SMTL ID : 8bm0.1

Structure of GroEL:GroES-ATP complex plunge frozen 200 ms after reaction initiation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.87, G.88 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.87 MG.4: 3 residues within 4Å: Chain C: D.87, G.88 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.87 MG.7: 2 residues within 4Å: Chain D: D.87 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.87, D:D.87 MG.10: 3 residues within 4Å: Chain F: D.87, G.88 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.87 MG.13: 3 residues within 4Å: Chain G: D.87, S.151 Ligands: ATP.15 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.87, G:D.87 MG.16: 3 residues within 4Å: Chain I: D.87, G.88 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.87 MG.19: 2 residues within 4Å: Chain J: D.87 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.87 MG.22: 3 residues within 4Å: Chain L: D.87, G.88 Ligands: ATP.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.87 MG.25: 3 residues within 4Å: Chain M: D.87, G.88 Ligands: ATP.27 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.87 MG.28: 3 residues within 4Å: Chain O: D.87, G.88 Ligands: ATP.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.87 MG.31: 2 residues within 4Å: Chain P: D.87 Ligands: ATP.33 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.87 MG.34: 3 residues within 4Å: Chain R: D.87, G.88 Ligands: ATP.35 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:D.87 MG.37: 2 residues within 4Å: Chain S: D.87 Ligands: ATP.39 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:D.87 MG.40: 3 residues within 4Å: Chain U: D.87, G.88 Ligands: ATP.41 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:D.87

14 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: T.30, L.31, K.51, T.90 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.30, A:K.51, A:T.90 K.6: 5 residues within 4Å: Chain C: T.30, L.31, K.51, T.90 Ligands: ATP.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:T.30, C:T.30, C:K.51, C:T.90 K.8: 5 residues within 4Å: Chain D: T.30, L.31, K.51, T.90 Ligands: ATP.9 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.30, D:T.30, D:K.51 K.12: 5 residues within 4Å: Chain F: T.30, L.31, K.51, T.90 Ligands: ATP.11 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:T.30, F:T.30, F:K.51, F:T.90 K.14: 5 residues within 4Å: Chain G: T.30, L.31, K.51, T.90 Ligands: ATP.15 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.30, G:T.30, G:K.51, G:T.90 K.18: 5 residues within 4Å: Chain I: T.30, L.31, K.51, T.90 Ligands: ATP.17 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:T.30, I:T.30, I:K.51, I:T.90 K.20: 5 residues within 4Å: Chain J: T.30, L.31, K.51, T.90 Ligands: ATP.21 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:T.30, J:T.30, J:K.51 K.24: 4 residues within 4Å: Chain L: T.30, K.51, T.90 Ligands: ATP.23 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:T.30, L:T.30, L:K.51, L:T.90 K.26: 5 residues within 4Å: Chain M: T.30, L.31, K.51, T.90 Ligands: ATP.27 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:T.30, M:K.51, M:T.90 K.30: 5 residues within 4Å: Chain O: T.30, L.31, K.51, T.90 Ligands: ATP.29 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:T.30, O:T.30, O:K.51, O:T.90 K.32: 5 residues within 4Å: Chain P: T.30, L.31, K.51, T.90 Ligands: ATP.33 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:T.30, P:T.30, P:K.51, P:T.90 K.36: 4 residues within 4Å: Chain R: T.30, K.51, T.90 Ligands: ATP.35 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:T.30, R:T.30, R:K.51, R:T.90 K.38: 5 residues within 4Å: Chain S: T.30, L.31, K.51, T.90 Ligands: ATP.39 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:T.30, S:K.51, S:T.90 K.42: 5 residues within 4Å: Chain U: T.30, L.31, K.51, T.90 Ligands: ATP.41 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:T.30, U:T.30, U:K.51, U:T.90

