SMTL ID : 4pj1.1

Crystal structure of the human mitochondrial chaperonin symmetrical 'football' complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-14-14-mer

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, I.176, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.58, A:G.114, A:T.115, A:T.116, A:T.116, A:T.117, A:G.442, A:D.506, A:D.506, A:A.507, A:D.522 Salt bridges: A:K.77 ADP.3: 20 residues within 4Å: Chain B: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.58, B:G.114, B:T.115, B:T.115, B:T.116, B:T.116, B:T.117, B:G.442, B:D.506, B:D.506, B:A.507, B:M.508, B:D.522 Salt bridges: B:K.77 ADP.5: 20 residues within 4Å: Chain C: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.58, C:G.114, C:T.115, C:T.116, C:T.117, C:G.442, C:D.506, C:D.506, C:A.507, C:M.508, C:D.522 Salt bridges: C:K.77 ADP.7: 19 residues within 4Å: Chain D: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, D.522 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.58, D:D.113, D:G.114, D:G.114, D:T.115, D:T.116, D:T.116, D:T.117, D:G.442, D:D.506, D:D.506, D:A.507, D:M.508, D:D.522 Salt bridges: D:K.77 ADP.9: 20 residues within 4Å: Chain E: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.58, E:D.113, E:D.113, E:T.115, E:T.116, E:T.116, E:T.117, E:G.442, E:D.506, E:D.506, E:A.507, E:M.508, E:D.522 Salt bridges: E:K.77 ADP.11: 20 residues within 4Å: Chain F: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.12 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.58, F:D.113, F:G.114, F:G.114, F:T.115, F:T.116, F:T.116, F:T.117, F:G.442, F:D.506, F:A.507, F:M.508, F:D.522 Salt bridges: F:K.77 ADP.13: 20 residues within 4Å: Chain G: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.58, G:D.113, G:G.114, G:G.114, G:T.115, G:T.116, G:T.116, G:T.117, G:G.442, G:D.506, G:D.506, G:A.507, G:M.508, G:D.522 Salt bridges: G:K.77 ADP.15: 20 residues within 4Å: Chain H: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.16 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.58, H:D.113, H:G.114, H:G.114, H:T.115, H:T.115, H:T.116, H:T.117, H:T.117, H:G.442, H:D.506, H:A.507, H:M.508, H:D.522 Salt bridges: H:K.77 ADP.17: 19 residues within 4Å: Chain I: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, D.522 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:G.58, I:D.113, I:G.114, I:G.114, I:T.115, I:T.115, I:T.116, I:T.117, I:T.117, I:G.442, I:D.506, I:A.507, I:M.508, I:D.522 Salt bridges: I:K.77 ADP.19: 20 residues within 4Å: Chain J: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.20 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:G.58, J:D.113, J:G.114, J:G.114, J:T.115, J:T.115, J:T.116, J:T.117, J:T.117, J:G.442, J:D.506, J:A.507, J:M.508, J:D.522 Salt bridges: J:K.77 ADP.21: 20 residues within 4Å: Chain K: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.22 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.58, K:D.113, K:G.114, K:G.114, K:T.115, K:T.115, K:T.116, K:T.117, K:G.442, K:D.506, K:A.507, K:M.508, K:D.522 Salt bridges: K:K.77 ADP.23: 20 residues within 4Å: Chain L: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.24 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:G.58, L:D.113, L:G.114, L:G.114, L:T.115, L:T.115, L:T.116, L:T.117, L:T.117, L:G.442, L:D.506, L:A.507, L:M.508, L:D.522 Salt bridges: L:K.77 ADP.25: 21 residues within 4Å: Chain M: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, I.176, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.26 13 PLIP interactions: 13 interactions with chain M Hydrogen bonds: M:G.58, M:G.114, M:G.114, M:T.115, M:T.116, M:T.117, M:T.117, M:G.442, M:D.506, M:A.507, M:M.508, M:D.522 Salt bridges: M:K.77 ADP.27: 20 residues within 4Å: Chain N: T.56, M.57, G.58, P.59, K.77, D.113, G.114, T.115, T.116, T.117, G.441, G.442, I.481, Y.505, D.506, A.507, M.508, I.520, D.522 Ligands: MG.28 13 PLIP interactions: 13 interactions with chain N Hydrogen bonds: N:T.56, N:G.58, N:G.114, N:T.115, N:T.116, N:T.117, N:T.117, N:G.442, N:D.506, N:A.507, N:M.508, N:D.522 Salt bridges: N:K.77

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.113, S.177 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.113 MG.4: 4 residues within 4Å: Chain B: D.113, S.177, D.425 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.113 MG.6: 3 residues within 4Å: Chain C: D.113, S.177 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.113 MG.8: 3 residues within 4Å: Chain D: D.113, S.177 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.113 MG.10: 3 residues within 4Å: Chain E: D.113, S.177 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.113, E:D.113 MG.12: 3 residues within 4Å: Chain F: D.113, S.177 Ligands: ADP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.113, F:D.113 MG.14: 3 residues within 4Å: Chain G: D.113, S.177 Ligands: ADP.13 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.113, G:D.113 MG.16: 3 residues within 4Å: Chain H: D.113, S.177 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.113 MG.18: 3 residues within 4Å: Chain I: D.113, S.177 Ligands: ADP.17 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.113, I:D.113 MG.20: 3 residues within 4Å: Chain J: D.113, S.177 Ligands: ADP.19 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.113, J:D.113 MG.22: 3 residues within 4Å: Chain K: D.113, S.177 Ligands: ADP.21 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.113, K:D.113 MG.24: 3 residues within 4Å: Chain L: D.113, S.177 Ligands: ADP.23 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.113, L:D.113 MG.26: 3 residues within 4Å: Chain M: D.113, S.177 Ligands: ADP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.113 MG.28: 3 residues within 4Å: Chain N: D.113, S.177 Ligands: ADP.27 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.113, N:D.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nisemblat, S. et al., Crystal structure of the human mitochondrial chaperonin symmetrical football complex. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-04-29

Peptides

60 kDa heat shock protein, mitochondrial: ABCDEFGHIJKLMN
10 kDa heat shock protein, mitochondrial: OPQRSTUVWXYZ01

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

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
1

1
2

60 kDa heat shock protein, mitochondrial

10 kDa heat shock protein, mitochondrial