SMTL ID : 9es2.1

ATP-bound human mitochondrial Hsp60 double-ring complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

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

ATP.1: 26 residues within 4Å: Chain A: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.2, K.3 24 PLIP interactions: 24 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.90, A:T.91, A:T.91, A:D.399, A:G.416, A:G.417, A:D.480, A:A.481, A:M.482, A:D.496 Water bridges: A:K.51, A:K.51, A:K.51, A:T.91, A:T.91, A:D.496 Salt bridges: A:K.51 ATP.4: 26 residues within 4Å: Chain B: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.5, K.6 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.32, B:K.51, B:G.53, B:G.88, B:G.88, B:T.89, B:T.90, B:T.90, B:T.91, B:T.91, B:G.416, B:G.417, B:D.480, B:A.481, B:M.482, B:D.496 Water bridges: B:K.51, B:T.91, B:T.91, B:N.153, B:D.496 Salt bridges: B:K.51 ATP.7: 26 residues within 4Å: Chain C: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.8, K.9 27 PLIP interactions: 27 interactions with chain C Hydrogen bonds: C:G.32, C:K.51, C:G.53, C:G.88, C:G.88, C:T.89, C:T.90, C:T.90, C:T.91, C:T.91, C:G.416, C:G.417, C:D.480, C:D.480, C:A.481, C:M.482, C:D.496 Water bridges: C:K.51, C:K.51, C:K.51, C:K.51, C:K.51, C:T.91, C:T.91, C:N.153, C:D.496 Salt bridges: C:K.51 ATP.10: 26 residues within 4Å: Chain D: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.11, K.12 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:G.32, D:K.51, D:G.53, D:G.88, D:G.88, D:T.89, D:T.90, D:T.90, D:T.91, D:T.91, D:G.416, D:G.417, D:D.480, D:D.480, D:A.481, D:M.482, D:D.496 Water bridges: D:K.51, D:K.51, D:T.91, D:T.91, D:D.496 Salt bridges: D:K.51 ATP.13: 26 residues within 4Å: Chain E: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.14, K.15 26 PLIP interactions: 26 interactions with chain E Hydrogen bonds: 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.90, E:T.91, E:T.91, E:G.416, E:G.417, E:D.480, E:D.480, E:A.481, E:M.482, E:D.496 Water bridges: E:K.51, E:K.51, E:K.51, E:T.91, E:T.91, E:N.153, E:D.496 Salt bridges: E:K.51 ATP.16: 26 residues within 4Å: Chain F: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.17, K.18 25 PLIP interactions: 25 interactions with chain F Hydrogen bonds: F:G.32, F:K.51, F:G.53, F:G.88, F:G.88, F:T.89, F:T.90, F:T.90, F:T.91, F:T.91, F:G.416, F:G.417, F:D.480, F:D.480, F:A.481, F:M.482, F:D.496 Water bridges: F:K.51, F:K.51, F:K.51, F:T.91, F:T.91, F:N.153, F:D.496 Salt bridges: F:K.51 ATP.19: 26 residues within 4Å: Chain G: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.20, K.21 27 PLIP interactions: 27 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.90, G:T.91, G:T.91, G:G.416, G:G.417, G:D.480, G:D.480, G:A.481, G:M.482, G:D.496 Water bridges: G:K.51, G:K.51, G:K.51, G:K.51, G:K.51, G:T.91, G:T.91, G:N.153, G:D.496 Salt bridges: G:K.51 ATP.22: 26 residues within 4Å: Chain H: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.23, K.24 29 PLIP interactions: 29 interactions with chain H Hydrogen bonds: H:G.32, H:D.52, H:G.53, H:D.87, H:G.88, H:G.88, H:T.89, H:T.90, H:T.90, H:T.91, H:G.416, H:G.417, H:D.480, H:A.481, H:M.482, H:D.496 Water bridges: H:K.51, H:K.51, H:K.51, H:K.51, H:T.89, H:T.91, H:T.91, H:T.91, H:N.153, H:D.399, H:D.399, H:D.496 Salt bridges: H:K.51 ATP.25: 26 residues within 4Å: Chain I: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.26, K.27 26 PLIP interactions: 26 interactions with chain I Hydrogen bonds: I:G.32, I:K.51, I:G.53, I:D.87, I:G.88, I:G.88, I:T.89, I:T.90, I:T.90, I:T.91, I:G.416, I:G.417, I:D.480, I:A.481, I:M.482, I:D.496 Water bridges: I:K.51, I:T.89, I:T.91, I:T.91, I:T.91, I:D.399, I:D.399, I:D.399, I:D.496 Salt bridges: I:K.51 ATP.28: 26 residues within 4Å: Chain J: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.29, K.30 29 PLIP interactions: 29 interactions with chain J Hydrogen bonds: J:G.32, J:K.51, J:G.53, J:D.87, J:G.88, J:G.88, J:T.89, J:T.90, J:T.90, J:T.91, J:G.416, J:G.417, J:D.480, J:A.481, J:M.482, J:D.496 Water bridges: J:K.51, J:K.51, J:K.51, J:K.51, J:T.89, J:T.91, J:T.91, J:T.91, J:N.153, J:D.399, J:D.399, J:D.496 Salt bridges: J:K.51 ATP.31: 26 residues within 4Å: Chain K: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.32, K.33 25 PLIP interactions: 25 interactions with chain K Hydrogen bonds: K:G.32, K:D.52, K:G.53, K:D.87, K:G.88, K:G.88, K:T.89, K:T.90, K:T.90, K:T.91, K:G.416, K:G.417, K:D.480, K:A.481, K:M.482, K:D.496 Water bridges: K:K.51, K:T.89, K:T.91, K:T.91, K:T.91, K:T.91, K:D.399, K:D.399 Salt bridges: K:K.51 ATP.34: 26 residues within 4Å: Chain L: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.35, K.36 27 PLIP interactions: 27 interactions with chain L Hydrogen bonds: L:G.32, L:K.51, L:G.53, L:D.87, L:G.88, L:G.88, L:T.89, L:T.90, L:T.90, L:T.91, L:G.416, L:G.417, L:D.480, L:A.481, L:M.482, L:D.496 Water bridges: L:K.51, L:K.51, L:T.89, L:T.91, L:T.91, L:T.91, L:N.153, L:D.399, L:D.399, L:D.496 Salt bridges: L:K.51 ATP.37: 26 residues within 4Å: Chain M: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.38, K.39 27 PLIP interactions: 27 interactions with chain M Hydrogen bonds: M:G.32, M:K.51, M:G.53, M:D.87, M:G.88, M:G.88, M:T.89, M:T.90, M:T.90, M:T.91, M:G.416, M:G.417, M:D.480, M:A.481, M:M.482, M:D.496 Water bridges: M:K.51, M:K.51, M:T.89, M:T.91, M:T.91, M:T.91, M:N.153, M:D.399, M:D.399, M:D.496 Salt bridges: M:K.51 ATP.40: 26 residues within 4Å: Chain N: T.30, M.31, G.32, P.33, K.51, D.52, G.53, D.87, G.88, T.89, T.90, T.91, I.150, D.399, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.41, K.42 28 PLIP interactions: 28 interactions with chain N Hydrogen bonds: N:G.32, N:K.51, N:G.53, N:D.87, N:G.88, N:G.88, N:T.89, N:T.90, N:T.90, N:T.91, N:G.416, N:G.417, N:D.480, N:D.480, N:A.481, N:M.482, N:D.496 Water bridges: N:K.51, N:K.51, N:T.89, N:T.91, N:T.91, N:T.91, N:N.153, N:D.399, N:D.399, N:D.496 Salt bridges: N:K.51

