SMTL ID : 3zq0.1

Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 9.20 Å

Oligo State

hetero-14-7-mer

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, S.150, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, M.487, I.492, D.494 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.31, A:G.87, A:G.87, A:T.89, A:T.89, A:T.90, A:S.153, A:S.153, A:G.414, A:A.479, A:A.480, A:D.494 Salt bridges: A:K.50 ADP.3: 24 residues within 4Å: Chain B: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, S.150, S.153, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, M.487, I.492, D.494 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.31, B:D.86, B:G.87, B:G.87, B:T.89, B:T.89, B:T.90, B:S.153, B:S.153, B:G.414, B:G.415, B:A.479, B:A.480, B:D.494 Salt bridges: B:K.50 ADP.5: 23 residues within 4Å: Chain C: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, S.150, S.153, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.31, C:D.86, C:G.87, C:G.87, C:T.89, C:T.89, C:T.90, C:S.153, C:S.153, C:G.414, C:G.415, C:A.479, C:A.480, C:D.494 Salt bridges: C:K.50 ADP.7: 22 residues within 4Å: Chain D: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.89, T.90, I.149, S.150, S.153, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.31, D:G.87, D:G.87, D:T.89, D:T.89, D:T.90, D:S.153, D:S.153, D:G.414, D:G.415, D:A.479, D:A.480, D:D.494 Salt bridges: D:K.50 ADP.9: 23 residues within 4Å: Chain E: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, S.150, S.153, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.31, E:D.86, E:G.87, E:G.87, E:T.89, E:T.89, E:T.90, E:S.153, E:S.153, E:G.414, E:A.479, E:A.480, E:D.494 Salt bridges: E:K.50 ADP.11: 21 residues within 4Å: Chain F: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.89, T.90, I.149, S.150, S.153, G.413, G.414, I.453, N.478, A.479, A.480, I.492, D.494 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.31, F:D.86, F:D.86, F:G.87, F:G.87, F:T.89, F:T.89, F:T.90, F:S.153, F:S.153, F:G.414, F:A.479, F:A.480, F:D.494 Salt bridges: F:K.50 ADP.13: 24 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, S.150, S.153, G.413, G.414, I.453, Y.477, N.478, A.479, A.480, M.487, I.492, D.494 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:G.31, G:D.86, G:G.87, G:G.87, G:T.89, G:T.89, G:T.90, G:S.153, G:S.153, G:G.414, G:A.479, G:A.480, G:D.494 Salt bridges: G:K.50

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.86, S.150 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.86, A:D.86 MG.4: 3 residues within 4Å: Chain B: D.86, S.150 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.86, B:S.150 MG.6: 3 residues within 4Å: Chain C: D.86, S.150 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.86 MG.8: 3 residues within 4Å: Chain D: D.86, S.150 Ligands: ADP.7 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.86, D:D.86, D:S.150 MG.10: 3 residues within 4Å: Chain E: D.86, S.150 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.86, E:S.150 MG.12: 3 residues within 4Å: Chain F: D.86, S.150 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.86 MG.14: 3 residues within 4Å: Chain G: D.86, S.150 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, D.-H. et al., Visualizing Groel/Es in the Act of Encapsulating a Folding Protein. Cell(Cambridge,Mass.) (2013)

Release Date

2013-06-19

Peptides

60 KDA CHAPERONIN: ABCDEFGHIJKLMN
10 KDA CHAPERONIN: OPQRSTU

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

60 KDA CHAPERONIN

10 KDA CHAPERONIN

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