SMTL ID : 3e76.1

Crystal structure of Wild-type GroEL with bound Thallium ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.94 Å

Oligo State

homo-14-mer

Ligands

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

AGS.1: 25 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, D.51, G.52, V.53, G.85, 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: TL.4, MG.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.31, A:D.51, A:G.52, 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: 22 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, 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: 24 residues within 4Å: Chain C: T.29, L.30, G.31, P.32, D.51, G.52, V.53, G.85, 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 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.31, C:D.51, C:G.52, C:G.87, C:G.87, C:T.88, 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.18: 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.22 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.31, D:G.52, 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.24: 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.26, MG.28 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.31, E:G.52, 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.29: 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.32, MG.33 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.31, F:G.52, 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.35: 24 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, D.51, G.52, G.85, 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: TL.38, MG.39 14 PLIP interactions: 14 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:G.414, G:G.415, G:N.478, G:A.479, G:A.480, G:D.494 AGS.40: 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.42, MG.44 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.31, H:G.52, H:G.87, H:G.87, H:T.88, H:T.89, H:T.89, H:T.90, H:T.90, H:G.414, H:G.415, H:N.478, H:A.479, H:A.480, H:D.494 AGS.46: 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.49, MG.50 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:G.31, I:D.51, I:D.51, 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.51: 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.54, MG.55 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.56: 23 residues within 4Å: Chain K: T.29, L.30, G.31, P.32, K.50, D.51, G.52, V.53, D.86, G.87, T.88, T.89, T.90, G.413, G.414, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.58, MG.60 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.31, K:K.50, 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:N.478, K:A.479, K:A.480, K:D.494 AGS.61: 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.64, MG.65 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:G.31, L:D.51, L:D.51, 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.66: 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.68, MG.70 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.71: 24 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, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: TL.72, MG.74 17 PLIP interactions: 17 interactions with chain N Hydrogen bonds: N:G.31, N:D.51, N:D.51, 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

