SMTL ID : 8p4p.1

Structure average of GroEL14 complexes found in the cytosol of Escherichia coli overexpressing GroEL obtained by cryo electron tomography

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: L.30, G.31, K.50, D.51, G.52, G.85, D.86, G.87, T.88, T.89, T.90, I.149, D.397, A.480, I.492, D.494 Ligands: MG.2, K.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.51, A:D.51, A:G.52, A:G.87, A:T.88, A:T.89, A:T.90, A:T.90, A:T.90, A:L.493 Salt bridges: A:K.50, A:K.50 ATP.4: 16 residues within 4Å: Chain B: L.30, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, D.397, A.480, I.492, D.494 Ligands: MG.5, K.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.51, B:D.51, B:G.52, B:G.87, B:T.88, B:T.89, B:T.90, B:T.90, B:L.493 Salt bridges: B:K.50, B:K.50 ATP.7: 17 residues within 4Å: Chain C: L.30, G.31, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, D.397, A.480, I.492, D.494 Ligands: MG.8, K.9 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.51, C:D.51, C:G.52, C:G.87, C:T.88, C:T.89, C:T.90, C:T.90, C:L.493 Salt bridges: C:K.50, C:K.50 ATP.10: 17 residues within 4Å: Chain D: L.30, G.31, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, D.397, A.480, I.492, D.494 Ligands: MG.11, K.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:D.51, D:D.51, D:G.52, D:G.87, D:T.88, D:T.89, D:T.90, D:T.90, D:L.493 Salt bridges: D:K.50, D:K.50 ATP.13: 18 residues within 4Å: Chain E: L.30, G.31, P.32, K.50, D.51, G.52, G.85, D.86, G.87, T.88, T.89, T.90, I.149, D.397, A.480, D.494 Ligands: MG.14, K.15 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:D.51, E:D.51, E:G.52, E:G.87, E:T.88, E:T.89, E:T.89, E:T.90, E:T.90, E:A.480, E:L.493 Salt bridges: E:K.50, E:K.50 ATP.16: 16 residues within 4Å: Chain F: L.30, G.31, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, D.397, A.480, D.494 Ligands: MG.17, K.18 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:D.51, F:D.51, F:G.52, F:G.87, F:T.88, F:T.89, F:T.90, F:T.90, F:L.493 Salt bridges: F:K.50, F:K.50 ATP.19: 17 residues within 4Å: Chain G: L.30, G.31, K.50, D.51, G.52, G.85, D.86, G.87, T.88, T.89, T.90, I.149, D.397, A.480, D.494 Ligands: MG.20, K.21 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:D.51, G:D.51, G:G.52, G:G.87, G:T.88, G:T.89, G:T.90, G:T.90, G:T.90, G:L.493 Salt bridges: G:K.50, G:K.50

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.51, D.86, G.87, D.397 Ligands: ATP.1, K.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.86 MG.5: 6 residues within 4Å: Chain B: D.51, D.86, G.87, D.397 Ligands: ATP.4, K.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.86 MG.8: 6 residues within 4Å: Chain C: D.51, D.86, G.87, D.397 Ligands: ATP.7, K.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.86 MG.11: 6 residues within 4Å: Chain D: D.51, D.86, G.87, D.397 Ligands: ATP.10, K.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86 MG.14: 6 residues within 4Å: Chain E: D.51, D.86, G.87, D.397 Ligands: ATP.13, K.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.86 MG.17: 6 residues within 4Å: Chain F: D.51, D.86, G.87, D.397 Ligands: ATP.16, K.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.86 MG.20: 6 residues within 4Å: Chain G: D.51, D.86, G.87, D.397 Ligands: ATP.19, K.21 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86 MG.23: 2 residues within 4Å: Chain H: D.86 Ligands: ADP.22 5 PLIP interactions: 2 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.86, H:D.86, H2O.1, H2O.1, H2O.1 MG.26: 2 residues within 4Å: Chain I: D.86 Ligands: ADP.25 5 PLIP interactions: 2 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:D.86, I:D.86, H2O.1, H2O.1, H2O.1 MG.29: 2 residues within 4Å: Chain J: D.86 Ligands: ADP.28 5 PLIP interactions: 2 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:D.86, J:D.86, H2O.1, H2O.1, H2O.1 MG.32: 2 residues within 4Å: Chain K: D.86 Ligands: ADP.31 5 PLIP interactions: 2 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:D.86, K:D.86, H2O.2, H2O.2, H2O.2 MG.35: 2 residues within 4Å: Chain L: D.86 Ligands: ADP.34 5 PLIP interactions: 2 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:D.86, L:D.86, H2O.2, H2O.2, H2O.2 MG.38: 2 residues within 4Å: Chain M: D.86 Ligands: ADP.37 5 PLIP interactions: 2 interactions with chain M, 3 Ligand-Water interactions Metal complexes: M:D.86, M:D.86, H2O.2, H2O.2, H2O.3 MG.41: 2 residues within 4Å: Chain N: D.86 Ligands: ADP.40 5 PLIP interactions: 2 interactions with chain N, 3 Ligand-Water interactions Metal complexes: N:D.86, N:D.86, H2O.3, H2O.3, H2O.3

