SMTL ID : 2ynj.1

GroEL at sub-nanometer resolution by Constrained Single Particle Tomography

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 8.40 Å

Oligo State

homo-14-mer

Ligands

14 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 23 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.3, MG.5 15 PLIP interactions: 15 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 AGS.7: 23 residues within 4Å: Chain B: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.9, MG.11 15 PLIP interactions: 15 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 AGS.13: 23 residues within 4Å: Chain C: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.15, MG.17 15 PLIP interactions: 15 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 AGS.19: 23 residues within 4Å: Chain D: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.21, MG.23 15 PLIP interactions: 15 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 AGS.25: 23 residues within 4Å: Chain E: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.27, MG.29 15 PLIP interactions: 15 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 AGS.31: 23 residues within 4Å: Chain F: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.33, MG.35 15 PLIP interactions: 15 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 AGS.37: 23 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.39, MG.41 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.31, G:G.52, G:G.87, G:G.87, G:T.88, G:T.89, G:T.89, G:T.90, G:T.90, G:G.414, G:G.415, G:N.478, G:A.479, G:A.480, G:D.494 AGS.43: 23 residues within 4Å: Chain H: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.45, MG.47 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.31, H:G.52, H:D.86, H:G.87, H:G.87, H:T.88, H:T.89, H:T.89, H:T.90, H:G.414, H:G.415, H:N.478, H:A.479, H:A.480, H:D.494 AGS.49: 23 residues within 4Å: Chain I: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.51, MG.53 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:G.31, I:G.52, I:G.87, I:G.87, I:T.88, I:T.89, I:T.89, I:T.90, I:T.90, I:G.414, I:G.415, I:N.478, I:A.479, I:A.480, I:D.494 AGS.55: 23 residues within 4Å: Chain J: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.57, MG.59 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:G.31, J:G.52, J:G.87, J:G.87, J:T.88, J:T.89, J:T.89, J:T.90, J:T.90, J:G.414, J:G.415, J:N.478, J:A.479, J:A.480, J:D.494 AGS.61: 23 residues within 4Å: Chain K: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.63, MG.65 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.31, K:G.52, K:G.87, K:G.87, K:T.88, K:T.89, K:T.89, K:T.90, K:T.90, K:G.414, K:G.415, K:N.478, K:A.479, K:A.480, K:D.494 AGS.67: 23 residues within 4Å: Chain L: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.69, MG.71 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:G.31, L:G.52, L:G.87, L:G.87, L:T.88, L:T.89, L:T.89, L:T.90, L:T.90, L:G.414, L:G.415, L:N.478, L:A.479, L:A.480, L:D.494 AGS.73: 23 residues within 4Å: Chain M: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.75, MG.77 15 PLIP interactions: 15 interactions with chain M Hydrogen bonds: M:G.31, M:G.52, M:G.87, M:G.87, M:T.88, M:T.89, M:T.89, M:T.90, M:T.90, M:G.414, M:G.415, M:N.478, M:A.479, M:A.480, M:D.494 AGS.79: 23 residues within 4Å: Chain N: T.29, L.30, G.31, P.32, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, G.415, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.81, MG.83 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:G.31, N:G.52, N:G.87, N:G.87, N:T.88, N:T.89, N:T.89, N:T.90, N:T.90, N:G.414, N:G.415, N:N.478, N:A.479, N:A.480, N:D.494

56 x TL: THALLIUM (I) ION(Non-covalent)

