SMTL ID : 6mrc.1

ADP-bound human mitochondrial Hsp60-Hsp10 football complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-14-mer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.32, A:D.87, A:G.88, A:T.89, A:T.89, A:T.90, A:G.416, A:D.480, A:D.480, A:A.481, A:D.496 Salt bridges: A:K.51 ADP.3: 21 residues within 4Å: Chain P: 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, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain P Hydrogen bonds: P:G.32, P:D.87, P:G.88, P:T.89, P:T.89, P:T.90, P:G.416, P:D.480, P:D.480, P:A.481, P:D.496 Water bridges: P:G.417 Salt bridges: P:K.51 ADP.5: 20 residues within 4Å: Chain Q: M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain Q Hydrogen bonds: Q:G.32, Q:D.87, Q:G.88, Q:T.89, Q:T.89, Q:T.90, Q:G.416, Q:D.480, Q:D.480, Q:A.481, Q:D.496 Water bridges: Q:G.417 Salt bridges: Q:K.51 ADP.7: 21 residues within 4Å: Chain R: 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, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain R Hydrogen bonds: R:G.32, R:D.87, R:G.88, R:T.89, R:T.89, R:T.90, R:G.416, R:D.480, R:D.480, R:A.481, R:D.496 Salt bridges: R:K.51 ADP.9: 20 residues within 4Å: Chain S: M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain S Hydrogen bonds: S:G.32, S:D.87, S:G.88, S:T.89, S:T.89, S:T.90, S:G.416, S:D.480, S:D.480, S:A.481, S:D.496 Salt bridges: S:K.51 ADP.11: 20 residues within 4Å: Chain T: M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.12 12 PLIP interactions: 12 interactions with chain T Hydrogen bonds: T:G.32, T:D.87, T:G.88, T:T.89, T:T.89, T:T.90, T:G.416, T:D.480, T:D.480, T:A.481, T:D.496 Salt bridges: T:K.51 ADP.13: 21 residues within 4Å: Chain U: 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, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain U Hydrogen bonds: U:G.32, U:D.87, U:G.88, U:T.89, U:T.89, U:T.90, U:G.416, U:D.480, U:D.480, U:A.481, U:D.496 Salt bridges: U:K.51 ADP.15: 21 residues within 4Å: Chain V: 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, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain V Hydrogen bonds: V:T.30, V:G.32, V:D.87, V:D.87, V:G.88, V:T.89, V:T.90, V:G.416, V:D.480, V:A.481, V:D.496 Water bridges: V:G.417 Salt bridges: V:K.51 ADP.17: 21 residues within 4Å: Chain W: 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, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.18 11 PLIP interactions: 11 interactions with chain W Hydrogen bonds: W:T.30, W:G.32, W:D.87, W:G.88, W:T.89, W:T.90, W:G.416, W:D.480, W:A.481, W:D.496 Salt bridges: W:K.51 ADP.19: 21 residues within 4Å: Chain X: 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, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.20 12 PLIP interactions: 12 interactions with chain X Hydrogen bonds: X:T.30, X:G.32, X:D.87, X:D.87, X:G.88, X:T.89, X:T.90, X:G.416, X:D.480, X:A.481, X:D.496 Salt bridges: X:K.51 ADP.21: 21 residues within 4Å: Chain Y: 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, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.22 11 PLIP interactions: 11 interactions with chain Y Hydrogen bonds: Y:T.30, Y:G.32, Y:D.87, Y:G.88, Y:T.89, Y:T.90, Y:G.416, Y:D.480, Y:A.481, Y:D.496 Salt bridges: Y:K.51 ADP.23: 20 residues within 4Å: Chain Z: M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.24 10 PLIP interactions: 10 interactions with chain Z Hydrogen bonds: Z:G.32, Z:D.87, Z:G.88, Z:T.89, Z:T.90, Z:G.416, Z:D.480, Z:A.481, Z:D.496 Salt bridges: Z:K.51 ADP.25: 20 residues within 4Å: Chain 0: M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.26 10 PLIP interactions: 10 interactions with chain 0 Hydrogen bonds: 0:G.32, 0:D.87, 0:G.88, 0:T.89, 0:T.90, 0:G.416, 0:D.480, 0:A.481, 0:D.496 Salt bridges: 0:K.51 ADP.27: 20 residues within 4Å: Chain 1: M.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.415, G.416, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: MG.28 10 PLIP interactions: 10 interactions with chain 1 Hydrogen bonds: 1:G.32, 1:D.87, 1:G.88, 1:T.89, 1:T.90, 1:G.416, 1:D.480, 1:A.481, 1:D.496 Salt bridges: 1:K.51

