SMTL ID : 8g7m.1

ATP-bound mtHsp60 V72I focus

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: T.31, M.32, G.33, P.34, K.52, D.53, G.54, D.88, G.89, T.90, T.91, T.92, I.151, D.400, G.416, G.417, I.456, Y.480, D.481, A.482, M.483, D.497 Ligands: MG.2, K.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.33, A:D.53, A:G.54, A:G.89, A:T.90, A:T.91, A:T.92, A:T.92, A:T.92, A:G.417, A:D.481, A:A.482, A:D.497 Salt bridges: A:K.52 ATP.4: 25 residues within 4Å: Chain B: T.31, M.32, G.33, P.34, K.52, D.53, G.54, D.88, G.89, T.90, T.91, T.92, I.151, D.400, G.416, G.417, I.456, Y.480, D.481, A.482, M.483, I.495, D.497 Ligands: MG.5, K.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.31, B:G.33, B:D.53, B:G.54, B:G.89, B:T.90, B:T.91, B:T.92, B:T.92, B:G.417, B:D.481, B:A.482, B:M.483, B:D.497 Salt bridges: B:K.52 ATP.7: 25 residues within 4Å: Chain C: T.31, M.32, G.33, P.34, K.52, D.53, G.54, D.88, G.89, T.90, T.91, T.92, I.151, D.400, G.416, G.417, I.456, Y.480, D.481, A.482, M.483, I.495, D.497 Ligands: MG.8, K.9 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.31, C:G.33, C:D.53, C:G.54, C:G.89, C:T.90, C:T.91, C:T.92, C:T.92, C:T.92, C:D.400, C:G.417, C:D.481, C:A.482, C:D.497 Salt bridges: C:K.52 ATP.10: 25 residues within 4Å: Chain D: T.31, M.32, G.33, P.34, K.52, D.53, G.54, D.88, G.89, T.90, T.91, T.92, I.151, D.400, G.416, G.417, I.456, Y.480, D.481, A.482, M.483, I.495, D.497 Ligands: MG.11, K.12 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:T.31, D:G.33, D:D.53, D:G.54, D:G.89, D:T.90, D:T.91, D:T.92, D:T.92, D:T.92, D:D.400, D:G.417, D:D.481, D:A.482, D:M.483, D:D.497 Salt bridges: D:K.52 ATP.13: 25 residues within 4Å: Chain E: T.31, M.32, G.33, P.34, K.52, D.53, G.54, D.88, G.89, T.90, T.91, T.92, I.151, D.400, G.416, G.417, I.456, Y.480, D.481, A.482, M.483, I.495, D.497 Ligands: MG.14, K.15 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.33, E:D.53, E:G.54, E:G.89, E:T.90, E:T.91, E:T.92, E:T.92, E:G.417, E:D.481, E:A.482, E:M.483, E:D.497 Salt bridges: E:K.52 ATP.16: 24 residues within 4Å: Chain F: T.31, M.32, G.33, P.34, K.52, D.53, G.54, D.88, G.89, T.90, T.91, T.92, I.151, D.400, G.416, G.417, I.456, Y.480, D.481, A.482, M.483, D.497 Ligands: MG.17, K.18 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:G.33, F:D.53, F:G.54, F:G.89, F:T.90, F:T.91, F:T.92, F:T.92, F:T.92, F:D.400, F:G.417, F:D.481, F:A.482, F:M.483, F:D.497 Salt bridges: F:K.52 ATP.19: 24 residues within 4Å: Chain G: T.31, M.32, G.33, P.34, K.52, D.53, G.54, D.88, G.89, T.90, T.91, T.92, I.151, D.400, G.416, G.417, I.456, Y.480, D.481, A.482, M.483, D.497 Ligands: MG.20, K.21 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.33, G:D.53, G:G.54, G:G.89, G:T.90, G:T.91, G:T.92, G:T.92, G:T.92, G:G.417, G:D.481, G:A.482, G:M.483, G:D.497 Salt bridges: G:K.52

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.88 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.88 MG.5: 2 residues within 4Å: Chain B: D.88 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.88 MG.8: 2 residues within 4Å: Chain C: D.88 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.88 MG.11: 2 residues within 4Å: Chain D: D.88 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.88, D:D.88 MG.14: 2 residues within 4Å: Chain E: D.88 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.88 MG.17: 2 residues within 4Å: Chain F: D.88 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.88, F:D.88 MG.20: 2 residues within 4Å: Chain G: D.88 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.88

7 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.31, K.52, T.91 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.31, A:T.31, A:K.52 K.6: 4 residues within 4Å: Chain B: T.31, K.52, T.91 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.31, B:T.31, B:K.52 K.9: 4 residues within 4Å: Chain C: T.31, K.52, T.91 Ligands: ATP.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.31, C:T.31, C:K.52 K.12: 4 residues within 4Å: Chain D: T.31, K.52, T.91 Ligands: ATP.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.31, D:T.31, D:K.52 K.15: 4 residues within 4Å: Chain E: T.31, K.52, T.91 Ligands: ATP.13 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.31, E:T.31, E:K.52 K.18: 4 residues within 4Å: Chain F: T.31, K.52, T.91 Ligands: ATP.16 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.31, F:T.31, F:K.52 K.21: 4 residues within 4Å: Chain G: T.31, K.52, T.91 Ligands: ATP.19 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.31, G:K.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Braxton, J.R. et al., Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. Biorxiv (2023)

Release Date

2023-07-12

Peptides

60 kDa heat shock protein, mitochondrial: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

60 kDa heat shock protein, mitochondrial

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