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.87, G.88 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.87, H2O.1, H2O.3 MG.5: 4 residues within 4Å: Chain B: D.87, S.151, D.399 Ligands: ATP.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.87, H2O.8, H2O.10 MG.8: 3 residues within 4Å: Chain C: D.87, D.399 Ligands: ATP.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.87, H2O.16, H2O.17 MG.11: 3 residues within 4Å: Chain D: D.87, D.399 Ligands: ATP.10 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.87, H2O.23, H2O.25 MG.14: 4 residues within 4Å: Chain E: D.87, S.151, D.399 Ligands: ATP.13 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.87, H2O.31, H2O.33 MG.17: 4 residues within 4Å: Chain F: D.87, S.151, D.399 Ligands: ATP.16 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.87, H2O.38, H2O.40 MG.20: 3 residues within 4Å: Chain G: D.87, D.399 Ligands: ATP.19 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.87, H2O.46, H2O.48 MG.23: 4 residues within 4Å: Chain H: D.87, S.151, D.399 Ligands: ATP.22 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.87, H2O.53, H2O.55 MG.26: 4 residues within 4Å: Chain I: D.87, S.151, D.399 Ligands: ATP.25 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.87, H2O.61, H2O.62 MG.29: 3 residues within 4Å: Chain J: D.87, D.399 Ligands: ATP.28 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.87, H2O.68, H2O.70 MG.32: 3 residues within 4Å: Chain K: D.87, D.399 Ligands: ATP.31 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:D.87, H2O.76, H2O.77 MG.35: 4 residues within 4Å: Chain L: D.87, S.151, D.399 Ligands: ATP.34 3 PLIP interactions: 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:D.87, H2O.83, H2O.85 MG.38: 3 residues within 4Å: Chain M: D.87, D.399 Ligands: ATP.37 3 PLIP interactions: 1 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:D.87, H2O.91, H2O.92 MG.41: 3 residues within 4Å: Chain N: D.87, D.399 Ligands: ATP.40 3 PLIP interactions: 1 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:D.87, H2O.98, H2O.100

