SMTL ID : 6ht7.1

Crystal structure of the WT human mitochondrial chaperonin (ADP:BeF3)14 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-14-14-mer

Ligands

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

ADP.1: 24 residues within 4Å: Chain A: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.32, A:D.87, A:G.88, A:T.90, A:T.90, A:G.416, A:D.480, A:A.481, A:D.496 Salt bridges: A:K.51 ADP.5: 23 residues within 4Å: Chain I: T.30, M.31, G.32, P.33, K.51, D.87, G.88, 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 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:D.87, I:T.90, I:T.91, I:G.416, I:D.480, I:A.481, I:D.496 Salt bridges: I:K.51 ADP.9: 24 residues within 4Å: Chain J: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:G.32, J:D.87, J:G.88, J:T.90, J:T.90, J:G.416, J:G.417, J:D.480, J:A.481, J:D.496 Salt bridges: J:K.51 ADP.13: 24 residues within 4Å: Chain K: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.32, K:D.87, K:G.88, K:T.90, K:T.90, K:T.90, K:T.91, K:G.416, K:G.417, K:D.480, K:D.480, K:A.481, K:D.496 Salt bridges: K:K.51 ADP.17: 24 residues within 4Å: Chain L: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.32, L:D.87, L:G.88, L:T.90, L:T.90, L:G.416, L:D.480, L:A.481, L:D.496 Salt bridges: L:K.51 ADP.21: 21 residues within 4Å: Chain M: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, G.415, G.416, Y.479, D.480, A.481, I.494, D.496 Ligands: BEF.22, MG.23, K.24 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:G.32, M:D.87, M:G.88, M:T.90, M:T.90, M:T.90, M:T.91, M:G.416, M:D.480, M:A.481, M:D.496 Salt bridges: M:K.51 ADP.25: 24 residues within 4Å: Chain N: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 11 PLIP interactions: 11 interactions with chain N Hydrogen bonds: N:T.30, N:G.32, N:D.87, N:G.88, N:T.90, N:T.91, N:G.416, N:D.480, N:A.481, N:D.496 Salt bridges: N:K.51 ADP.29: 24 residues within 4Å: Chain O: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:G.32, O:D.87, O:G.88, O:T.90, O:T.90, O:T.90, O:G.416, O:D.480, O:D.480, O:A.481, O:D.496 Salt bridges: O:K.51 ADP.33: 24 residues within 4Å: Chain W: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 13 PLIP interactions: 13 interactions with chain W Hydrogen bonds: W:G.32, W:D.87, W:G.88, W:T.90, W:T.90, W:T.90, W:T.91, W:G.416, W:D.480, W:D.480, W:A.481, W:D.496 Salt bridges: W:K.51 ADP.37: 23 residues within 4Å: Chain X: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, I.150, S.151, 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 11 PLIP interactions: 11 interactions with chain X Hydrogen bonds: X:T.30, X:G.32, X:D.87, X:G.88, X:T.90, X:G.416, X:D.480, X:D.480, X:A.481, X:D.496 Salt bridges: X:K.51 ADP.41: 24 residues within 4Å: Chain Y: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 12 PLIP interactions: 12 interactions with chain Y Hydrogen bonds: Y:T.30, Y:G.32, Y:D.87, Y:G.88, Y:T.90, Y:T.90, Y:G.416, Y:D.480, Y:D.480, Y:A.481, Y:D.496 Salt bridges: Y:K.51 ADP.45: 23 residues within 4Å: Chain Z: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, G.415, G.416, I.455, Y.479, D.480, A.481, M.482, I.494, D.496 Ligands: BEF.46, MG.47, K.48 11 PLIP interactions: 11 interactions with chain Z Hydrogen bonds: Z:G.32, Z:D.87, Z:G.88, Z:T.90, Z:S.151, Z:G.416, Z:D.480, Z:D.480, Z:A.481, Z:D.496 Salt bridges: Z:K.51 ADP.49: 24 residues within 4Å: Chain 0: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 12 PLIP interactions: 12 interactions with chain 0 Hydrogen bonds: 0:G.32, 0:D.87, 0:T.90, 0:T.90, 0:T.90, 0:T.91, 0:G.416, 0:D.480, 0:D.480, 0:A.481, 0:D.496 Salt bridges: 0:K.51 ADP.53: 24 residues within 4Å: Chain 1: T.30, M.31, G.32, P.33, K.51, D.87, G.88, T.90, T.91, I.150, S.151, 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 11 PLIP interactions: 11 interactions with chain 1 Hydrogen bonds: 1:G.32, 1:D.87, 1:G.88, 1:T.90, 1:T.90, 1:G.416, 1:D.480, 1:D.480, 1:A.481, 1:D.496 Salt bridges: 1:K.51