14 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 28 residues within 4Å: Chain A: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, S.154, D.398, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.1, K.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.32, A:G.53, A:G.88, A:G.88, A:T.89, A:T.90, A:T.91, A:T.91, A:S.154, A:S.154, A:G.415, A:G.416, A:N.479, A:A.480, A:A.481, A:D.495 Salt bridges: A:K.51 ATP.5: 26 residues within 4Å: Chain C: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.4, K.6 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:G.32, C:D.52, C:D.52, C:G.53, C:G.88, C:G.88, C:T.89, C:T.90, C:T.90, C:T.91, C:T.91, C:T.91, C:S.154, C:S.154, C:G.415, C:A.480, C:A.481, C:D.495 Salt bridges: C:K.51 ATP.9: 27 residues within 4Å: Chain D: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, S.154, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.7, K.8 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:T.30, D:G.32, D:G.53, D:G.88, D:T.89, D:T.89, D:T.90, D:T.91, D:T.91, D:S.154, D:S.154, D:D.398, D:G.415, D:A.480, D:A.481, D:D.495 Salt bridges: D:K.51 ATP.11: 26 residues within 4Å: Chain F: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.10, K.12 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:G.32, F:D.52, F:D.52, F:G.53, F:G.88, F:G.88, F:T.89, F:T.90, F:T.90, F:T.91, F:T.91, F:T.91, F:S.154, F:S.154, F:G.415, F:A.480, F:A.481, F:D.495 Salt bridges: F:K.51 ATP.15: 27 residues within 4Å: Chain G: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, S.154, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.13, K.14 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:T.30, G:G.32, G:G.53, G:G.88, G:T.89, G:T.90, G:T.90, G:T.91, G:T.91, G:S.154, G:S.154, G:D.398, G:G.415, G:A.480, G:A.481, G:D.495 Salt bridges: G:K.51 ATP.17: 26 residues within 4Å: Chain I: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.16, K.18 18 PLIP interactions: 18 interactions with chain I Hydrogen bonds: I:G.32, I:D.52, I:D.52, I:G.53, I:G.88, I:G.88, I:T.89, I:T.90, I:T.90, I:T.91, I:T.91, I:T.91, I:G.415, I:N.479, I:A.480, I:A.481, I:D.495 Salt bridges: I:K.51 ATP.21: 27 residues within 4Å: Chain J: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, S.154, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.19, K.20 18 PLIP interactions: 18 interactions with chain J Hydrogen bonds: J:T.30, J:G.32, J:G.53, J:G.88, J:T.89, J:T.89, J:T.90, J:T.91, J:T.91, J:S.154, J:S.154, J:D.398, J:G.415, J:N.479, J:A.480, J:A.481, J:D.495 Salt bridges: J:K.51 ATP.23: 25 residues within 4Å: Chain L: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.22, K.24 19 PLIP interactions: 19 interactions with chain L Hydrogen bonds: L:G.32, L:D.52, L:D.52, L:G.53, L:G.88, L:G.88, L:T.89, L:T.90, L:T.90, L:T.91, L:T.91, L:T.91, L:G.415, L:G.416, L:N.479, L:A.480, L:A.481, L:D.495 Salt bridges: L:K.51 ATP.27: 28 residues within 4Å: Chain M: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, S.154, D.398, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.25, K.26 17 PLIP interactions: 17 interactions with chain M Hydrogen bonds: M:G.32, M:G.53, M:G.88, M:G.88, M:T.89, M:T.90, M:T.91, M:T.91, M:S.154, M:S.154, M:G.415, M:G.416, M:N.479, M:A.480, M:A.481, M:D.495 Salt bridges: M:K.51 ATP.29: 25 residues within 4Å: Chain O: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.28, K.30 18 PLIP interactions: 18 interactions with chain O Hydrogen bonds: O:G.32, O:D.52, O:D.52, O:G.53, O:G.88, O:G.88, O:T.89, O:T.90, O:T.90, O:T.91, O:T.91, O:T.91, O:G.415, O:N.479, O:A.480, O:A.481, O:D.495 Salt bridges: O:K.51 ATP.33: 28 residues within 4Å: Chain P: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, S.154, D.398, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.31, K.32 17 PLIP interactions: 17 interactions with chain P Hydrogen bonds: P:G.32, P:G.53, P:G.88, P:G.88, P:T.89, P:T.90, P:T.91, P:T.91, P:S.154, P:S.154, P:G.415, P:G.416, P:N.479, P:A.480, P:A.481, P:D.495 Salt bridges: P:K.51 ATP.35: 26 residues within 4Å: Chain R: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.34, K.36 20 PLIP interactions: 20 interactions with chain R Hydrogen bonds: R:G.32, R:D.52, R:D.52, R:G.53, R:G.88, R:G.88, R:T.89, R:T.90, R:T.90, R:T.91, R:T.91, R:T.91, R:S.154, R:S.154, R:G.415, R:G.416, R:A.480, R:A.481, R:D.495 Salt bridges: R:K.51 ATP.39: 28 residues within 4Å: Chain S: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, S.154, D.398, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.37, K.38 16 PLIP interactions: 16 interactions with chain S Hydrogen bonds: S:G.32, S:G.53, S:G.88, S:G.88, S:T.89, S:T.90, S:T.91, S:T.91, S:S.154, S:S.154, S:G.415, S:G.416, S:A.480, S:A.481, S:D.495 Salt bridges: S:K.51 ATP.41: 26 residues within 4Å: Chain U: T.30, L.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, S.154, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.40, K.42 19 PLIP interactions: 19 interactions with chain U Hydrogen bonds: U:G.32, U:D.52, U:D.52, U:G.53, U:G.88, U:G.88, U:T.89, U:T.90, U:T.90, U:T.91, U:T.91, U:T.91, U:G.415, U:G.416, U:N.479, U:A.480, U:A.481, U:D.495 Salt bridges: U:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torino, S. et al., Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting. Nat.Methods (2023)

Release Date

2023-08-09

Peptides

Chaperonin GroEL: ACDFGIJLMOPRSU
Co-chaperonin GroES: BEHKNQT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

C
G

D
A

F
C

G
D

I
F

J
H

L
K

M
L

O
N

P
O

R
Q

S
R

U
T

B
W

E
B

H
E

K
J

N
M

Q
P

T
S

Chaperonin GroEL

Co-chaperonin GroES

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