SMTL ID : 4ab2.1

ATP-triggered molecular mechanics of the chaperonin GroEL

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 8.50 Å

Oligo State

homo-14-mer

Ligands

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

ATP.1: 25 residues within 4Å: Chain A: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.2, PO4.3 15 PLIP interactions: 15 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.90, A:T.90, A:T.91, A:S.154, A:G.415, A:G.416, A:D.495, A:D.495 ATP.4: 25 residues within 4Å: Chain B: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.5, PO4.6 15 PLIP interactions: 15 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.90, B:T.90, B:T.91, B:S.154, B:G.415, B:G.416, B:D.495, B:D.495 ATP.7: 25 residues within 4Å: Chain C: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.8, PO4.9 15 PLIP interactions: 15 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.90, C:T.90, C:T.91, C:S.154, C:G.415, C:G.416, C:D.495, C:D.495 ATP.10: 25 residues within 4Å: Chain D: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.11, PO4.12 15 PLIP interactions: 15 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.90, D:T.90, D:T.91, D:S.154, D:G.415, D:G.416, D:D.495, D:D.495 ATP.13: 25 residues within 4Å: Chain E: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.14, PO4.15 15 PLIP interactions: 15 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.90, E:T.90, E:T.91, E:S.154, E:G.415, E:G.416, E:D.495, E:D.495 ATP.16: 25 residues within 4Å: Chain F: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.17, PO4.18 15 PLIP interactions: 15 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.90, F:T.90, F:T.91, F:S.154, F:G.415, F:G.416, F:D.495, F:D.495 ATP.19: 25 residues within 4Å: Chain G: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.20, PO4.21 15 PLIP interactions: 15 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.90, G:T.90, G:T.91, G:S.154, G:G.415, G:G.416, G:D.495, G:D.495 ATP.23: 25 residues within 4Å: Chain H: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.22, PO4.24 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.32, H:G.53, H:V.54, H:G.88, H:G.88, H:T.89, H:T.89, H:T.89, H:T.90, H:T.91, H:S.154, H:G.415, H:G.416, H:D.495, H:D.495 ATP.25: 25 residues within 4Å: Chain I: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.26, PO4.27 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:G.32, I:G.53, I:V.54, I:G.88, I:G.88, I:T.89, I:T.89, I:T.89, I:T.90, I:T.91, I:S.154, I:G.415, I:G.416, I:D.495, I:D.495 ATP.28: 25 residues within 4Å: Chain J: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.29, PO4.30 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:G.32, J:G.53, J:V.54, J:G.88, J:G.88, J:T.89, J:T.89, J:T.89, J:T.90, J:T.91, J:S.154, J:G.415, J:G.416, J:D.495, J:D.495 ATP.32: 25 residues within 4Å: Chain K: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.31, PO4.33 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.32, K:G.53, K:V.54, K:G.88, K:G.88, K:T.89, K:T.89, K:T.89, K:T.90, K:T.91, K:S.154, K:G.415, K:G.416, K:D.495, K:D.495 ATP.35: 25 residues within 4Å: Chain L: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.34, PO4.36 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:G.32, L:G.53, L:V.54, L:G.88, L:G.88, L:T.89, L:T.89, L:T.89, L:T.90, L:T.91, L:S.154, L:G.415, L:G.416, L:D.495, L:D.495 ATP.38: 25 residues within 4Å: Chain M: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.37, PO4.39 15 PLIP interactions: 15 interactions with chain M Hydrogen bonds: M:G.32, M:G.53, M:V.54, M:G.88, M:G.88, M:T.89, M:T.89, M:T.89, M:T.90, M:T.91, M:S.154, M:G.415, M:G.416, M:D.495, M:D.495 ATP.41: 25 residues within 4Å: Chain N: L.31, G.32, P.33, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.151, N.153, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: MG.40, PO4.42 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:G.32, N:G.53, N:V.54, N:G.88, N:G.88, N:T.89, N:T.89, N:T.89, N:T.90, N:T.91, N:S.154, N:G.415, N:G.416, N:D.495, N:D.495