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

BEF.2: 10 residues within 4Å: Chain A: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.1, MG.3, K.4 No protein-ligand interaction detected (PLIP) BEF.6: 10 residues within 4Å: Chain I: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.5, MG.7, K.8 No protein-ligand interaction detected (PLIP) BEF.10: 10 residues within 4Å: Chain J: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.9, MG.11, K.12 No protein-ligand interaction detected (PLIP) BEF.14: 10 residues within 4Å: Chain K: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.13, MG.15, K.16 No protein-ligand interaction detected (PLIP) BEF.18: 10 residues within 4Å: Chain L: K.51, D.52, G.53, D.87, G.88, T.89, T.90 Ligands: ADP.17, MG.19, K.20 No protein-ligand interaction detected (PLIP) BEF.22: 10 residues within 4Å: Chain M: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.21, MG.23, K.24 No protein-ligand interaction detected (PLIP) BEF.26: 10 residues within 4Å: Chain N: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.25, MG.27, K.28 No protein-ligand interaction detected (PLIP) BEF.30: 10 residues within 4Å: Chain O: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.29, MG.31, K.32 No protein-ligand interaction detected (PLIP) BEF.34: 9 residues within 4Å: Chain W: G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.33, MG.35, K.36 No protein-ligand interaction detected (PLIP) BEF.38: 10 residues within 4Å: Chain X: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.37, MG.39, K.40 No protein-ligand interaction detected (PLIP) BEF.42: 10 residues within 4Å: Chain Y: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.41, MG.43, K.44 No protein-ligand interaction detected (PLIP) BEF.46: 10 residues within 4Å: Chain Z: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.45, MG.47, K.48 No protein-ligand interaction detected (PLIP) BEF.50: 10 residues within 4Å: Chain 0: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.49, MG.51, K.52 No protein-ligand interaction detected (PLIP) BEF.54: 10 residues within 4Å: Chain 1: D.52, G.53, D.87, G.88, T.89, T.90, T.91 Ligands: ADP.53, MG.55, K.56 No protein-ligand interaction detected (PLIP)