14 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: T.29, K.50, D.51, T.89 Ligands: ATP.1, MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.29, A:T.89 K.6: 6 residues within 4Å: Chain B: T.29, K.50, D.51, T.89 Ligands: ATP.4, MG.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.29, B:T.89 K.9: 6 residues within 4Å: Chain C: T.29, K.50, D.51, T.89 Ligands: ATP.7, MG.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.29, C:T.89 K.12: 6 residues within 4Å: Chain D: T.29, K.50, D.51, T.89 Ligands: ATP.10, MG.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.29, D:T.89 K.15: 6 residues within 4Å: Chain E: T.29, K.50, D.51, T.89 Ligands: ATP.13, MG.14 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.29, E:K.50, E:T.89 K.18: 6 residues within 4Å: Chain F: T.29, K.50, D.51, T.89 Ligands: ATP.16, MG.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.29, F:T.89 K.21: 6 residues within 4Å: Chain G: T.29, K.50, D.51, T.89 Ligands: ATP.19, MG.20 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.29, G:T.89 K.24: 3 residues within 4Å: Chain H: G.31, N.152 Ligands: ADP.22 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:G.31 K.27: 4 residues within 4Å: Chain I: G.31, K.50, N.152 Ligands: ADP.25 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:G.31 K.30: 3 residues within 4Å: Chain J: G.31, N.152 Ligands: ADP.28 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:G.31 K.33: 4 residues within 4Å: Chain K: G.31, K.50, N.152 Ligands: ADP.31 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:G.31 K.36: 4 residues within 4Å: Chain L: G.31, K.50, N.152 Ligands: ADP.34 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:G.31 K.39: 4 residues within 4Å: Chain M: G.31, K.50, N.152 Ligands: ADP.37 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:G.31 K.42: 3 residues within 4Å: Chain N: G.31, N.152 Ligands: ADP.40 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:G.31

7 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.22: 21 residues within 4Å: Chain H: T.29, L.30, G.31, P.32, K.50, D.51, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, N.478, A.479, A.480, I.492, D.494 Ligands: MG.23, K.24 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:G.31, H:D.86, H:G.87, H:T.88, H:T.89, H:T.89, H:T.90, H:T.90, H:N.478, H:N.478, H:A.479, H:A.480, H:D.494 Water bridges: H:G.52, H:G.52, H:N.152 ADP.25: 21 residues within 4Å: Chain I: T.29, L.30, G.31, P.32, K.50, D.51, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, N.478, A.479, A.480, I.492, D.494 Ligands: MG.26, K.27 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:G.31, I:D.86, I:G.87, I:T.89, I:T.89, I:T.90, I:T.90, I:N.478, I:N.478, I:A.479, I:A.480, I:D.494 Water bridges: I:G.52, I:G.52 ADP.28: 21 residues within 4Å: Chain J: T.29, L.30, G.31, P.32, K.50, D.51, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, N.478, A.479, A.480, I.492, D.494 Ligands: MG.29, K.30 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:G.31, J:D.86, J:G.87, J:T.88, J:T.89, J:T.89, J:T.90, J:T.90, J:N.478, J:N.478, J:A.479, J:A.480, J:D.494 Water bridges: J:G.52, J:G.52 ADP.31: 21 residues within 4Å: Chain K: T.29, L.30, G.31, P.32, K.50, D.51, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, N.478, A.479, A.480, I.492, D.494 Ligands: MG.32, K.33 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.31, K:D.86, K:G.87, K:T.88, K:T.89, K:T.89, K:T.90, K:T.90, K:N.478, K:N.478, K:A.479, K:A.480, K:D.494 Water bridges: K:G.52, K:G.52 ADP.34: 21 residues within 4Å: Chain L: T.29, L.30, G.31, P.32, K.50, D.51, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, N.478, A.479, A.480, I.492, D.494 Ligands: MG.35, K.36 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:G.31, L:D.86, L:G.87, L:T.88, L:T.89, L:T.89, L:T.90, L:T.90, L:N.478, L:N.478, L:A.479, L:A.480, L:D.494 Water bridges: L:G.52, L:G.52 ADP.37: 21 residues within 4Å: Chain M: T.29, L.30, G.31, P.32, K.50, D.51, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, N.478, A.479, A.480, I.492, D.494 Ligands: MG.38, K.39 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:G.31, M:D.86, M:G.87, M:T.89, M:T.89, M:T.90, M:T.90, M:N.478, M:N.478, M:A.479, M:A.480, M:D.494 Water bridges: M:G.52, M:G.52 ADP.40: 21 residues within 4Å: Chain N: T.29, L.30, G.31, P.32, K.50, D.51, D.86, G.87, T.88, T.89, T.90, I.149, N.152, G.414, N.478, A.479, A.480, I.492, D.494 Ligands: MG.41, K.42 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:G.31, N:D.86, N:G.87, N:T.88, N:T.89, N:T.89, N:T.90, N:T.90, N:N.478, N:N.478, N:A.479, N:A.480, N:D.494 Water bridges: N:G.52, N:G.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, J. et al., Visualizing chaperonin function in situ by cryo-electron tomography. Nature (2024)

Release Date

2024-07-03

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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