SMTL ID : 8g7l.1

ATP-bound mtHsp60 V72I

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

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

ATP.1: 25 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, I.495, D.497 Ligands: MG.2, K.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.33, A:D.53, A:G.54, A:G.89, A:G.89, A:T.90, A:T.91, A:T.91, A:T.92, A:T.92, A:G.417, A:D.481, A:A.482, A:M.483, 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 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.33, B:D.53, B:G.54, B:G.89, B:G.89, B:T.90, B:T.91, 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:G.33, C:D.53, C:G.54, C:G.89, C:G.89, C:T.90, C:T.91, C:T.91, C:T.92, C:T.92, C:G.417, C:D.481, C:A.482, C:M.483, 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 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.33, D:D.53, D:G.54, D:G.89, D:G.89, D:T.90, D:T.91, D:T.91, D:T.92, D:T.92, 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 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:G.33, E:D.53, E:G.54, E:G.89, E:G.89, E:T.90, E:T.91, 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: 25 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, I.495, 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:G.89, F:T.90, F:T.91, F:T.91, F:T.92, F:T.92, F:G.417, F:D.481, F:A.482, F:M.483, F:D.497 Salt bridges: F:K.52 ATP.19: 25 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, I.495, D.497 Ligands: MG.20, K.21 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:G.33, G:D.53, G:G.54, G:G.89, G:G.89, G:T.90, G:T.91, G:T.91, 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 ATP.22: 25 residues within 4Å: Chain H: 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.23, K.24 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:G.33, H:D.53, H:D.53, H:G.54, H:G.89, H:G.89, H:T.90, H:T.91, H:T.91, H:T.92, H:G.417, H:D.481, H:D.481, H:A.482, H:M.483, H:D.497 Salt bridges: H:K.52 ATP.25: 25 residues within 4Å: Chain I: 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.26, K.27 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:G.33, I:D.53, I:D.53, I:G.54, I:G.89, I:G.89, I:T.90, I:T.91, I:T.91, I:T.92, I:G.417, I:D.481, I:D.481, I:A.482, I:M.483, I:D.497 Salt bridges: I:K.52 ATP.28: 25 residues within 4Å: Chain J: 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.29, K.30 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:G.33, J:D.53, J:D.53, J:G.54, J:G.89, J:G.89, J:T.90, J:T.91, J:T.91, J:T.92, J:G.417, J:D.481, J:D.481, J:A.482, J:M.483, J:D.497 Salt bridges: J:K.52 ATP.31: 25 residues within 4Å: Chain K: 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.32, K.33 17 PLIP interactions: 17 interactions with chain K Hydrogen bonds: K:G.33, K:D.53, K:D.53, K:G.54, K:G.89, K:G.89, K:T.90, K:T.91, K:T.91, K:T.92, K:G.417, K:D.481, K:D.481, K:A.482, K:M.483, K:D.497 Salt bridges: K:K.52 ATP.34: 25 residues within 4Å: Chain L: 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.35, K.36 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:G.33, L:D.53, L:D.53, L:G.54, L:G.89, L:G.89, L:T.90, L:T.91, L:T.91, L:T.92, L:G.417, L:D.481, L:D.481, L:A.482, L:M.483, L:D.497 Salt bridges: L:K.52 ATP.37: 25 residues within 4Å: Chain M: 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.38, K.39 17 PLIP interactions: 17 interactions with chain M Hydrogen bonds: M:G.33, M:D.53, M:D.53, M:G.54, M:G.89, M:G.89, M:T.90, M:T.91, M:T.91, M:T.92, M:G.417, M:D.481, M:D.481, M:A.482, M:M.483, M:D.497 Salt bridges: M:K.52 ATP.40: 25 residues within 4Å: Chain N: 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.41, K.42 17 PLIP interactions: 17 interactions with chain N Hydrogen bonds: N:G.33, N:D.53, N:D.53, N:G.54, N:G.89, N:G.89, N:T.90, N:T.91, N:T.91, N:T.92, N:G.417, N:D.481, N:D.481, N:A.482, N:M.483, N:D.497 Salt bridges: N:K.52

14 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 1 PLIP interactions: 1 interactions with chain D Metal complexes: 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 1 PLIP interactions: 1 interactions with chain F Metal complexes: 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 MG.23: 2 residues within 4Å: Chain H: D.88 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.88 MG.26: 2 residues within 4Å: Chain I: D.88 Ligands: ATP.25 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.88 MG.29: 2 residues within 4Å: Chain J: D.88 Ligands: ATP.28 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.88 MG.32: 2 residues within 4Å: Chain K: D.88 Ligands: ATP.31 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.88 MG.35: 2 residues within 4Å: Chain L: D.88 Ligands: ATP.34 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.88 MG.38: 2 residues within 4Å: Chain M: D.88 Ligands: ATP.37 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.88 MG.41: 2 residues within 4Å: Chain N: D.88 Ligands: ATP.40 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.88

14 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.31, K.52, T.91 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.31, A:K.52 K.6: 4 residues within 4Å: Chain B: T.31, K.52, T.91 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.31, B:K.52 K.9: 4 residues within 4Å: Chain C: T.31, K.52, T.91 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.31, C:K.52 K.12: 4 residues within 4Å: Chain D: T.31, K.52, T.91 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.31, D:K.52 K.15: 4 residues within 4Å: Chain E: T.31, K.52, T.91 Ligands: ATP.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.31, E:K.52 K.18: 4 residues within 4Å: Chain F: T.31, K.52, T.91 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: 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 K.24: 4 residues within 4Å: Chain H: T.31, K.52, T.91 Ligands: ATP.22 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.31, H:K.52 K.27: 4 residues within 4Å: Chain I: T.31, K.52, T.91 Ligands: ATP.25 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.31, I:K.52 K.30: 4 residues within 4Å: Chain J: T.31, K.52, T.91 Ligands: ATP.28 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.31, J:K.52 K.33: 4 residues within 4Å: Chain K: T.31, K.52, T.91 Ligands: ATP.31 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:T.31, K:K.52 K.36: 4 residues within 4Å: Chain L: T.31, K.52, T.91 Ligands: ATP.34 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:T.31, L:K.52 K.39: 4 residues within 4Å: Chain M: T.31, K.52, T.91 Ligands: ATP.37 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:T.31, M:K.52 K.42: 4 residues within 4Å: Chain N: T.31, K.52, T.91 Ligands: ATP.40 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:T.31, N: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: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

C
F

D
E

E
D

F
C

G
B

H
K

I
J

J
I

K
H

L
N

M
M

N
L

60 kDa heat shock protein, mitochondrial

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