SMTL ID : 2c7e.1

REVISED ATOMIC STRUCTURE FITTING INTO A GROEL(D398A)-ATP7 CRYO-EM MAP (EMD 1047)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 14.90 Å

Oligo State

homo-14-mer

Ligands

7 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: T.29, K.50 Ligands: ATP.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.29, A:K.50, H2O.1, H2O.1, H2O.1 K.4: 3 residues within 4Å: Chain B: T.29, K.50 Ligands: ATP.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.29, B:K.50, H2O.1, H2O.1, H2O.1 K.7: 3 residues within 4Å: Chain C: T.29, K.50 Ligands: ATP.9 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.29, C:K.50, H2O.1, H2O.1, H2O.1 K.10: 3 residues within 4Å: Chain D: T.29, K.50 Ligands: ATP.12 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.29, D:K.50, H2O.1, H2O.1, H2O.1 K.13: 3 residues within 4Å: Chain E: T.29, K.50 Ligands: ATP.15 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.29, E:K.50, H2O.1, H2O.2, H2O.2 K.16: 3 residues within 4Å: Chain F: T.29, K.50 Ligands: ATP.18 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.29, F:K.50, H2O.2, H2O.2, H2O.2 K.19: 3 residues within 4Å: Chain G: T.29, K.50 Ligands: ATP.21 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:T.29, G:K.50, H2O.2, H2O.2, H2O.2

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.86 Ligands: ATP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.86, H2O.1, H2O.1 MG.5: 2 residues within 4Å: Chain B: D.86 Ligands: ATP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.86, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain C: D.86 Ligands: ATP.9 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.86, H2O.1, H2O.1 MG.11: 2 residues within 4Å: Chain D: D.86 Ligands: ATP.12 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.86, H2O.1, H2O.1 MG.14: 2 residues within 4Å: Chain E: D.86 Ligands: ATP.15 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.86, H2O.2, H2O.2 MG.17: 2 residues within 4Å: Chain F: D.86 Ligands: ATP.18 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.86, H2O.2, H2O.2 MG.20: 2 residues within 4Å: Chain G: D.86 Ligands: ATP.21 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.86, H2O.2, H2O.2

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

ATP.3: 22 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, G.52, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.1, MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.31, A:G.52, A:D.86, A:G.87, A:G.87, A:T.88, A:T.89, A:T.89, A:T.90, A:G.414, A:G.415, A:N.478, A:A.479, A:A.480, A:D.494 Water bridges: A:D.51, A:D.51, A:D.86 ATP.6: 22 residues within 4Å: Chain B: T.29, L.30, G.31, P.32, G.52, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.4, MG.5 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.31, B:G.52, B:D.86, B:G.87, B:G.87, B:T.88, B:T.89, B:T.89, B:T.90, B:G.414, B:G.415, B:N.478, B:A.479, B:A.480, B:D.494 Water bridges: B:D.51, B:D.51, B:D.86 ATP.9: 22 residues within 4Å: Chain C: T.29, L.30, G.31, P.32, G.52, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.7, MG.8 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:G.31, C:G.52, C:D.86, C:G.87, C:G.87, C:T.88, C:T.89, C:T.89, C:T.90, C:G.414, C:G.415, C:N.478, C:A.479, C:A.480, C:D.494 Water bridges: C:D.51, C:D.51, C:D.86 ATP.12: 22 residues within 4Å: Chain D: T.29, L.30, G.31, P.32, G.52, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.10, MG.11 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:G.31, D:G.52, D:D.86, D:G.87, D:G.87, D:T.88, D:T.89, D:T.89, D:T.90, D:G.414, D:G.415, D:N.478, D:A.479, D:A.480, D:D.494 Water bridges: D:D.51, D:D.51, D:D.86 ATP.15: 22 residues within 4Å: Chain E: T.29, L.30, G.31, P.32, G.52, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.13, MG.14 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:G.31, E:G.52, E:D.86, E:G.87, E:G.87, E:T.88, E:T.89, E:T.89, E:T.90, E:G.414, E:G.415, E:N.478, E:A.479, E:A.480, E:D.494 Water bridges: E:D.51, E:D.51, E:D.86 ATP.18: 22 residues within 4Å: Chain F: T.29, L.30, G.31, P.32, G.52, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.16, MG.17 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:G.31, F:G.52, F:D.86, F:G.87, F:G.87, F:T.88, F:T.89, F:T.89, F:T.90, F:G.414, F:G.415, F:N.478, F:A.479, F:A.480, F:D.494 Water bridges: F:D.51, F:D.51, F:D.86 ATP.21: 22 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, G.52, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.19, MG.20 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:G.31, G:G.52, G:D.86, G:G.87, G:G.87, G:T.88, G:T.89, G:T.89, G:T.90, G:G.414, G:G.415, G:N.478, G:A.479, G:A.480, G:D.494 Water bridges: G:D.51, G:D.51, G:D.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ranson, N.A. et al., ATP-Bound States of Groel Captured by Cryo-Electron Microscopy. Cell(Cambridge,Mass.) (2001)

Release Date

2006-02-16

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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