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.87, S.151 Ligands: ADP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, A:D.87, H2O.1 MG.4: 3 residues within 4Å: Chain P: D.87, S.151 Ligands: ADP.3 3 PLIP interactions: 2 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:D.87, P:D.87, H2O.1 MG.6: 3 residues within 4Å: Chain Q: D.87, S.151 Ligands: ADP.5 3 PLIP interactions: 2 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:D.87, Q:D.87, H2O.1 MG.8: 3 residues within 4Å: Chain R: D.87, S.151 Ligands: ADP.7 3 PLIP interactions: 2 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:D.87, R:D.87, H2O.1 MG.10: 3 residues within 4Å: Chain S: D.87, S.151 Ligands: ADP.9 3 PLIP interactions: 2 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:D.87, S:D.87, H2O.2 MG.12: 3 residues within 4Å: Chain T: D.87, S.151 Ligands: ADP.11 4 PLIP interactions: 2 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:D.87, T:D.87, H2O.2, H2O.2 MG.14: 3 residues within 4Å: Chain U: D.87, S.151 Ligands: ADP.13 3 PLIP interactions: 2 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:D.87, U:D.87, H2O.2 MG.16: 3 residues within 4Å: Chain V: D.87, S.151 Ligands: ADP.15 3 PLIP interactions: 2 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:D.87, V:D.87, H2O.2 MG.18: 3 residues within 4Å: Chain W: D.87, S.151 Ligands: ADP.17 3 PLIP interactions: 2 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:D.87, W:D.87, H2O.3 MG.20: 3 residues within 4Å: Chain X: D.87, S.151 Ligands: ADP.19 3 PLIP interactions: 2 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:D.87, X:D.87, H2O.3 MG.22: 3 residues within 4Å: Chain Y: D.87, S.151 Ligands: ADP.21 3 PLIP interactions: 2 interactions with chain Y, 1 Ligand-Water interactions Metal complexes: Y:D.87, Y:D.87, H2O.3 MG.24: 3 residues within 4Å: Chain Z: D.87, S.151 Ligands: ADP.23 4 PLIP interactions: 2 interactions with chain Z, 2 Ligand-Water interactions Metal complexes: Z:D.87, Z:D.87, H2O.3, H2O.4 MG.26: 3 residues within 4Å: Chain 0: D.87, S.151 Ligands: ADP.25 3 PLIP interactions: 2 interactions with chain 0, 1 Ligand-Water interactions Metal complexes: 0:D.87, 0:D.87, H2O.4 MG.28: 3 residues within 4Å: Chain 1: D.87, S.151 Ligands: ADP.27 3 PLIP interactions: 2 interactions with chain 1, 1 Ligand-Water interactions Metal complexes: 1:D.87, 1:D.87, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gomez-Llorente, Y. et al., Structural basis for active single and double ring complexes in human mitochondrial Hsp60-Hsp10 chaperonin. Nat Commun (2020)

Release Date

2020-04-15

Peptides

60 kDa heat shock protein, mitochondrial: APQRSTUVWXYZ01
10 kDa heat shock protein, mitochondrial: BCDEFGHIJKLMNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

P
N

Q
M

R
L

S
K

T
J

U
I

V
D

W
C

X
B

Y
A

Z
G

0
F

1
E

B
V

C
2

D
1

E
Z

F
Y

G
X

H
W

I
R

J
Q

K
P

L
O

M
U

N
T

O
S

60 kDa heat shock protein, mitochondrial

10 kDa heat shock protein, mitochondrial

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