SMTL ID : 8bmo.1

Structure of GroEL:GroES complex exhibiting ADP-conformation in trans ring obtained under the continuous turnover conditions

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.87 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: D.87, S.151 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.87, B:D.87 MG.5: 2 residues within 4Å: Chain D: D.87 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain E: D.87 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.87, E:D.87 MG.9: 2 residues within 4Å: Chain G: D.87 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.87 MG.11: 3 residues within 4Å: Chain H: D.87, S.151 Ligands: ATP.12 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.87, H:D.87 MG.13: 2 residues within 4Å: Chain J: D.87 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.87 MG.15: 2 residues within 4Å: Chain K: D.87 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.87, K:D.87 MG.17: 2 residues within 4Å: Chain M: D.87 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.87 MG.19: 2 residues within 4Å: Chain N: D.87 Ligands: ATP.20 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.87, N:D.87 MG.21: 2 residues within 4Å: Chain P: D.87 Ligands: ATP.22 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain Q: D.87, S.151 Ligands: ATP.24 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:D.87, Q:D.87 MG.25: 2 residues within 4Å: Chain S: D.87 Ligands: ATP.26 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:D.87 MG.27: 3 residues within 4Å: Chain T: D.87, S.151 Ligands: ATP.28 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:D.87, T:D.87

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

ATP.2: 24 residues within 4Å: Chain A: T.30, L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, N.153, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.32, A:D.52, A:D.52, A:G.53, A:G.88, A:T.89, A:T.90, A:T.90, A:T.91, A:T.91, A:T.91, A:T.91, A:N.153, A:G.415, A:N.479, A:A.480, A:A.481, A:D.495 ATP.4: 24 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, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.30, B:G.32, B:K.51, B:G.53, B:G.88, B:G.88, B:T.89, 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 Salt bridges: B:K.51 ATP.6: 24 residues within 4Å: Chain D: T.30, L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, N.153, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.32, D:D.52, D:D.52, D:G.53, D:G.88, D:T.89, D:T.90, D:T.90, D:T.91, D:T.91, D:T.91, D:G.415, D:N.479, D:A.480, D:A.481, D:D.495 ATP.8: 25 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, I.493, D.495 Ligands: MG.7 19 PLIP interactions: 19 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:D.398, E:G.415, E:G.416, E:N.479, E:A.480, E:A.481, E:D.495 Salt bridges: E:K.51 ATP.10: 23 residues within 4Å: Chain G: T.30, L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.9 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:G.32, G:D.52, G:D.52, G:G.53, G:V.54, G:G.88, G:T.89, G:T.90, G:T.90, G:T.91, G:T.91, G:T.91, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495 ATP.12: 25 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, I.493, D.495 Ligands: MG.11 19 PLIP interactions: 19 interactions with chain H Hydrogen bonds: H:T.30, H:G.32, H:K.51, H:G.53, H:G.88, H:G.88, H:T.89, H:T.89, H:T.90, H:T.91, H:T.91, H:D.398, H:G.415, H:G.416, H:N.479, H:A.480, H:A.481, H:D.495 Salt bridges: H:K.51 ATP.14: 24 residues within 4Å: Chain J: T.30, L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, N.153, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.13 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:G.32, J:D.52, J:D.52, J:G.53, J:G.88, J:T.89, J:T.90, J:T.90, J:T.91, J:T.91, J:T.91, J:N.153, J:G.415, J:N.479, J:A.480, J:A.481, J:D.495 ATP.16: 25 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, I.493, D.495 Ligands: MG.15 18 PLIP interactions: 18 interactions with chain K Hydrogen bonds: 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:D.398, K:G.415, K:G.416, K:N.479, K:A.480, K:A.481, K:D.495 Salt bridges: K:K.51 ATP.18: 24 residues within 4Å: Chain M: T.30, L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, N.153, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.17 16 PLIP interactions: 16 interactions with chain M Hydrogen bonds: M:G.32, M:D.52, M:D.52, M:G.53, M:G.88, M:T.89, M:T.90, M:T.90, M:T.91, M:T.91, M:T.91, M:G.415, M:N.479, M:A.480, M:A.481, M:D.495 ATP.20: 25 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, I.493, D.495 Ligands: MG.19 17 PLIP interactions: 17 interactions with chain N Hydrogen bonds: N:G.32, N:K.51, N:G.53, N:G.88, N:G.88, N:T.89, N:T.89, N:T.90, N:T.91, N:T.91, N:G.415, N:G.416, N:N.479, N:A.480, N:A.481, N:D.495 Salt bridges: N:K.51 ATP.22: 23 residues within 4Å: Chain P: T.30, L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.21 16 PLIP interactions: 16 interactions with chain P Hydrogen bonds: P:G.32, P:D.52, P:D.52, P:G.53, P:G.88, P:T.89, P:T.90, P:T.90, P:T.91, P:T.91, P:T.91, P:G.415, P:N.479, P:A.480, P:A.481, P:D.495 ATP.24: 25 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, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.23 17 PLIP interactions: 17 interactions with chain Q Hydrogen bonds: Q:G.32, Q:K.51, Q:G.53, Q:G.88, Q:G.88, Q:T.89, Q:T.89, Q:T.90, Q:T.91, Q:T.91, Q:G.415, Q:G.416, Q:N.479, Q:A.480, Q:A.481, Q:D.495 Salt bridges: Q:K.51 ATP.26: 24 residues within 4Å: Chain S: T.30, L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, N.153, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.25 17 PLIP interactions: 17 interactions with chain S Hydrogen bonds: S:G.32, S:D.52, S:D.52, S:G.53, S:G.88, S:T.89, S:T.90, S:T.90, S:T.91, S:T.91, S:T.91, S:N.153, S:G.415, S:N.479, S:A.480, S:A.481, S:D.495 ATP.28: 24 residues within 4Å: Chain T: 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.27 18 PLIP interactions: 18 interactions with chain T Hydrogen bonds: T:T.30, T:G.32, T:K.51, T:G.53, T:G.88, T:G.88, T:T.89, T:T.89, T:T.90, T:T.91, T:T.91, T:G.415, T:G.416, T:N.479, T:A.480, T:A.481, T:D.495 Salt bridges: T: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: ABDEGHJKMNPQST
Co-chaperonin GroES: CFILORU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
I

D
A

E
B

G
E

H
F

J
H

K
J

M
L

N
M

P
O

Q
P

S
R

T
S

C
W

F
D

I
G

L
K

O
N

R
Q

U
T

Chaperonin GroEL

Co-chaperonin GroES

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