SMTL ID : 9es6.1

ADP:BeF3-bound human mitochondrial Hsp60 double-ring complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

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

ADP.1: 24 residues within 4Å: Chain A: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.2, MG.3, K.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.32, A:D.87, A:G.88, A:G.88, A:T.89, A:T.90, A:T.90, A:T.91, A:T.91, A:G.416, A:G.417, A:D.480, A:D.480, A:A.481, A:M.482, A:D.496 Water bridges: A:D.87, A:T.91, A:D.496, A:D.496 Salt bridges: A:K.51 ADP.5: 24 residues within 4Å: Chain B: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.6, MG.7, K.8 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.32, B:D.87, 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:D.480, B:A.481, B:M.482, B:D.496 Water bridges: B:D.87, B:T.91, B:D.496, B:D.496 Salt bridges: B:K.51 ADP.9: 24 residues within 4Å: Chain C: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.10, MG.11, K.12 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:G.32, C:D.87, 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:T.91, C:D.496, C:D.496 Salt bridges: C:K.51 ADP.13: 24 residues within 4Å: Chain D: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.14, MG.15, K.16 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:G.32, D:D.87, 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:D.496 Water bridges: D:T.91, D:D.496, D:D.496 Salt bridges: D:K.51 ADP.17: 24 residues within 4Å: Chain E: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.18, MG.19, K.20 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:G.32, E:D.87, E:G.88, E:G.88, 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:T.91, E:D.496, E:D.496 Salt bridges: E:K.51 ADP.21: 24 residues within 4Å: Chain F: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.22, MG.23, K.24 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:G.32, F:D.87, F:G.88, F:G.88, F:T.89, F:T.90, F:T.90, 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:D.87, F:T.91, F:D.496, F:D.496 Salt bridges: F:K.51 ADP.25: 24 residues within 4Å: Chain G: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.26, MG.27, K.28 21 PLIP interactions: 21 interactions with chain G Hydrogen bonds: G:G.32, G:D.87, 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:D.87, G:T.91, G:D.496, G:D.496 Salt bridges: G:K.51 ADP.29: 24 residues within 4Å: Chain H: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.30, MG.31, K.32 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:G.32, H:D.87, H:G.88, H:G.88, H:T.89, 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:T.91, H:D.496, H:D.496 Salt bridges: H:K.51 ADP.33: 24 residues within 4Å: Chain I: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.34, MG.35, K.36 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:G.32, I:D.87, I:G.88, I:G.88, I:T.89, 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:T.91, I:D.496, I:D.496 Salt bridges: I:K.51 ADP.37: 24 residues within 4Å: Chain J: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.38, MG.39, K.40 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:G.32, J:D.87, J:G.88, J:G.88, J:T.89, 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:T.91, J:D.496, J:D.496 Salt bridges: J:K.51 ADP.41: 24 residues within 4Å: Chain K: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.42, MG.43, K.44 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:G.32, K:D.87, K:G.88, K:G.88, K:T.89, K:T.90, K:T.91, K:G.416, K:G.417, K:D.480, K:A.481, K:D.496 Water bridges: K:T.91, K:D.496, K:D.496 Salt bridges: K:K.51 ADP.45: 24 residues within 4Å: Chain L: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.46, MG.47, K.48 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:G.32, L:D.87, L:G.88, L:G.88, L:T.89, 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:T.91, L:D.496, L:D.496 Salt bridges: L:K.51 ADP.49: 24 residues within 4Å: Chain M: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.50, MG.51, K.52 18 PLIP interactions: 18 interactions with chain M Hydrogen bonds: M:G.32, M:D.87, M:G.88, M:G.88, M:T.89, M:T.90, M:T.91, M:T.91, M:G.416, M:G.417, M:D.480, M:A.481, M:M.482, M:D.496 Water bridges: M:T.91, M:D.496, M:D.496 Salt bridges: M:K.51 ADP.53: 24 residues within 4Å: Chain N: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, G.417, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.54, MG.55, K.56 17 PLIP interactions: 17 interactions with chain N Hydrogen bonds: N:G.32, N:D.87, N:G.88, N:G.88, N:T.89, N:T.90, N:T.91, N:G.416, N:G.417, N:D.480, N:A.481, N:M.482, N:D.496 Water bridges: N:T.91, N:D.496, N:D.496 Salt bridges: N:K.51