14 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: D.52, D.87, T.89, D.399 Ligands: ADP.1, BEF.2, K.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.52, A:D.399 MG.7: 6 residues within 4Å: Chain I: D.52, D.87, T.89, D.399 Ligands: ADP.5, BEF.6 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.52, I:D.399 MG.11: 5 residues within 4Å: Chain J: D.52, D.87, D.399 Ligands: ADP.9, BEF.10 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.399 MG.15: 6 residues within 4Å: Chain K: D.52, D.87, D.399 Ligands: ADP.13, BEF.14, K.16 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.399 MG.19: 5 residues within 4Å: Chain L: D.52, D.87, D.399 Ligands: ADP.17, BEF.18 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.87, L:D.399 MG.23: 5 residues within 4Å: Chain M: D.52, D.87, D.399 Ligands: ADP.21, BEF.22 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.399 MG.27: 7 residues within 4Å: Chain N: D.52, D.87, G.88, D.399 Ligands: ADP.25, BEF.26, K.28 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.87, N:D.399 MG.31: 5 residues within 4Å: Chain O: D.52, D.87, D.399 Ligands: ADP.29, BEF.30 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.399 MG.35: 5 residues within 4Å: Chain W: D.52, D.87, D.399 Ligands: ADP.33, BEF.34 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:D.87, W:D.399 MG.39: 5 residues within 4Å: Chain X: D.87, D.399 Ligands: ADP.37, BEF.38, K.40 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:D.87 MG.43: 6 residues within 4Å: Chain Y: D.52, D.87, D.399 Ligands: ADP.41, BEF.42, K.44 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:D.399 MG.47: 6 residues within 4Å: Chain Z: D.52, D.87, D.399 Ligands: ADP.45, BEF.46, K.48 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:D.399 MG.51: 5 residues within 4Å: Chain 0: D.52, D.87, D.399 Ligands: ADP.49, BEF.50 2 PLIP interactions: 2 interactions with chain 0 Metal complexes: 0:D.87, 0:D.399 MG.55: 5 residues within 4Å: Chain 1: D.52, D.87, D.399 Ligands: ADP.53, BEF.54 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1:D.399

14 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: K.51, D.52, G.53 Ligands: ADP.1, BEF.2, MG.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.51 K.8: 7 residues within 4Å: Chain I: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.5, BEF.6 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:T.30, I:T.30, I:K.51, I:T.90 K.12: 6 residues within 4Å: Chain J: T.30, K.51, D.52, T.90 Ligands: ADP.9, BEF.10 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.30, J:K.51 K.16: 8 residues within 4Å: Chain K: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.13, BEF.14, MG.15 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:K.51 K.20: 6 residues within 4Å: Chain L: T.30, K.51, D.52, T.90 Ligands: ADP.17, BEF.18 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:T.30, L:K.51 K.24: 7 residues within 4Å: Chain M: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.21, BEF.22 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:T.30, M:K.51 K.28: 8 residues within 4Å: Chain N: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.25, BEF.26, MG.27 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:T.30, N:K.51 K.32: 7 residues within 4Å: Chain O: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.29, BEF.30 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:K.51, O:T.90 K.36: 6 residues within 4Å: Chain W: T.30, K.51, D.52, T.90 Ligands: ADP.33, BEF.34 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:K.51 K.40: 6 residues within 4Å: Chain X: T.30, K.51, D.52 Ligands: ADP.37, BEF.38, MG.39 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:K.51 K.44: 7 residues within 4Å: Chain Y: T.30, K.51, D.52, T.90 Ligands: ADP.41, BEF.42, MG.43 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:K.51 K.48: 8 residues within 4Å: Chain Z: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.45, BEF.46, MG.47 2 PLIP interactions: 2 interactions with chain Z Metal complexes: Z:T.30, Z:K.51 K.52: 7 residues within 4Å: Chain 0: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.49, BEF.50 3 PLIP interactions: 3 interactions with chain 0 Metal complexes: 0:T.30, 0:K.51, 0:T.90 K.56: 7 residues within 4Å: Chain 1: T.30, K.51, D.52, G.53, T.90 Ligands: ADP.53, BEF.54 2 PLIP interactions: 2 interactions with chain 1 Metal complexes: 1:T.30, 1:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jebara, F. et al., Crystal structure of the WT human mitochondrial football Hsp60-Hsp10(ADPBeFx)14 complex. Nat Commun (2020)

Release Date

2020-04-29

Peptides

60 kDa heat shock protein, mitochondrial: AIJKLMNOWXYZ01
10 kDa heat shock protein, mitochondrial: BCDEFGHPQRSTUV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

I
I

J
H

K
N

L
M

M
L

N
K

O
G

W
F

X
E

Y
D

Z
C

0
B

1
A

B
X

C
W

D
V

E
2

F
1

G
Z

H
Y

P
U

Q
T

R
S

S
R

T
Q

U
P

V
O

60 kDa heat shock protein, mitochondrial

10 kDa heat shock protein, mitochondrial