SMTL ID : 8bmt.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-14-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.87, S.151 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, S.151 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.87 MG.7: 3 residues within 4Å: Chain E: D.87, S.151 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.87 MG.10: 3 residues within 4Å: Chain G: D.87, S.151 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.87 MG.13: 3 residues within 4Å: Chain I: D.87, S.151 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.87 MG.16: 3 residues within 4Å: Chain K: D.87, S.151 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.87 MG.19: 3 residues within 4Å: Chain M: D.87, S.151 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.87 MG.22: 3 residues within 4Å: Chain O: D.87, S.151 Ligands: ATP.24 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.87 MG.25: 3 residues within 4Å: Chain Q: D.87, S.151 Ligands: ATP.27 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.87 MG.28: 3 residues within 4Å: Chain S: D.87, S.151 Ligands: ATP.30 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:D.87 MG.31: 3 residues within 4Å: Chain U: D.87, S.151 Ligands: ATP.33 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:D.87 MG.34: 3 residues within 4Å: Chain W: D.87, S.151 Ligands: ATP.36 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:D.87 MG.37: 3 residues within 4Å: Chain Y: D.87, S.151 Ligands: ATP.39 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:D.87 MG.40: 3 residues within 4Å: Chain 0: D.87, S.151 Ligands: ATP.42 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0: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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.30, A:T.30, A:K.51, A:T.90 K.5: 5 residues within 4Å: Chain C: T.30, L.31, K.51, T.90 Ligands: ATP.6 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 E: T.30, L.31, K.51, T.90 Ligands: ATP.9 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:T.30, E:T.30, E:K.51, E:T.90 K.11: 5 residues within 4Å: Chain G: T.30, L.31, K.51, T.90 Ligands: ATP.12 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.30, G:T.30, G:K.51, G:T.90 K.14: 5 residues within 4Å: Chain I: T.30, L.31, K.51, T.90 Ligands: ATP.15 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:T.30, I:T.30, I:K.51, I:T.90 K.17: 5 residues within 4Å: Chain K: T.30, L.31, K.51, T.90 Ligands: ATP.18 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:T.30, K:T.30, K:K.51, K:T.90 K.20: 5 residues within 4Å: Chain M: T.30, L.31, K.51, T.90 Ligands: ATP.21 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:T.30, M:T.30, M:K.51, M:T.90 K.23: 5 residues within 4Å: Chain O: T.30, L.31, K.51, T.90 Ligands: ATP.24 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:T.30, O:T.30, O:K.51, O:T.90 K.26: 5 residues within 4Å: Chain Q: T.30, L.31, K.51, T.90 Ligands: ATP.27 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:T.30, Q:T.30, Q:K.51, Q:T.90 K.29: 5 residues within 4Å: Chain S: T.30, L.31, K.51, T.90 Ligands: ATP.30 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:T.30, S:T.30, S:K.51, S:T.90 K.32: 5 residues within 4Å: Chain U: T.30, L.31, K.51, T.90 Ligands: ATP.33 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:T.30, U:T.30, U:K.51, U:T.90 K.35: 5 residues within 4Å: Chain W: T.30, L.31, K.51, T.90 Ligands: ATP.36 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:T.30, W:T.30, W:K.51, W:T.90 K.38: 5 residues within 4Å: Chain Y: T.30, L.31, K.51, T.90 Ligands: ATP.39 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:T.30, Y:T.30, Y:K.51, Y:T.90 K.41: 5 residues within 4Å: Chain 0: T.30, L.31, K.51, T.90 Ligands: ATP.42 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:T.30, 0:T.30, 0:K.51, 0:T.90

