SMTL ID : 8ble.1

Structure of GroEL-nucleotide complex in ADP-like conformation plunged 50 ms after mixing with ATP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: T.30, L.31, G.32, P.33, K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.32, A:K.51, A:D.52, A:D.52, A:G.53, A:V.54, 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:G.415, A:N.479, A:A.480, A:A.481, A:D.495 ATP.2: 21 residues within 4Å: Chain B: T.30, L.31, G.32, P.33, K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.32, B:K.51, B:D.52, B:D.52, B:D.52, B:G.53, B:G.88, B:T.89, B:T.90, B:T.90, B:T.91, B:T.91, B:T.91, B:T.91, B:G.415, B:N.479, B:A.480, B:A.481, B:D.495 ATP.3: 21 residues within 4Å: Chain C: T.30, L.31, G.32, P.33, K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:G.32, C:K.51, C:D.52, C:D.52, C:G.53, C:V.54, C:G.88, C:T.89, C:T.90, C:T.90, C:T.91, C:T.91, C:T.91, C:T.91, C:G.415, C:N.479, C:A.480, C:A.481, C:D.495 ATP.4: 20 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, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:G.32, D:K.51, D:D.52, D:D.52, D:D.52, D:G.53, D:V.54, D:G.88, D:T.89, D:T.90, D:T.90, D:T.91, 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.5: 20 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, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:G.32, E:K.51, E:D.52, E:D.52, E:D.52, E:G.53, E:V.54, E:G.88, E:T.89, E:T.90, E:T.90, E:T.91, E:T.91, E:T.91, E:T.91, E:G.415, E:N.479, E:A.480, E:A.481, E:D.495 ATP.6: 21 residues within 4Å: Chain F: T.30, L.31, G.32, P.33, K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:G.32, F:K.51, F:D.52, F:D.52, F:D.52, F:G.53, F:V.54, F:G.88, F:T.89, F:T.90, F:T.90, F:T.91, F:T.91, F:T.91, F:T.91, F:G.415, F:N.479, F:A.480, F:A.481, F:D.495 ATP.7: 20 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, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 19 PLIP interactions: 19 interactions with chain G Hydrogen bonds: G:G.32, G:K.51, 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:T.91, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495 ATP.8: 21 residues within 4Å: Chain H: T.30, L.31, G.32, P.33, K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:G.32, H:K.51, H:D.52, H:G.53, H:V.54, H:D.87, H:G.88, H:T.89, H:T.90, H:T.91, H:T.91, H:T.91, H:T.91, H:G.415, H:N.479, H:A.480, H:A.481, H:D.495 ATP.9: 20 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, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 19 PLIP interactions: 19 interactions with chain I Hydrogen bonds: I:G.32, I:K.51, I:D.52, I:D.52, I:G.53, I:D.87, I:G.88, I:T.89, I:T.90, I:T.90, I:T.91, I:T.91, I:T.91, I:T.91, I:G.415, I:N.479, I:A.480, I:A.481, I:D.495 ATP.10: 21 residues within 4Å: Chain J: T.30, L.31, G.32, P.33, K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 18 PLIP interactions: 18 interactions with chain J Hydrogen bonds: J:G.32, J:K.51, J:D.52, J:G.53, J:V.54, J:D.87, J:G.88, J:T.89, J:T.90, J:T.91, J:T.91, J:T.91, J:T.91, J:G.415, J:N.479, J:A.480, J:A.481, J:D.495 ATP.11: 20 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, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 20 PLIP interactions: 20 interactions with chain K Hydrogen bonds: K:G.32, K:K.51, K:D.52, K:G.53, K:V.54, K:D.87, K:G.88, K:T.89, K:T.89, K:T.90, K:T.90, K:T.91, K:T.91, K:T.91, K:T.91, K:G.415, K:N.479, K:A.480, K:A.481, K:D.495 ATP.12: 21 residues within 4Å: Chain L: T.30, L.31, G.32, P.33, K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 20 PLIP interactions: 20 interactions with chain L Hydrogen bonds: L:G.32, L:K.51, L:D.52, L:D.52, L:G.53, L:V.54, L:D.87, L:G.88, L:T.89, L:T.90, L:T.90, L:T.91, L:T.91, L:T.91, L:T.91, L:G.415, L:N.479, L:A.480, L:A.481, L:D.495 ATP.13: 21 residues within 4Å: Chain M: T.30, L.31, G.32, P.33, K.51, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 19 PLIP interactions: 19 interactions with chain M Hydrogen bonds: M:G.32, M:K.51, M:D.52, M:G.53, M:V.54, M:D.87, M:G.88, M:T.89, M:T.90, M:T.90, M:T.91, 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.14: 20 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, G.414, G.415, I.454, N.479, A.480, A.481, I.493, D.495 19 PLIP interactions: 19 interactions with chain N Hydrogen bonds: N:G.32, N:K.51, N:D.52, N:G.53, N:V.54, N:D.87, N:G.88, N:T.89, N:T.90, N:T.90, N:T.91, N:T.91, N:T.91, N:T.91, N:G.415, N:N.479, N:A.480, N:A.481, N:D.495

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
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Chaperonin GroEL

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