SMTL ID : 4aau.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 MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.87, G.88 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:D.87 MG.4: 3 residues within 4Å: Chain B: D.87, G.88 Ligands: ATP.6 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.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.87, C:D.87 MG.10: 3 residues within 4Å: Chain D: D.87, G.88 Ligands: ATP.12 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.16: 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.19: 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 MG.24: 3 residues within 4Å: Chain H: D.87, G.88 Ligands: ATP.23 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.87, H:D.87 MG.27: 3 residues within 4Å: Chain I: D.87, G.88 Ligands: ATP.26 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.87, I:D.87 MG.30: 3 residues within 4Å: Chain J: D.87, G.88 Ligands: ATP.29 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.87, J:D.87 MG.33: 3 residues within 4Å: Chain K: D.87, G.88 Ligands: ATP.32 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.87, K:D.87 MG.36: 3 residues within 4Å: Chain L: D.87, G.88 Ligands: ATP.35 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.87, L:D.87 MG.39: 4 residues within 4Å: Chain M: D.87, G.88 Ligands: PO4.37, ATP.38 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.87, M:D.87 MG.42: 3 residues within 4Å: Chain N: D.87, G.88 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)

PO4.2: 5 residues within 4Å: Chain A: T.30, L.31, G.53, T.90 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) PO4.5: 5 residues within 4Å: Chain B: T.30, L.31, G.53, T.90 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) PO4.8: 5 residues within 4Å: Chain C: T.30, L.31, G.53, T.90 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) PO4.11: 5 residues within 4Å: Chain D: T.30, L.31, G.53, T.90 Ligands: ATP.12 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) PO4.17: 5 residues within 4Å: Chain F: T.30, L.31, G.53, T.90 Ligands: ATP.18 No protein-ligand interaction detected (PLIP) PO4.20: 5 residues within 4Å: Chain G: T.30, L.31, G.53, T.90 Ligands: ATP.21 No protein-ligand interaction detected (PLIP) PO4.22: 4 residues within 4Å: Chain H: L.31, G.53, T.90 Ligands: ATP.23 No protein-ligand interaction detected (PLIP) PO4.25: 4 residues within 4Å: Chain I: L.31, G.53, T.90 Ligands: ATP.26 No protein-ligand interaction detected (PLIP) PO4.28: 4 residues within 4Å: Chain J: L.31, G.53, T.90 Ligands: ATP.29 No protein-ligand interaction detected (PLIP) PO4.31: 4 residues within 4Å: Chain K: K.51, D.52, G.53 Ligands: ATP.32 No protein-ligand interaction detected (PLIP) PO4.34: 4 residues within 4Å: Chain L: L.31, G.53, T.90 Ligands: ATP.35 No protein-ligand interaction detected (PLIP) PO4.37: 3 residues within 4Å: Chain M: I.150 Ligands: ATP.38, MG.39 No protein-ligand interaction detected (PLIP) PO4.40: 4 residues within 4Å: Chain N: L.31, G.53, T.90 Ligands: ATP.41 No protein-ligand interaction detected (PLIP)

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

ATP.3: 24 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, N.153, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.1, PO4.2 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.90, A:T.90, A:T.91, A:T.91, A:N.153, A:G.415, A:N.479, A:A.480, A:A.481, A:D.495, A:D.495 ATP.6: 24 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, N.153, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.4, PO4.5 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.90, B:T.90, B:T.91, B:T.91, B:N.153, B:G.415, B:N.479, B:A.480, B:A.481, B:D.495, B:D.495 ATP.9: 24 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, N.153, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.7, PO4.8 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.90, C:T.90, C:T.91, C:T.91, C:N.153, C:G.415, C:N.479, C:A.480, C:A.481, C:D.495, C:D.495 ATP.12: 24 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, N.153, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.10, PO4.11 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.90, D:T.90, D:T.91, D:T.91, D:N.153, D:G.415, 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, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, N.153, 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.90, E:T.90, E:T.91, E:T.91, E:N.153, E:G.415, 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, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, N.153, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.16, PO4.17 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.90, F:T.90, F:T.91, F:T.91, F:N.153, F:G.415, 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, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, N.153, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: MG.19, PO4.20 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.90, G:T.90, G:T.91, G:T.91, G:N.153, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495, G:D.495 ATP.23: 24 residues within 4Å: Chain H: 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: PO4.22, MG.24 16 PLIP interactions: 16 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:G.415, H:N.479, H:A.480, H:A.481, H:D.495, H:D.495 ATP.26: 24 residues within 4Å: Chain I: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: PO4.25, MG.27 16 PLIP interactions: 16 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:A.481, I:D.495, I:D.495 ATP.29: 24 residues within 4Å: Chain J: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: PO4.28, MG.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:G.415, J:G.416, J:A.481, J:D.495, J:D.495 ATP.32: 19 residues within 4Å: Chain K: L.31, G.32, P.33, D.52, G.53, V.54, D.87, T.89, T.90, T.149, I.150, N.153, S.154, N.479, A.481, I.493, D.495 Ligands: PO4.31, MG.33 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:G.32, K:G.53, K:V.54, K:G.88, K:T.89, K:T.90, K:T.90, K:T.90, K:N.153, K:S.154, K:S.154 ATP.35: 24 residues within 4Å: Chain L: L.31, G.32, P.33, D.52, G.53, V.54, D.87, G.88, T.89, T.90, T.91, I.150, S.154, G.414, G.415, G.416, I.454, N.479, A.480, A.481, I.493, D.495 Ligands: PO4.34, MG.36 16 PLIP interactions: 16 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:A.481, L:D.495, L:D.495 ATP.38: 23 residues within 4Å: Chain M: L.31, G.32, P.33, D.87, G.88, T.90, T.91, Q.146, T.149, I.150, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, M.488, M.491, I.493, D.495 Ligands: PO4.37, MG.39 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:G.32, M:G.88, M:T.90, M:T.91, M:Q.146, M:T.149, M:T.149, M:Y.478, M:N.479, M:A.480 ATP.41: 24 residues within 4Å: Chain N: 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: PO4.40, MG.42 16 PLIP interactions: 16 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:G.415, N:N.479, N:A.480, N:A.481, N:D.495, N:D.495

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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