SMTL ID : 5opx.1

Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.64 Å

Oligo State

hetero-14-14-mer

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.2, BEF.3, K.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.30, A:G.32, A:G.88, A:G.88, A:T.89, A:T.90, A:T.90, A:T.91, A:T.91, A:G.415, A:N.479, A:A.480, A:A.481, A:D.495 Salt bridges: A:K.51 ADP.5: 23 residues within 4Å: Chain B: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.6, BEF.7, K.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.30, B:G.32, B:G.88, B:G.88, B:T.89, B:T.90, B:T.90, B:T.91, B:T.91, B:G.415, B:N.479, B:A.480, B:A.481, B:D.495 Salt bridges: B:K.51 ADP.9: 23 residues within 4Å: Chain C: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.10, BEF.11, K.12 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.30, C:G.32, C:G.88, C:G.88, C:T.89, C:T.90, C:T.90, C:T.91, C:T.91, C:G.415, C:N.479, C:A.480, C:A.481, C:D.495 Salt bridges: C:K.51 ADP.13: 23 residues within 4Å: Chain D: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.14, BEF.15, K.16 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.30, D:G.32, D:G.88, D:G.88, D:T.89, D:T.90, D:T.90, D:T.91, D:G.415, D:G.416, D:N.479, D:A.480, D:A.481, D:D.495 Salt bridges: D:K.51 ADP.17: 23 residues within 4Å: Chain E: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.18, BEF.19, K.20 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:T.30, E:G.32, E:G.88, E:G.88, E:T.89, E:T.89, E:T.90, E:T.90, E:T.91, E:G.415, E:N.479, E:A.480, E:A.481, E:D.495 Salt bridges: E:K.51 ADP.21: 23 residues within 4Å: Chain F: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.22, BEF.23, K.24 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:T.30, F:G.32, F:G.88, F:G.88, F:T.89, F:T.89, F:T.90, F:T.90, F:T.91, F:G.415, F:N.479, F:A.480, F:A.481, F:D.495 Salt bridges: F:K.51 ADP.25: 23 residues within 4Å: Chain G: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.26, BEF.27, K.28 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:T.30, G:G.32, G:G.88, G:G.88, G:T.89, G:T.89, G:T.90, G:T.90, G:T.91, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495 Salt bridges: G:K.51 ADP.29: 23 residues within 4Å: Chain H: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.30, BEF.31, K.32 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:G.32, H:G.88, H:T.89, H:T.89, H:T.90, H:T.91, H:T.91, H:G.415, H:N.479, H:A.480, H:A.481, H:D.495 Salt bridges: H:K.51 ADP.33: 23 residues within 4Å: Chain I: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.34, BEF.35, K.36 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:G.32, I:G.88, I:T.89, I:T.90, I:T.91, I:T.91, I:G.415, I:N.479, I:A.480, I:A.481, I:D.495 Salt bridges: I:K.51 ADP.37: 23 residues within 4Å: Chain J: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.38, BEF.39, K.40 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:G.32, J:D.87, J:G.88, J:T.89, J:T.89, J:T.90, J:T.91, J:T.91, J:G.415, J:N.479, J:A.480, J:A.481, J:D.495 Salt bridges: J:K.51 ADP.41: 23 residues within 4Å: Chain K: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.42, BEF.43, K.44 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:G.32, K:G.88, K:T.89, K:T.89, K:T.90, K:T.91, K:T.91, K:G.415, K:N.479, K:A.480, K:A.481, K:D.495 Salt bridges: K:K.51 ADP.45: 23 residues within 4Å: Chain L: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.46, BEF.47, K.48 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:G.32, L:D.87, L:G.88, L:T.89, L:T.89, L:T.90, L:T.91, L:G.415, L:N.479, L:A.480, L:A.481, L:D.495 Salt bridges: L:K.51 ADP.49: 23 residues within 4Å: Chain M: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.50, BEF.51, K.52 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:G.32, M:G.88, M:T.89, M:T.89, M:T.90, M:T.91, M:G.415, M:N.479, M:A.480, M:A.481, M:D.495 Salt bridges: M:K.51 ADP.53: 23 residues within 4Å: Chain N: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.54, BEF.55, K.56 11 PLIP interactions: 11 interactions with chain N Hydrogen bonds: N:G.32, N:G.88, N:T.89, N:T.90, N:T.91, N:G.415, N:N.479, N:A.480, N:A.481, N:D.495 Salt bridges: N:K.51

