.93, J:T.94, J:T.94, J:T.94, J:T.95, J:T.95, J:T.95, J:T.95, J:G.404, J:G.405, J:E.490, J:K.495 ADP.21: 21 residues within 4Å: Chain K: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, L.473, F.476, V.488, E.490, K.495 Ligands: MG.22 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.40, K:G.92, K:T.93, K:T.94, K:T.94, K:T.94, K:T.95, K:T.95, K:T.95, K:T.95, K:T.95, K:G.404, K:G.405, K:E.490, K:K.495 ADP.23: 20 residues within 4Å: Chain L: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, F.476, V.488, E.490, K.495 Ligands: MG.24 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:G.40, L:G.92, L:T.93, L:T.94, L:T.94, L:T.94, L:T.95, L:T.95, L:T.95, L:T.95, L:T.95, L:G.404, L:G.405, L:E.490, L:K.495 ADP.25: 21 residues within 4Å: Chain M: L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, G.160, G.403, G.404, G.405, L.444, L.473, N.474, F.476, V.488, E.490, K.495 Ligands: MG.26 15 PLIP interactions: 15 interactions with chain M Hydrogen bonds: M:T.38, M:G.40, M:G.92, M:T.93, M:T.94, M:T.95, M:T.95, M:T.95, M:G.404, M:G.405, M:N.474, M:V.475, M:E.490, M:K.495, M:K.495 ADP.27: 21 residues within 4Å: Chain N: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, L.473, F.476, V.488, E.490, K.495 Ligands: MG.28 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:G.40, N:G.92, N:T.93, N:T.94, N:T.94, N:T.94, N:T.95, N:T.95, N:T.95, N:T.95, N:T.95, N:G.404, N:G.405, N:E.490, N:K.495 ADP.29: 21 residues within 4Å: Chain O: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, L.473, F.476, V.488, E.490, K.495 Ligands: MG.30 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:T.38, O:G.40, O:G.92, O:T.93, O:T.94, O:T.95, O:T.95, O:T.95, O:G.404, O:G.405, O:E.490, O:K.495 ADP.31: 21 residues within 4Å: Chain P: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, T.156, T.159, G.160, G.403, G.404, G.405, L.473, F.476, V.488, E.490, K.495 Ligands: MG.32 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:G.40, P:G.92, P:T.93, P:T.94, P:T.94, P:T.94, P:T.95, P:T.95, P:T.95, P:T.95, P:T.95, P:G.404, P:G.405, P:E.490, P:K.495

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.91, T.94 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: D.91, S.157 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.91 MG.6: 3 residues within 4Å: Chain C: D.91, S.157 Ligands: ADP.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: ADP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.91, D:D.91 MG.10: 2 residues within 4Å: Chain E: D.91 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.91 MG.12: 3 residues within 4Å: Chain F: D.91, S.157 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.91 MG.14: 3 residues within 4Å: Chain G: D.91, S.157 Ligands: ADP.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: ADP.15 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.91, H:D.91 MG.18: 3 residues within 4Å: Chain I: D.91, T.94 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain J: D.91, S.157 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.91 MG.22: 3 residues within 4Å: Chain K: D.91, S.157 Ligands: ADP.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: ADP.23 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.91, L:D.91 MG.26: 2 residues within 4Å: Chain M: D.91 Ligands: ADP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.91 MG.28: 3 residues within 4Å: Chain N: D.91, S.157 Ligands: ADP.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.91 MG.30: 3 residues within 4Å: Chain O: D.91, S.157 Ligands: ADP.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: ADP.31 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.91, P:D.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dalton, K.M. et al., The Conformational Cycle of the Group II Chaperonin Termini. To Be Published

Release Date

2018-06-20

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