SMTL ID : 7pbj.1

Cryo-EM structure of the GroEL-GroES complex with ADP bound to both rings ("wide" conformation).

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, N.152, G.413, G.414, I.453, Y.477, N.478, A.479, I.492, D.494 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.31, A:G.87, A:T.89, A:T.90, A:G.414, A:N.478, A:A.479, A:D.494 Water bridges: A:D.86 ADP.3: 21 residues within 4Å: Chain B: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.31, B:G.87, B:T.88, B:T.89, B:T.89, B:T.90, B:T.90, B:T.90, B:G.414, B:N.478, B:A.479, B:A.480, B:D.494, B:D.494 Salt bridges: B:K.50 ADP.5: 19 residues within 4Å: Chain D: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, N.152, G.413, G.414, I.453, Y.477, N.478, A.479, I.492, D.494 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.31, D:G.87, D:T.89, D:T.90, D:G.414, D:N.478, D:A.479, D:D.494 Water bridges: D:D.86 ADP.7: 21 residues within 4Å: Chain E: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:G.31, E:G.87, E:T.88, E:T.89, E:T.89, E:T.90, E:T.90, E:T.90, E:G.414, E:N.478, E:A.479, E:A.480, E:D.494, E:D.494 Salt bridges: E:K.50 ADP.9: 19 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, N.152, G.413, G.414, I.453, Y.477, N.478, A.479, I.492, D.494 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:G.31, G:G.87, G:T.89, G:T.90, G:G.414, G:N.478, G:A.479, G:D.494 Water bridges: G:D.86 ADP.11: 21 residues within 4Å: Chain H: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.31, H:G.87, H:T.88, H:T.89, H:T.89, H:T.90, H:T.90, H:T.90, H:G.414, H:N.478, H:A.479, H:A.480, H:D.494, H:D.494 Salt bridges: H:K.50 ADP.13: 19 residues within 4Å: Chain J: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, N.152, G.413, G.414, I.453, Y.477, N.478, A.479, I.492, D.494 Ligands: MG.14 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:G.31, J:G.87, J:T.89, J:T.90, J:G.414, J:N.478, J:A.479, J:D.494 Water bridges: J:D.86 ADP.15: 21 residues within 4Å: Chain K: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.16 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.31, K:G.87, K:T.88, K:T.89, K:T.89, K:T.90, K:T.90, K:T.90, K:G.414, K:N.478, K:A.479, K:A.480, K:D.494, K:D.494 Salt bridges: K:K.50 ADP.17: 19 residues within 4Å: Chain M: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, N.152, G.413, G.414, I.453, Y.477, N.478, A.479, I.492, D.494 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:G.31, M:G.87, M:T.89, M:T.90, M:G.414, M:N.478, M:A.479, M:D.494 Water bridges: M:D.86 ADP.19: 21 residues within 4Å: Chain N: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.20 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:G.31, N:G.87, N:T.88, N:T.89, N:T.89, N:T.90, N:T.90, N:T.90, N:G.414, N:N.478, N:A.479, N:A.480, N:D.494, N:D.494 Salt bridges: N:K.50 ADP.21: 19 residues within 4Å: Chain P: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, N.152, G.413, G.414, I.453, Y.477, N.478, A.479, I.492, D.494 Ligands: MG.22 9 PLIP interactions: 9 interactions with chain P Hydrogen bonds: P:G.31, P:G.87, P:T.89, P:T.90, P:G.414, P:N.478, P:A.479, P:D.494 Water bridges: P:D.86 ADP.23: 21 residues within 4Å: Chain Q: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.24 15 PLIP interactions: 15 interactions with chain Q Hydrogen bonds: Q:G.31, Q:G.87, Q:T.88, Q:T.89, Q:T.89, Q:T.90, Q:T.90, Q:T.90, Q:G.414, Q:N.478, Q:A.479, Q:A.480, Q:D.494, Q:D.494 Salt bridges: Q:K.50 ADP.25: 19 residues within 4Å: Chain S: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, N.152, G.413, G.414, I.453, Y.477, N.478, A.479, I.492, D.494 Ligands: MG.26 9 PLIP interactions: 9 interactions with chain S Hydrogen bonds: S:G.31, S:G.87, S:T.89, S:T.90, S:G.414, S:N.478, S:A.479, S:D.494 Water bridges: S:D.86 ADP.27: 21 residues within 4Å: Chain T: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.28 15 PLIP interactions: 15 interactions with chain T Hydrogen bonds: T:G.31, T:G.87, T:T.88, T:T.89, T:T.89, T:T.90, T:T.90, T:T.90, T:G.414, T:N.478, T:A.479, T:A.480, T:D.494, T:D.494 Salt bridges: T:K.50

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.86 Ligands: ADP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.86, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain B: D.86 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.86, B:D.86 MG.6: 2 residues within 4Å: Chain D: D.86 Ligands: ADP.5 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.86, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain E: D.86 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.86, E:D.86 MG.10: 2 residues within 4Å: Chain G: D.86 Ligands: ADP.9 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.86, H2O.1, H2O.1 MG.12: 2 residues within 4Å: Chain H: D.86 Ligands: ADP.11 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.86, H:D.86 MG.14: 2 residues within 4Å: Chain J: D.86 Ligands: ADP.13 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.86, H2O.1, H2O.1 MG.16: 2 residues within 4Å: Chain K: D.86 Ligands: ADP.15 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.86, K:D.86 MG.18: 2 residues within 4Å: Chain M: D.86 Ligands: ADP.17 3 PLIP interactions: 1 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:D.86, H2O.1, H2O.1 MG.20: 2 residues within 4Å: Chain N: D.86 Ligands: ADP.19 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.86, N:D.86 MG.22: 2 residues within 4Å: Chain P: D.86 Ligands: ADP.21 3 PLIP interactions: 1 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:D.86, H2O.1, H2O.1 MG.24: 2 residues within 4Å: Chain Q: D.86 Ligands: ADP.23 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:D.86, Q:D.86 MG.26: 2 residues within 4Å: Chain S: D.86 Ligands: ADP.25 3 PLIP interactions: 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:D.86, H2O.1, H2O.1 MG.28: 2 residues within 4Å: Chain T: D.86 Ligands: ADP.27 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:D.86, T:D.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kudryavtseva, S.S. et al., Novel cryo-EM structure of an ADP-bound GroEL-GroES complex. Sci Rep (2021)

Release Date

2021-11-24

Peptides

60 kDa chaperonin: ABDEGHJKMNPQST
10 kDa chaperonin: CFILORU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Ad

B
Ae

D
Ak

E
Al

G
Ar

H
As

J
Ay

K
Az

M
Bf

N
Bg

P
Bm

Q
Bn

S
Bt

T
Bu

C
Af

F
Am

I
At

L
Ba

O
Bh

R
Bo

U
Bv

60 kDa chaperonin

10 kDa chaperonin

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