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.87, S.151 Ligands: ADP.1, BEF.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:D.87 MG.6: 4 residues within 4Å: Chain B: D.87, S.151 Ligands: ADP.5, BEF.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.87, B:D.87 MG.10: 4 residues within 4Å: Chain C: D.87, S.151 Ligands: ADP.9, BEF.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.87, C:D.87 MG.14: 4 residues within 4Å: Chain D: D.87, S.151 Ligands: ADP.13, BEF.15 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.87, D:D.87 MG.18: 4 residues within 4Å: Chain E: D.87, S.151 Ligands: ADP.17, BEF.19 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.87, E:D.87 MG.22: 4 residues within 4Å: Chain F: D.87, S.151 Ligands: ADP.21, BEF.23 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.87, F:D.87 MG.26: 4 residues within 4Å: Chain G: D.87, S.151 Ligands: ADP.25, BEF.27 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.87, G:D.87 MG.30: 4 residues within 4Å: Chain H: D.87, S.151 Ligands: ADP.29, BEF.31 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.87, H:D.87 MG.34: 4 residues within 4Å: Chain I: D.87, S.151 Ligands: ADP.33, BEF.35 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.87, I:D.87 MG.38: 4 residues within 4Å: Chain J: D.87, S.151 Ligands: ADP.37, BEF.39 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.87, J:D.87 MG.42: 4 residues within 4Å: Chain K: D.87, S.151 Ligands: ADP.41, BEF.43 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.87, K:D.87 MG.46: 4 residues within 4Å: Chain L: D.87, S.151 Ligands: ADP.45, BEF.47 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.87, L:D.87 MG.50: 4 residues within 4Å: Chain M: D.87, S.151 Ligands: ADP.49, BEF.51 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.87, M:D.87 MG.54: 4 residues within 4Å: Chain N: D.87, S.151 Ligands: ADP.53, BEF.55 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.87, N:D.87

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

BEF.3: 10 residues within 4Å: Chain A: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.1, MG.2, K.4 No protein-ligand interaction detected (PLIP) BEF.7: 10 residues within 4Å: Chain B: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.5, MG.6, K.8 No protein-ligand interaction detected (PLIP) BEF.11: 10 residues within 4Å: Chain C: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.9, MG.10, K.12 No protein-ligand interaction detected (PLIP) BEF.15: 10 residues within 4Å: Chain D: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.13, MG.14, K.16 No protein-ligand interaction detected (PLIP) BEF.19: 10 residues within 4Å: Chain E: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.17, MG.18, K.20 No protein-ligand interaction detected (PLIP) BEF.23: 10 residues within 4Å: Chain F: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.21, MG.22, K.24 No protein-ligand interaction detected (PLIP) BEF.27: 10 residues within 4Å: Chain G: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.25, MG.26, K.28 No protein-ligand interaction detected (PLIP) BEF.31: 10 residues within 4Å: Chain H: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.29, MG.30, K.32 No protein-ligand interaction detected (PLIP) BEF.35: 10 residues within 4Å: Chain I: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.33, MG.34, K.36 No protein-ligand interaction detected (PLIP) BEF.39: 10 residues within 4Å: Chain J: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.37, MG.38, K.40 No protein-ligand interaction detected (PLIP) BEF.43: 10 residues within 4Å: Chain K: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.41, MG.42, K.44 No protein-ligand interaction detected (PLIP) BEF.47: 10 residues within 4Å: Chain L: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.45, MG.46, K.48 No protein-ligand interaction detected (PLIP) BEF.51: 10 residues within 4Å: Chain M: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.49, MG.50, K.52 No protein-ligand interaction detected (PLIP) BEF.55: 10 residues within 4Å: Chain N: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.53, MG.54, K.56 No protein-ligand interaction detected (PLIP)

14 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: T.30, K.51, T.90 Ligands: ADP.1, BEF.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.30, A:K.51, A:T.90 K.8: 5 residues within 4Å: Chain B: T.30, K.51, T.90 Ligands: ADP.5, BEF.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:K.51 K.12: 5 residues within 4Å: Chain C: T.30, K.51, T.90 Ligands: ADP.9, BEF.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.30, C:K.51, C:T.90 K.16: 6 residues within 4Å: Chain D: T.30, K.51, G.53, T.90 Ligands: ADP.13, BEF.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.51 K.20: 5 residues within 4Å: Chain E: T.30, K.51, T.90 Ligands: ADP.17, BEF.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:K.51 K.24: 5 residues within 4Å: Chain F: T.30, K.51, T.90 Ligands: ADP.21, BEF.23 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:K.51, F:T.90 K.28: 5 residues within 4Å: Chain G: T.30, K.51, T.90 Ligands: ADP.25, BEF.27 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:K.51 K.32: 5 residues within 4Å: Chain H: T.30, K.51, T.90 Ligands: ADP.29, BEF.31 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:K.51 K.36: 5 residues within 4Å: Chain I: T.30, K.51, T.90 Ligands: ADP.33, BEF.35 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:K.51, I:T.90 K.40: 6 residues within 4Å: Chain J: T.30, K.51, G.53, T.90 Ligands: ADP.37, BEF.39 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:K.51 K.44: 6 residues within 4Å: Chain K: T.30, K.51, G.53, T.90 Ligands: ADP.41, BEF.43 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:K.51, K:T.90 K.48: 5 residues within 4Å: Chain L: T.30, K.51, T.90 Ligands: ADP.45, BEF.47 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:K.51 K.52: 5 residues within 4Å: Chain M: T.30, K.51, T.90 Ligands: ADP.49, BEF.51 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:K.51, M:T.90 K.56: 5 residues within 4Å: Chain N: T.30, K.51, T.90 Ligands: ADP.53, BEF.55 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:K.51, N:T.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, X. et al., GroEL Ring Separation and Exchange in the Chaperonin Reaction. Cell (2018)

Release Date

2018-01-10

Peptides

60 kDa chaperonin: ABCDEFGHIJKLMN
10 kDa chaperonin: 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
1

P
2

Q
O

R
P

S
Q

T
R

U
S

V
T

W
U

X
V

Y
W

Z
X

0
Y

1
Z

60 kDa chaperonin

10 kDa chaperonin

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