TL.2: 5 residues within 4Å: Chain A: C.457, E.482 Chain H: N.111, D.114 Ligands: TL.48 Ligand excluded by PLIP TL.3: 4 residues within 4Å: Chain A: T.29, K.50, T.89 Ligands: AGS.1 Ligand excluded by PLIP TL.4: 5 residues within 4Å: Chain A: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.6: 5 residues within 4Å: Chain A: N.111, D.114 Chain B: C.457, E.482 Ligands: TL.8 Ligand excluded by PLIP TL.8: 5 residues within 4Å: Chain A: N.111, D.114 Chain B: C.457, E.482 Ligands: TL.6 Ligand excluded by PLIP TL.9: 4 residues within 4Å: Chain B: T.29, K.50, T.89 Ligands: AGS.7 Ligand excluded by PLIP TL.10: 5 residues within 4Å: Chain B: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.12: 5 residues within 4Å: Chain B: N.111, D.114 Chain C: C.457, E.482 Ligands: TL.14 Ligand excluded by PLIP TL.14: 5 residues within 4Å: Chain B: N.111, D.114 Chain C: C.457, E.482 Ligands: TL.12 Ligand excluded by PLIP TL.15: 4 residues within 4Å: Chain C: T.29, K.50, T.89 Ligands: AGS.13 Ligand excluded by PLIP TL.16: 5 residues within 4Å: Chain C: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.18: 5 residues within 4Å: Chain C: N.111, D.114 Chain D: C.457, E.482 Ligands: TL.20 Ligand excluded by PLIP TL.20: 5 residues within 4Å: Chain C: N.111, D.114 Chain D: C.457, E.482 Ligands: TL.18 Ligand excluded by PLIP TL.21: 4 residues within 4Å: Chain D: T.29, K.50, T.89 Ligands: AGS.19 Ligand excluded by PLIP TL.22: 5 residues within 4Å: Chain D: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.24: 5 residues within 4Å: Chain D: N.111, D.114 Chain E: C.457, E.482 Ligands: TL.26 Ligand excluded by PLIP TL.26: 5 residues within 4Å: Chain D: N.111, D.114 Chain E: C.457, E.482 Ligands: TL.24 Ligand excluded by PLIP TL.27: 4 residues within 4Å: Chain E: T.29, K.50, T.89 Ligands: AGS.25 Ligand excluded by PLIP TL.28: 5 residues within 4Å: Chain E: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.30: 5 residues within 4Å: Chain E: N.111, D.114 Chain F: C.457, E.482 Ligands: TL.32 Ligand excluded by PLIP TL.32: 5 residues within 4Å: Chain E: N.111, D.114 Chain F: C.457, E.482 Ligands: TL.30 Ligand excluded by PLIP TL.33: 4 residues within 4Å: Chain F: T.29, K.50, T.89 Ligands: AGS.31 Ligand excluded by PLIP TL.34: 5 residues within 4Å: Chain F: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.36: 5 residues within 4Å: Chain F: N.111, D.114 Chain H: C.457, E.482 Ligands: TL.44 Ligand excluded by PLIP TL.38: 5 residues within 4Å: Chain G: C.457, E.482 Chain N: N.111, D.114 Ligands: TL.84 Ligand excluded by PLIP TL.39: 4 residues within 4Å: Chain G: T.29, K.50, T.89 Ligands: AGS.37 Ligand excluded by PLIP TL.40: 5 residues within 4Å: Chain G: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.42: 5 residues within 4Å: Chain G: N.111, D.114 Chain I: C.457, E.482 Ligands: TL.50 Ligand excluded by PLIP TL.44: 5 residues within 4Å: Chain F: N.111, D.114 Chain H: C.457, E.482 Ligands: TL.36 Ligand excluded by PLIP TL.45: 4 residues within 4Å: Chain H: T.29, K.50, T.89 Ligands: AGS.43 Ligand excluded by PLIP TL.46: 5 residues within 4Å: Chain H: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.48: 5 residues within 4Å: Chain A: C.457, E.482 Chain H: N.111, D.114 Ligands: TL.2 Ligand excluded by PLIP TL.50: 5 residues within 4Å: Chain G: N.111, D.114 Chain I: C.457, E.482 Ligands: TL.42 Ligand excluded by PLIP TL.51: 4 residues within 4Å: Chain I: T.29, K.50, T.89 Ligands: AGS.49 Ligand excluded by PLIP TL.52: 5 residues within 4Å: Chain I: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.54: 5 residues within 4Å: Chain I: N.111, D.114 Chain J: C.457, E.482 Ligands: TL.56 Ligand excluded by PLIP TL.56: 5 residues within 4Å: Chain I: N.111, D.114 Chain J: C.457, E.482 Ligands: TL.54 Ligand excluded by PLIP TL.57: 4 residues within 4Å: Chain J: T.29, K.50, T.89 Ligands: AGS.55 Ligand excluded by PLIP TL.58: 5 residues within 4Å: Chain J: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.60: 5 residues within 4Å: Chain J: N.111, D.114 Chain K: C.457, E.482 Ligands: TL.62 Ligand excluded by PLIP TL.62: 5 residues within 4Å: Chain J: N.111, D.114 Chain K: C.457, E.482 Ligands: TL.60 Ligand excluded by PLIP TL.63: 4 residues within 4Å: Chain K: T.29, K.50, T.89 Ligands: AGS.61 Ligand excluded by PLIP TL.64: 5 residues within 4Å: Chain K: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.66: 5 residues within 4Å: Chain K: N.111, D.114 Chain L: C.457, E.482 Ligands: TL.68 Ligand excluded by PLIP TL.68: 5 residues within 4Å: Chain K: N.111, D.114 Chain L: C.457, E.482 Ligands: TL.66 Ligand excluded by PLIP TL.69: 4 residues within 4Å: Chain L: T.29, K.50, T.89 Ligands: AGS.67 Ligand excluded by PLIP TL.70: 5 residues within 4Å: Chain L: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.72: 5 residues within 4Å: Chain L: N.111, D.114 Chain M: C.457, E.482 Ligands: TL.74 Ligand excluded by PLIP TL.74: 5 residues within 4Å: Chain L: N.111, D.114 Chain M: C.457, E.482 Ligands: TL.72 Ligand excluded by PLIP TL.75: 4 residues within 4Å: Chain M: T.29, K.50, T.89 Ligands: AGS.73 Ligand excluded by PLIP TL.76: 5 residues within 4Å: Chain M: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.78: 5 residues within 4Å: Chain M: N.111, D.114 Chain N: C.457, E.482 Ligands: TL.80 Ligand excluded by PLIP TL.80: 5 residues within 4Å: Chain M: N.111, D.114 Chain N: C.457, E.482 Ligands: TL.78 Ligand excluded by PLIP TL.81: 4 residues within 4Å: Chain N: T.29, K.50, T.89 Ligands: AGS.79 Ligand excluded by PLIP TL.82: 5 residues within 4Å: Chain N: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.84: 5 residues within 4Å: Chain G: C.457, E.482 Chain N: N.111, D.114 Ligands: TL.38 Ligand excluded by PLIP

