SMTL ID : 8bl2.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.87, G.88 Ligands: ATP.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, H2O.2 MG.4: 3 residues within 4Å: Chain B: D.87, G.88 Ligands: ATP.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.87, H2O.10 MG.7: 3 residues within 4Å: Chain C: D.87, G.88 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.87 MG.10: 3 residues within 4Å: Chain D: D.87, G.88 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.87 MG.13: 3 residues within 4Å: Chain E: D.87, G.88 Ligands: ATP.14 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.87, H2O.33 MG.16: 3 residues within 4Å: Chain F: D.87, G.88 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.87 MG.19: 3 residues within 4Å: Chain G: D.87, G.88 Ligands: ATP.20 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.87, H2O.47 MG.22: 3 residues within 4Å: Chain H: D.87, G.88 Ligands: ATP.23 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.87, H2O.55 MG.25: 3 residues within 4Å: Chain I: D.87, G.88 Ligands: ATP.26 2 PLIP interactions: 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.87, H2O.64 MG.28: 3 residues within 4Å: Chain J: D.87, G.88 Ligands: ATP.29 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.87 MG.31: 3 residues within 4Å: Chain K: D.87, G.88 Ligands: ATP.32 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.87 MG.34: 3 residues within 4Å: Chain L: D.87, G.88 Ligands: ATP.35 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.87 MG.37: 3 residues within 4Å: Chain M: D.87, G.88 Ligands: ATP.38 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.87 MG.40: 3 residues within 4Å: Chain N: D.87, G.88 Ligands: ATP.41 2 PLIP interactions: 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:D.87, H2O.101

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

ATP.2: 27 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, 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.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.32, A:D.52, A:G.53, A:G.88, A:G.88, A:T.89, A:T.90, A:T.91, A:T.91, A:D.398, A:G.415, A:G.416, A:N.479, A:A.480, A:A.481, A:D.495 Water bridges: A:K.51, A:K.51, A:K.51 Salt bridges: A:K.51 ATP.5: 27 residues within 4Å: Chain B: 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.4, K.6 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.32, B:D.52, B:G.53, B:G.88, B:G.88, B:T.89, B:T.90, B:T.91, B:T.91, B:D.398, B:G.415, B:G.416, B:N.479, B:A.480, B:A.481, B:D.495 Water bridges: B:K.51, B:K.51, B:K.51, B:D.495 Salt bridges: B:K.51 ATP.8: 27 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.7, K.9 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:G.32, C:D.52, C:G.53, C:G.88, C:G.88, C:T.89, C:T.90, C:T.91, C:T.91, C:D.398, C:G.415, C:G.416, C:N.479, C:A.480, C:A.481, C:D.495 Water bridges: C:K.51, C:K.51, C:K.51, C:N.153 Salt bridges: C:K.51 ATP.11: 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, 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.10, K.12 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:G.32, D:D.52, D:G.53, D:G.88, D:G.88, D:T.89, D:T.90, D:T.91, D:T.91, D:D.398, D:G.415, D:G.416, D:N.479, D:A.480, D:A.481, D:D.495 Water bridges: D:K.51, D:K.51, D:K.51 Salt bridges: D:K.51 ATP.14: 27 residues within 4Å: Chain E: 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.13, K.15 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:G.32, E:D.52, E:G.53, E:G.88, E:G.88, E:T.89, E:T.90, E:T.91, E:T.91, E:D.398, E:G.415, E:G.416, E:N.479, E:A.480, E:A.481, E:D.495 Water bridges: E:K.51, E:K.51, E:K.51, E:D.495 Salt bridges: E:K.51 ATP.17: 27 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.16, K.18 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:G.32, F:D.52, F:G.53, F:G.88, F:G.88, F:T.89, F:T.90, F:T.91, F:T.91, F:D.398, F:G.415, F:G.416, F:N.479, F:A.480, F:A.481, F:D.495 Water bridges: F:K.51, F:K.51, F:D.495 Salt bridges: F:K.51 ATP.20: 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, 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.19, K.21 21 PLIP interactions: 21 interactions with chain G Hydrogen bonds: G:G.32, G:D.52, G:G.53, G:G.88, G:G.88, G:T.89, G:T.90, G:T.91, G:T.91, G:D.398, G:G.415, G:G.416, G:N.479, G:A.480, G:A.481, G:D.495 Water bridges: G:K.51, G:K.51, G:K.51, G:D.495 Salt bridges: G:K.51 ATP.23: 27 residues within 4Å: Chain H: 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.22, K.24 23 PLIP interactions: 23 interactions with chain H Hydrogen bonds: H:G.32, H:D.52, H:D.52, H:G.53, H:G.88, H:G.88, H:T.89, H:T.90, H:T.90, H:T.91, H:D.398, H:G.415, H:G.416, H:N.479, H:A.480, H:A.481, H:D.495 Water bridges: H:K.51, H:K.51, H:D.398, H:D.398, H:D.398 Salt bridges: H:K.51 ATP.26: 27 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.25, K.27 24 PLIP interactions: 24 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:D.398, I:G.415, I:G.416, I:N.479, I:A.480, I:A.481, I:D.495 Water bridges: I:K.51, I:K.51, I:D.398, I:D.398, I:D.398, I:D.495 Salt bridges: I:K.51 ATP.29: 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, 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.28, K.30 22 PLIP interactions: 22 interactions with chain J Hydrogen bonds: J:G.32, J:D.52, J:D.52, J:G.53, J:G.88, J:G.88, J:T.89, J:T.90, J:T.90, J:T.91, J:D.398, J:G.415, J:G.416, J:N.479, J:A.480, J:A.481, J:D.495 Water bridges: J:K.51, J:K.51, J:D.398, J:D.398 Salt bridges: J:K.51 ATP.32: 27 residues within 4Å: Chain K: 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.31, K.33 23 PLIP interactions: 23 interactions with chain K Hydrogen bonds: K:G.32, K:D.52, K:D.52, K:G.53, K:G.88, K:G.88, K:T.89, K:T.90, K:T.90, K:T.91, K:D.398, K:G.415, K:G.416, K:N.479, K:A.480, K:A.481, K:D.495 Water bridges: K:K.51, K:K.51, K:D.398, K:D.398, K:D.495 Salt bridges: K:K.51 ATP.35: 27 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.34, K.36 23 PLIP interactions: 23 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:D.398, L:G.415, L:G.416, L:N.479, L:A.480, L:A.481, L:D.495 Water bridges: L:K.51, L:K.51, L:D.398, L:D.398, L:D.495 Salt bridges: L:K.51 ATP.38: 27 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, 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.39 21 PLIP interactions: 21 interactions with chain M Hydrogen bonds: M:G.32, M:D.52, M:D.52, M:G.53, M:G.88, M:G.88, M:T.89, M:T.90, M:T.90, M:T.91, M:D.398, M:G.415, M:G.416, M:N.479, M:A.480, M:A.481, M:D.495 Water bridges: M:D.398, M:D.398, M:D.495 Salt bridges: M:K.51 ATP.41: 27 residues within 4Å: Chain N: 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, G.416, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.40, K.42 25 PLIP interactions: 25 interactions with chain N Hydrogen bonds: N:G.32, N:D.52, N:D.52, N:G.53, N:G.88, N:G.88, N:T.89, N:T.90, N:T.90, N:T.91, N:D.398, N:G.415, N:G.416, N:N.479, N:A.480, N:A.481, N:D.495 Water bridges: N:K.51, N:K.51, N:D.398, N:D.398, N:D.398, N:D.495, N:D.495 Salt bridges: N:K.51