14 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.30, K.51, T.90 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.30, A:K.51, A:T.90 K.6: 4 residues within 4Å: Chain B: T.30, K.51, T.90 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.30, B:K.51, B:T.90 K.9: 4 residues within 4Å: Chain C: T.30, K.51, T.90 Ligands: ATP.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.30, C:K.51, C:T.90 K.12: 4 residues within 4Å: Chain D: T.30, K.51, T.90 Ligands: ATP.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.30, D:K.51, D:T.90 K.15: 4 residues within 4Å: Chain E: T.30, K.51, T.90 Ligands: ATP.13 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.30, E:K.51, E:T.90 K.18: 5 residues within 4Å: Chain F: T.30, K.51, G.53, T.90 Ligands: ATP.16 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.30, F:K.51, F:T.90 K.21: 4 residues within 4Å: Chain G: T.30, K.51, T.90 Ligands: ATP.19 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.30, G:K.51, G:T.90 K.24: 4 residues within 4Å: Chain H: T.30, K.51, T.90 Ligands: ATP.22 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:T.30, H:K.51, H:T.90 K.27: 4 residues within 4Å: Chain I: T.30, K.51, T.90 Ligands: ATP.25 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:T.30, I:K.51, I:T.90 K.30: 4 residues within 4Å: Chain J: T.30, K.51, T.90 Ligands: ATP.28 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:T.30, J:K.51, J:T.90 K.33: 4 residues within 4Å: Chain K: T.30, K.51, T.90 Ligands: ATP.31 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:T.30, K:K.51, K:T.90 K.36: 4 residues within 4Å: Chain L: T.30, K.51, T.90 Ligands: ATP.34 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:T.30, L:K.51, L:T.90 K.39: 4 residues within 4Å: Chain M: T.30, K.51, T.90 Ligands: ATP.37 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:T.30, M:K.51, M:T.90 K.42: 5 residues within 4Å: Chain N: T.30, K.51, G.53, T.90 Ligands: ATP.40 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:T.30, N:K.51, N:T.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tascon, I. et al., Structural basis for ATP-triggered assembly of human mitochondrial Hsp60-Hsp10 chaperonin. To Be Published

Release Date

2025-04-09

Peptides

60 kDa heat shock protein, mitochondrial: 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

60 kDa heat shock protein, mitochondrial

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