SMTL ID : 7pbx.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.31, A:D.86, A:D.86, A:D.86, A:G.87, A:T.89, A:T.90, A:G.414, A:N.478, A:A.479, A:A.480 ADP.3: 22 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.29, B:G.31, B:G.87, B:T.88, B:T.89, B:T.89, B:T.90, B:G.414, B:G.415, B:N.478, B:A.479, B:A.480, B:D.494 Salt bridges: B:K.50 ADP.5: 17 residues within 4Å: Chain D: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.31, D:D.86, D:D.86, D:D.86, D:G.87, D:T.89, D:T.90, D:G.414, D:N.478, D:A.479, D:A.480 ADP.7: 22 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:T.29, E:G.31, E:G.87, E:T.88, E:T.89, E:T.89, E:T.90, E:G.414, E:G.415, E:N.478, E:A.479, E:A.480, E:D.494 Salt bridges: E:K.50 ADP.9: 17 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.31, G:D.86, G:D.86, G:D.86, G:G.87, G:T.89, G:T.90, G:G.414, G:N.478, G:A.479, G:A.480 ADP.11: 22 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.12 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:T.29, H:G.31, H:G.87, H:T.88, H:T.89, H:T.89, H:T.90, H:G.414, H:G.415, H:N.478, H:A.479, H:A.480, H:D.494 Salt bridges: H:K.50 ADP.13: 17 residues within 4Å: Chain J: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:G.31, J:D.86, J:D.86, J:D.86, J:G.87, J:T.89, J:T.90, J:G.414, J:N.478, J:A.479, J:A.480 ADP.15: 22 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.16 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:T.29, K:G.31, K:G.87, K:T.88, K:T.89, K:T.89, K:T.90, K:G.414, K:G.415, K:N.478, K:A.479, K:A.480, K:D.494 Salt bridges: K:K.50 ADP.17: 17 residues within 4Å: Chain M: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492 Ligands: MG.18 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:G.31, M:D.86, M:D.86, M:D.86, M:G.87, M:T.89, M:T.90, M:G.414, M:N.478, M:A.479, M:A.480 ADP.19: 22 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.20 14 PLIP interactions: 14 interactions with chain N Hydrogen bonds: N:T.29, N:G.31, N:G.87, N:T.88, N:T.89, N:T.89, N:T.90, N:G.414, N:G.415, N:N.478, N:A.479, N:A.480, N:D.494 Salt bridges: N:K.50 ADP.21: 17 residues within 4Å: Chain P: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492 Ligands: MG.22 11 PLIP interactions: 11 interactions with chain P Hydrogen bonds: P:G.31, P:D.86, P:D.86, P:D.86, P:G.87, P:T.89, P:T.90, P:G.414, P:N.478, P:A.479, P:A.480 ADP.23: 22 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.24 14 PLIP interactions: 14 interactions with chain Q Hydrogen bonds: Q:T.29, Q:G.31, Q:G.87, Q:T.88, Q:T.89, Q:T.89, Q:T.90, Q:G.414, Q:G.415, Q:N.478, Q:A.479, Q:A.480, Q:D.494 Salt bridges: Q:K.50 ADP.25: 17 residues within 4Å: Chain S: T.29, L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, G.414, I.453, Y.477, N.478, A.479, A.480, I.492 Ligands: MG.26 11 PLIP interactions: 11 interactions with chain S Hydrogen bonds: S:G.31, S:D.86, S:D.86, S:D.86, S:G.87, S:T.89, S:T.90, S:G.414, S:N.478, S:A.479, S:A.480 ADP.27: 22 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, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.28 14 PLIP interactions: 14 interactions with chain T Hydrogen bonds: T:T.29, T:G.31, T:G.87, T:T.88, T:T.89, T:T.89, T:T.90, T:G.414, T:G.415, T:N.478, T:A.479, T:A.480, 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.86, A:D.86 MG.4: 3 residues within 4Å: Chain B: D.86, G.87 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 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.86, D:D.86 MG.8: 3 residues within 4Å: Chain E: D.86, G.87 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 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.86, G:D.86 MG.12: 3 residues within 4Å: Chain H: D.86, G.87 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 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.86, J:D.86 MG.16: 3 residues within 4Å: Chain K: D.86, G.87 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 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.86, M:D.86 MG.20: 3 residues within 4Å: Chain N: D.86, G.87 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 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.86, P:D.86 MG.24: 3 residues within 4Å: Chain Q: D.86, G.87 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 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:D.86, S:D.86 MG.28: 3 residues within 4Å: Chain T: D.86, G.87 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
Ac

B
Ad

D
Ai

E
Aj

G
Ao

H
Ap

J
Au

K
Av

M
Ba

N
Bb

P
Bg

Q
Bh

S
Bm

T
Bn

C
Af

F
Al

I
Ar

L
Ax

O
Bd

R
Bj

U
Bp

60 kDa chaperonin

10 kDa chaperonin

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