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.87, G.88, I.150, S.151 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:D.87 MG.5: 5 residues within 4Å: Chain B: D.87, G.88, I.150, S.151 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.87, B:D.87 MG.8: 5 residues within 4Å: Chain C: D.87, G.88, I.150, S.151 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.87, C:D.87 MG.11: 5 residues within 4Å: Chain D: D.87, G.88, I.150, S.151 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.87, D:D.87 MG.14: 5 residues within 4Å: Chain E: D.87, G.88, I.150, S.151 Ligands: ATP.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.87, E:D.87 MG.17: 5 residues within 4Å: Chain F: D.87, G.88, I.150, S.151 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.87, F:D.87 MG.20: 5 residues within 4Å: Chain G: D.87, G.88, I.150, S.151 Ligands: ATP.19 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.87, G:D.87 MG.22: 5 residues within 4Å: Chain H: D.87, G.88, I.150, S.151 Ligands: ATP.23 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.87, H:D.87 MG.26: 5 residues within 4Å: Chain I: D.87, G.88, I.150, S.151 Ligands: ATP.25 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.87, I:D.87 MG.29: 5 residues within 4Å: Chain J: D.87, G.88, I.150, S.151 Ligands: ATP.28 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.87, J:D.87 MG.31: 5 residues within 4Å: Chain K: D.87, G.88, I.150, S.151 Ligands: ATP.32 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.87, K:D.87 MG.34: 5 residues within 4Å: Chain L: D.87, G.88, I.150, S.151 Ligands: ATP.35 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.87, L:D.87 MG.37: 5 residues within 4Å: Chain M: D.87, G.88, I.150, S.151 Ligands: ATP.38 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.87, M:D.87 MG.40: 5 residues within 4Å: Chain N: D.87, G.88, I.150, S.151 Ligands: ATP.41 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.87, N:D.87

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

PO4.3: 6 residues within 4Å: Chain A: T.30, L.31, G.53, T.90, N.153 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) PO4.6: 6 residues within 4Å: Chain B: T.30, L.31, G.53, T.90, N.153 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) PO4.9: 6 residues within 4Å: Chain C: T.30, L.31, G.53, T.90, N.153 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) PO4.12: 6 residues within 4Å: Chain D: T.30, L.31, G.53, T.90, N.153 Ligands: ATP.10 No protein-ligand interaction detected (PLIP) PO4.15: 6 residues within 4Å: Chain E: T.30, L.31, G.53, T.90, N.153 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) PO4.18: 6 residues within 4Å: Chain F: T.30, L.31, G.53, T.90, N.153 Ligands: ATP.16 No protein-ligand interaction detected (PLIP) PO4.21: 6 residues within 4Å: Chain G: T.30, L.31, G.53, T.90, N.153 Ligands: ATP.19 No protein-ligand interaction detected (PLIP) PO4.24: 4 residues within 4Å: Chain H: D.52, T.90, N.153 Ligands: ATP.23 No protein-ligand interaction detected (PLIP) PO4.27: 4 residues within 4Å: Chain I: D.52, T.90, N.153 Ligands: ATP.25 No protein-ligand interaction detected (PLIP) PO4.30: 4 residues within 4Å: Chain J: D.52, T.90, N.153 Ligands: ATP.28 No protein-ligand interaction detected (PLIP) PO4.33: 4 residues within 4Å: Chain K: D.52, T.90, N.153 Ligands: ATP.32 No protein-ligand interaction detected (PLIP) PO4.36: 4 residues within 4Å: Chain L: D.52, T.90, N.153 Ligands: ATP.35 No protein-ligand interaction detected (PLIP) PO4.39: 4 residues within 4Å: Chain M: D.52, T.90, N.153 Ligands: ATP.38 No protein-ligand interaction detected (PLIP) PO4.42: 4 residues within 4Å: Chain N: D.52, T.90, N.153 Ligands: ATP.41 No protein-ligand interaction detected (PLIP)

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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