14 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.30, K.51, T.90 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:K.51, A:T.90 K.6: 4 residues within 4Å: Chain B: T.30, K.51, T.90 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:K.51, B:T.90 K.9: 4 residues within 4Å: Chain C: T.30, K.51, T.90 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:K.51, C:T.90 K.12: 4 residues within 4Å: Chain D: T.30, K.51, T.90 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:K.51, D:T.90 K.15: 4 residues within 4Å: Chain E: T.30, K.51, T.90 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:K.51, E:T.90 K.18: 4 residues within 4Å: Chain F: T.30, K.51, T.90 Ligands: ATP.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:K.51, F:T.90 K.21: 4 residues within 4Å: Chain G: T.30, K.51, T.90 Ligands: ATP.20 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:K.51, G:T.90 K.24: 4 residues within 4Å: Chain H: T.30, K.51, T.90 Ligands: ATP.23 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:K.51, H:T.90 K.27: 4 residues within 4Å: Chain I: T.30, K.51, T.90 Ligands: ATP.26 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:K.51, I:T.90 K.30: 4 residues within 4Å: Chain J: T.30, K.51, T.90 Ligands: ATP.29 2 PLIP interactions: 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:K.51, H2O.72 K.33: 4 residues within 4Å: Chain K: T.30, K.51, T.90 Ligands: ATP.32 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:K.51, K:T.90 K.36: 4 residues within 4Å: Chain L: T.30, K.51, T.90 Ligands: ATP.35 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:K.51, L:T.90 K.39: 4 residues within 4Å: Chain M: T.30, K.51, T.90 Ligands: ATP.38 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:K.51, M:T.90 K.42: 4 residues within 4Å: Chain N: T.30, K.51, T.90 Ligands: ATP.41 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:K.51, N:T.90

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: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
A

C
B

D
C

E
D

F
E

G
F

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Chaperonin GroEL

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