14 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 11 residues within 4Å: Chain A: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.1, MG.3, K.4 No protein-ligand interaction detected (PLIP) BEF.6: 11 residues within 4Å: Chain B: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.5, MG.7, K.8 No protein-ligand interaction detected (PLIP) BEF.10: 11 residues within 4Å: Chain C: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.9, MG.11, K.12 No protein-ligand interaction detected (PLIP) BEF.14: 11 residues within 4Å: Chain D: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.13, MG.15, K.16 No protein-ligand interaction detected (PLIP) BEF.18: 11 residues within 4Å: Chain E: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.17, MG.19, K.20 No protein-ligand interaction detected (PLIP) BEF.22: 11 residues within 4Å: Chain F: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.21, MG.23, K.24 No protein-ligand interaction detected (PLIP) BEF.26: 10 residues within 4Å: Chain G: K.51, D.52, G.53, D.87, T.89, T.90, D.399 Ligands: ADP.25, MG.27, K.28 No protein-ligand interaction detected (PLIP) BEF.30: 11 residues within 4Å: Chain H: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.29, MG.31, K.32 No protein-ligand interaction detected (PLIP) BEF.34: 11 residues within 4Å: Chain I: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.33, MG.35, K.36 No protein-ligand interaction detected (PLIP) BEF.38: 11 residues within 4Å: Chain J: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.37, MG.39, K.40 No protein-ligand interaction detected (PLIP) BEF.42: 11 residues within 4Å: Chain K: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.41, MG.43, K.44 No protein-ligand interaction detected (PLIP) BEF.46: 11 residues within 4Å: Chain L: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.45, MG.47, K.48 No protein-ligand interaction detected (PLIP) BEF.50: 11 residues within 4Å: Chain M: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.49, MG.51, K.52 No protein-ligand interaction detected (PLIP) BEF.54: 11 residues within 4Å: Chain N: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.399 Ligands: ADP.53, MG.55, K.56 No protein-ligand interaction detected (PLIP)

14 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.87, S.151 Ligands: ADP.1, BEF.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:D.87 MG.7: 4 residues within 4Å: Chain B: D.87, S.151 Ligands: ADP.5, BEF.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.87, B:D.87 MG.11: 4 residues within 4Å: Chain C: D.87, S.151 Ligands: ADP.9, BEF.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.87, C:D.87 MG.15: 5 residues within 4Å: Chain D: D.87, S.151, D.399 Ligands: ADP.13, BEF.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.87, D:D.87 MG.19: 3 residues within 4Å: Chain E: D.87 Ligands: ADP.17, BEF.18 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.87, E:D.87 MG.23: 4 residues within 4Å: Chain F: D.87, S.151 Ligands: ADP.21, BEF.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.87, F:D.87 MG.27: 3 residues within 4Å: Chain G: D.87 Ligands: ADP.25, BEF.26 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.87, G:D.87 MG.31: 4 residues within 4Å: Chain H: D.87, S.151 Ligands: ADP.29, BEF.30 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.87, H:D.87 MG.35: 4 residues within 4Å: Chain I: D.87, S.151 Ligands: ADP.33, BEF.34 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.87, I:D.87 MG.39: 4 residues within 4Å: Chain J: D.87, S.151 Ligands: ADP.37, BEF.38 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.87, J:D.87 MG.43: 5 residues within 4Å: Chain K: D.87, S.151, D.399 Ligands: ADP.41, BEF.42 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.87, K:D.87 MG.47: 3 residues within 4Å: Chain L: D.87 Ligands: ADP.45, BEF.46 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.87, L:D.87 MG.51: 4 residues within 4Å: Chain M: D.87, S.151 Ligands: ADP.49, BEF.50 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.87, M:D.87 MG.55: 3 residues within 4Å: Chain N: D.87 Ligands: ADP.53, BEF.54 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.87, N:D.87

14 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: T.30, K.51, T.90 Ligands: ADP.1, BEF.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.30, A:K.51, A:T.90 K.8: 5 residues within 4Å: Chain B: T.30, K.51, T.90 Ligands: ADP.5, BEF.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.30, B:K.51, B:T.90 K.12: 6 residues within 4Å: Chain C: T.30, K.51, G.53, T.90 Ligands: ADP.9, BEF.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.30, C:K.51, C:T.90 K.16: 6 residues within 4Å: Chain D: T.30, K.51, G.53, T.90 Ligands: ADP.13, BEF.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.30, D:K.51, D:T.90 K.20: 5 residues within 4Å: Chain E: T.30, K.51, T.90 Ligands: ADP.17, BEF.18 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.30, E:K.51, E:T.90 K.24: 6 residues within 4Å: Chain F: T.30, K.51, G.53, T.90 Ligands: ADP.21, BEF.22 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.30, F:K.51, F:T.90 K.28: 5 residues within 4Å: Chain G: T.30, K.51, T.90 Ligands: ADP.25, BEF.26 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.30, G:K.51, G:T.90 K.32: 5 residues within 4Å: Chain H: T.30, K.51, T.90 Ligands: ADP.29, BEF.30 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:T.30, H:K.51, H:T.90 K.36: 5 residues within 4Å: Chain I: T.30, K.51, T.90 Ligands: ADP.33, BEF.34 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:T.30, I:K.51, I:T.90 K.40: 6 residues within 4Å: Chain J: T.30, K.51, G.53, T.90 Ligands: ADP.37, BEF.38 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:T.30, J:K.51, J:T.90 K.44: 6 residues within 4Å: Chain K: T.30, K.51, G.53, T.90 Ligands: ADP.41, BEF.42 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:T.30, K:K.51, K:T.90 K.48: 5 residues within 4Å: Chain L: T.30, K.51, T.90 Ligands: ADP.45, BEF.46 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:T.30, L:K.51, L:T.90 K.52: 6 residues within 4Å: Chain M: T.30, K.51, G.53, T.90 Ligands: ADP.49, BEF.50 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:T.30, M:K.51, M:T.90 K.56: 5 residues within 4Å: Chain N: T.30, K.51, T.90 Ligands: ADP.53, BEF.54 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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