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

ATP.3: 26 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, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.1, K.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.30, A:G.32, A:K.51, A:G.53, A:G.88, A:G.88, A:T.89, A:T.89, A:T.90, A:T.91, A:T.91, A:T.91, A:D.398, A:G.415, A:N.479, A:A.480, A:A.481, A:D.495 Water bridges: A:K.51, A:K.51 Salt bridges: A:K.51 ATP.6: 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.5 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:T.30, C:G.32, C:K.51, C:G.53, C:G.88, C:G.88, C:T.89, C:T.89, C:T.90, C:T.91, C:T.91, C:T.91, C:D.398, C:G.415, C:N.479, C:A.480, C:A.481, C:D.495 Water bridges: C:K.51, C:K.51 Salt bridges: C:K.51 ATP.9: 26 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, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.7, K.8 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:T.30, E:G.32, E:K.51, E:G.53, E:G.88, E:G.88, E:T.89, E:T.89, E:T.90, E:T.91, E:T.91, E:T.91, E:D.398, E:G.415, E:N.479, E:A.480, E:A.481, E:D.495 Water bridges: E:K.51, E:K.51 Salt bridges: E:K.51 ATP.12: 26 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, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.10, K.11 19 PLIP interactions: 19 interactions with chain G Hydrogen bonds: G:T.30, G:G.32, G:K.51, G:G.53, G:G.88, G:G.88, G:T.89, G:T.89, G:T.90, G:T.91, G:T.91, G:T.91, G:D.398, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495 Salt bridges: G:K.51 ATP.15: 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.13, K.14 21 PLIP interactions: 21 interactions with chain I Hydrogen bonds: I:T.30, I:G.32, I:K.51, I:G.53, I:G.88, I:G.88, I:T.89, I:T.89, I:T.90, I:T.91, I:T.91, I:T.91, I:D.398, I:G.415, I:N.479, I:A.480, I:A.481, I:D.495 Water bridges: I:K.51, I:K.51 Salt bridges: I:K.51 ATP.18: 26 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, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.16, K.17 21 PLIP interactions: 21 interactions with chain K Hydrogen bonds: K:T.30, K:G.32, K:K.51, K:G.53, K:G.88, K:G.88, K:T.89, K:T.89, K:T.90, K:T.91, K:T.91, K:T.91, K:D.398, K:G.415, K:N.479, K:A.480, K:A.481, K:D.495 Water bridges: K:K.51, K:K.51 Salt bridges: K:K.51 ATP.21: 26 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, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.19, K.20 19 PLIP interactions: 19 interactions with chain M Hydrogen bonds: M:T.30, M:G.32, M:K.51, M:G.53, M:G.88, M:G.88, M:T.89, M:T.89, M:T.90, M:T.91, M:T.91, M:T.91, M:D.398, M:G.415, M:N.479, M:A.480, M:A.481, M:D.495 Salt bridges: M:K.51 ATP.24: 26 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, M.488, I.493, D.495 Ligands: MG.22, K.23 23 PLIP interactions: 23 interactions with chain O Hydrogen bonds: O:T.30, O:G.32, O:K.51, 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:D.398, O:D.398, O:G.415, O:N.479, O:A.480, O:A.481, O:D.495 Water bridges: O:K.51, O:D.52, O:D.495 Salt bridges: O:K.51 ATP.27: 26 residues within 4Å: Chain Q: 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.25, K.26 24 PLIP interactions: 24 interactions with chain Q Hydrogen bonds: Q:T.30, Q:G.32, Q:K.51, Q:G.53, Q:G.88, Q:G.88, Q:T.89, Q:T.90, Q:T.90, Q:T.91, Q:T.91, Q:T.91, Q:D.398, Q:D.398, Q:G.415, Q:N.479, Q:A.480, Q:A.481, Q:D.495 Water bridges: Q:K.51, Q:D.52, Q:N.153, Q:D.495 Salt bridges: Q:K.51 ATP.30: 26 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, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.28, K.29 23 PLIP interactions: 23 interactions with chain S Hydrogen bonds: S:T.30, S:G.32, S:K.51, S:G.53, S:G.88, S:G.88, S:T.89, S:T.90, S:T.90, S:T.91, S:T.91, S:T.91, S:D.398, S:D.398, S:G.415, S:N.479, S:A.480, S:A.481, S:D.495 Water bridges: S:K.51, S:D.52, S:N.153 Salt bridges: S:K.51 ATP.33: 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, D.398, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, I.493, D.495 Ligands: MG.31, K.32 20 PLIP interactions: 20 interactions with chain U Hydrogen bonds: U:T.30, U:G.32, U:K.51, 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:D.398, U:D.398, U:G.415, U:N.479, U:A.480, U:A.481, U:D.495 Salt bridges: U:K.51 ATP.36: 26 residues within 4Å: Chain W: 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.35 21 PLIP interactions: 21 interactions with chain W Hydrogen bonds: W:T.30, W:G.32, W:K.51, W:G.53, W:G.88, W:G.88, W:T.89, W:T.90, W:T.90, W:T.91, W:T.91, W:T.91, W:D.398, W:D.398, W:G.415, W:N.479, W:A.480, W:A.481, W:D.495 Water bridges: W:N.153 Salt bridges: W:K.51 ATP.39: 26 residues within 4Å: Chain Y: 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.37, K.38 20 PLIP interactions: 20 interactions with chain Y Hydrogen bonds: Y:T.30, Y:G.32, Y:K.51, Y:G.53, Y:G.88, Y:G.88, Y:T.89, Y:T.90, Y:T.90, Y:T.91, Y:T.91, Y:T.91, Y:D.398, Y:D.398, Y:G.415, Y:N.479, Y:A.480, Y:A.481, Y:D.495 Salt bridges: Y:K.51 ATP.42: 26 residues within 4Å: Chain 0: 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.40, K.41 22 PLIP interactions: 22 interactions with chain 0 Hydrogen bonds: 0:T.30, 0:G.32, 0:K.51, 0:G.53, 0:G.88, 0:G.88, 0:T.89, 0:T.90, 0:T.90, 0:T.91, 0:T.91, 0:T.91, 0:D.398, 0:D.398, 0:G.415, 0:N.479, 0:A.480, 0:A.481, 0:D.495 Water bridges: 0:K.51, 0:D.52 Salt bridges: 0: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: ACEGIKMOQSUWY0
Co-chaperonin GroES: BDFHJLNPRTVXZ1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

C
A

E
C

G
E

I
G

K
J

M
L

O
N

Q
P

S
R

U
T

W
X

Y
Z

0
BA

B
W

D
B

F
D

H
F

J
H

L
K

N
M

P
O

R
Q

T
S

V
V

X
Y

Z
AA

1
CA

Chaperonin GroEL

Co-chaperonin GroES

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