14 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: D.86 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.86 MG.11: 2 residues within 4Å: Chain B: D.86 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.86 MG.17: 2 residues within 4Å: Chain C: D.86 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.86 MG.23: 2 residues within 4Å: Chain D: D.86 Ligands: AGS.19 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86 MG.29: 2 residues within 4Å: Chain E: D.86 Ligands: AGS.25 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.86 MG.35: 2 residues within 4Å: Chain F: D.86 Ligands: AGS.31 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.86 MG.41: 2 residues within 4Å: Chain G: D.86 Ligands: AGS.37 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86 MG.47: 2 residues within 4Å: Chain H: D.86 Ligands: AGS.43 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.86 MG.53: 2 residues within 4Å: Chain I: D.86 Ligands: AGS.49 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.86 MG.59: 2 residues within 4Å: Chain J: D.86 Ligands: AGS.55 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.86 MG.65: 2 residues within 4Å: Chain K: D.86 Ligands: AGS.61 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.86 MG.71: 2 residues within 4Å: Chain L: D.86 Ligands: AGS.67 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.86 MG.77: 2 residues within 4Å: Chain M: D.86 Ligands: AGS.73 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.86 MG.83: 2 residues within 4Å: Chain N: D.86 Ligands: AGS.79 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bartesaghi, A. et al., Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography. Structure (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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