SMTL ID : 4aaq.1

ATP-triggered molecular mechanics of the chaperonin GroEL

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 8.00 Å

Oligo State

homo-14-mer

Ligands

7 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 24 residues within 4Å: Chain A: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: PO4.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.32, A:G.53, A:V.54, A:G.88, A:G.88, A:T.89, A:T.89, A:T.89, A:T.90, A:T.91, A:T.91, A:G.415, A:G.416, A:N.479, A:A.480, A:A.481, A:D.495, A:D.495 ATP.4: 24 residues within 4Å: Chain B: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: PO4.5, MG.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.32, B:G.53, B:V.54, B:G.88, B:G.88, B:T.89, B:T.89, B:T.89, B:T.90, B:T.91, B:T.91, B:G.415, B:G.416, B:N.479, B:A.480, B:A.481, B:D.495, B:D.495 ATP.8: 24 residues within 4Å: Chain C: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.7, PO4.9 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:G.32, C:G.53, C:V.54, C:G.88, C:G.88, C:T.89, C:T.89, C:T.89, C:T.90, C:T.91, C:T.91, C:G.415, C:G.416, C:N.479, C:A.480, C:A.481, C:D.495, C:D.495 ATP.10: 24 residues within 4Å: Chain D: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: PO4.11, MG.12 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:G.32, D:G.53, D:V.54, D:G.88, D:G.88, D:T.89, D:T.89, D:T.89, D:T.90, D:T.91, D:T.91, D:G.415, D:G.416, D:N.479, D:A.480, D:A.481, D:D.495, D:D.495 ATP.15: 24 residues within 4Å: Chain E: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.13, PO4.14 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:G.32, E:G.53, E:V.54, E:G.88, E:G.88, E:T.89, E:T.89, E:T.89, E:T.90, E:T.91, E:T.91, E:G.415, E:G.416, E:N.479, E:A.480, E:A.481, E:D.495, E:D.495 ATP.18: 24 residues within 4Å: Chain F: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: PO4.16, MG.17 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:G.32, F:G.53, F:V.54, F:G.88, F:G.88, F:T.89, F:T.89, F:T.89, F:T.90, F:T.91, F:T.91, F:G.415, F:G.416, F:N.479, F:A.480, F:A.481, F:D.495, F:D.495 ATP.21: 24 residues within 4Å: Chain G: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: PO4.19, MG.20 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:G.32, G:G.53, G:V.54, G:G.88, G:G.88, G:T.89, G:T.89, G:T.89, G:T.90, G:T.91, G:T.91, G:G.415, G:G.416, G:N.479, G:A.480, G:A.481, G:D.495, G:D.495

7 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: T.30, L.31, G.53, T.90 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) PO4.5: 5 residues within 4Å: Chain B: T.30, L.31, G.53, T.90 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) PO4.9: 5 residues within 4Å: Chain C: T.30, L.31, G.53, T.90 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) PO4.11: 5 residues within 4Å: Chain D: T.30, L.31, G.53, T.90 Ligands: ATP.10 No protein-ligand interaction detected (PLIP) PO4.14: 5 residues within 4Å: Chain E: T.30, L.31, G.53, T.90 Ligands: ATP.15 No protein-ligand interaction detected (PLIP) PO4.16: 5 residues within 4Å: Chain F: T.30, L.31, G.53, T.90 Ligands: ATP.18 No protein-ligand interaction detected (PLIP) PO4.19: 5 residues within 4Å: Chain G: T.30, L.31, G.53, T.90 Ligands: ATP.21 No protein-ligand interaction detected (PLIP)

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.87, G.88 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:D.87 MG.6: 3 residues within 4Å: Chain B: D.87, G.88 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.87, B:D.87 MG.7: 3 residues within 4Å: Chain C: D.87, G.88 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.87, C:D.87 MG.12: 3 residues within 4Å: Chain D: D.87, G.88 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.87, D:D.87 MG.13: 3 residues within 4Å: Chain E: D.87, G.88 Ligands: ATP.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.87, E:D.87 MG.17: 3 residues within 4Å: Chain F: D.87, G.88 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.87, F:D.87 MG.20: 3 residues within 4Å: Chain G: D.87, G.88 Ligands: ATP.21 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.87, G:D.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clare, D.K. et al., ATP-Triggered Conformational Changes Delineate Substrate-Binding and -Folding Mechanics of the Groel Chaperonin. Cell(Cambridge,Mass.) (2012)

Release Date

2012-12-12

Peptides

60 KDA CHAPERONIN: ABCDEFGHIJKLMN

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

60 KDA CHAPERONIN

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