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

TL.2: 4 residues within 4Å: Chain A: S.216, P.217, F.218, Q.318 Ligand excluded by PLIP TL.3: 4 residues within 4Å: Chain A: C.457, E.482 Chain B: N.111, D.114 Ligand excluded by PLIP TL.4: 4 residues within 4Å: Chain A: T.29, K.50, T.89 Ligands: AGS.1 Ligand excluded by PLIP TL.6: 2 residues within 4Å: Chain A: K.131, S.134 Ligand excluded by PLIP TL.8: 3 residues within 4Å: Chain B: C.457, E.482 Chain C: N.111 Ligand excluded by PLIP TL.9: 5 residues within 4Å: Chain B: T.29, K.50, G.52, T.89 Ligands: AGS.7 Ligand excluded by PLIP TL.10: 4 residues within 4Å: Chain B: S.216, P.217, F.218, K.244 Ligand excluded by PLIP TL.12: 3 residues within 4Å: Chain B: K.131, S.134, P.136 Ligand excluded by PLIP TL.14: 4 residues within 4Å: Chain C: C.457, E.482 Chain D: N.111, D.114 Ligand excluded by PLIP TL.15: 5 residues within 4Å: Chain C: T.29, K.50, G.52, T.89 Ligands: AGS.13 Ligand excluded by PLIP TL.16: 4 residues within 4Å: Chain C: S.216, P.217, F.218, Q.318 Ligand excluded by PLIP TL.19: 4 residues within 4Å: Chain D: S.216, P.217, F.218, Q.318 Ligand excluded by PLIP TL.20: 4 residues within 4Å: Chain D: C.457, E.482 Chain E: N.111, D.114 Ligand excluded by PLIP TL.21: 4 residues within 4Å: Chain D: T.29, K.50, T.89 Ligands: AGS.18 Ligand excluded by PLIP TL.23: 3 residues within 4Å: Chain D: K.131, S.134, P.136 Ligand excluded by PLIP TL.25: 4 residues within 4Å: Chain E: C.457, E.482 Chain F: N.111, D.114 Ligand excluded by PLIP TL.26: 5 residues within 4Å: Chain E: T.29, L.30, K.50, T.89 Ligands: AGS.24 Ligand excluded by PLIP TL.27: 4 residues within 4Å: Chain E: S.216, P.217, F.218, K.244 Ligand excluded by PLIP TL.30: 5 residues within 4Å: Chain F: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.31: 4 residues within 4Å: Chain F: C.457, E.482 Chain G: N.111, D.114 Ligand excluded by PLIP TL.32: 4 residues within 4Å: Chain F: T.29, K.50, T.89 Ligands: AGS.29 Ligand excluded by PLIP TL.34: 1 residues within 4Å: Chain F: A.132 Ligand excluded by PLIP TL.36: 3 residues within 4Å: Chain G: S.216, P.217, F.218 Ligand excluded by PLIP TL.37: 3 residues within 4Å: Chain A: N.111 Chain G: C.457, E.482 Ligand excluded by PLIP TL.38: 5 residues within 4Å: Chain G: T.29, K.50, G.52, T.89 Ligands: AGS.35 Ligand excluded by PLIP TL.41: 4 residues within 4Å: Chain H: C.457, E.482 Chain I: N.111, D.114 Ligand excluded by PLIP TL.42: 4 residues within 4Å: Chain H: T.29, K.50, T.89 Ligands: AGS.40 Ligand excluded by PLIP TL.43: 5 residues within 4Å: Chain H: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.45: 4 residues within 4Å: Chain H: N.111, D.114 Chain N: C.457, E.482 Ligand excluded by PLIP TL.47: 3 residues within 4Å: Chain I: S.216, F.218, Q.318 Ligand excluded by PLIP TL.48: 4 residues within 4Å: Chain I: C.457, E.482 Chain J: N.111, D.114 Ligand excluded by PLIP TL.49: 5 residues within 4Å: Chain I: T.29, K.50, G.52, T.89 Ligands: AGS.46 Ligand excluded by PLIP TL.52: 4 residues within 4Å: Chain J: S.216, F.218, K.244, Q.318 Ligand excluded by PLIP TL.53: 4 residues within 4Å: Chain J: C.457, E.482 Chain K: N.111, D.114 Ligand excluded by PLIP TL.54: 5 residues within 4Å: Chain J: T.29, K.50, G.52, T.89 Ligands: AGS.51 Ligand excluded by PLIP TL.57: 4 residues within 4Å: Chain K: C.457, E.482 Chain L: N.111, D.114 Ligand excluded by PLIP TL.58: 5 residues within 4Å: Chain K: T.29, K.50, G.52, T.89 Ligands: AGS.56 Ligand excluded by PLIP TL.59: 5 residues within 4Å: Chain K: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.62: 4 residues within 4Å: Chain L: S.216, P.217, F.218, Q.318 Ligand excluded by PLIP TL.63: 5 residues within 4Å: Chain L: K.33, C.457, E.482 Chain M: N.111, D.114 Ligand excluded by PLIP TL.64: 4 residues within 4Å: Chain L: T.29, K.50, T.89 Ligands: AGS.61 Ligand excluded by PLIP TL.67: 4 residues within 4Å: Chain M: C.457, E.459, E.482 Chain N: N.111 Ligand excluded by PLIP TL.68: 4 residues within 4Å: Chain M: T.29, K.50, T.89 Ligands: AGS.66 Ligand excluded by PLIP TL.69: 5 residues within 4Å: Chain M: S.216, P.217, F.218, K.244, Q.318 Ligand excluded by PLIP TL.72: 4 residues within 4Å: Chain N: T.29, K.50, T.89 Ligands: AGS.71 Ligand excluded by PLIP TL.73: 4 residues within 4Å: Chain N: S.216, P.217, F.218, Q.318 Ligand excluded by PLIP

14 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.86, G.87 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.22: 2 residues within 4Å: Chain D: D.86 Ligands: AGS.18 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86 MG.28: 2 residues within 4Å: Chain E: D.86 Ligands: AGS.24 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.86 MG.33: 2 residues within 4Å: Chain F: D.86 Ligands: AGS.29 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.86 MG.39: 2 residues within 4Å: Chain G: D.86 Ligands: AGS.35 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86 MG.44: 2 residues within 4Å: Chain H: D.86 Ligands: AGS.40 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.86 MG.50: 2 residues within 4Å: Chain I: D.86 Ligands: AGS.46 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.86 MG.55: 2 residues within 4Å: Chain J: D.86 Ligands: AGS.51 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.86 MG.60: 2 residues within 4Å: Chain K: D.86 Ligands: AGS.56 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.86 MG.65: 2 residues within 4Å: Chain L: D.86 Ligands: AGS.61 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.86 MG.70: 2 residues within 4Å: Chain M: D.86 Ligands: AGS.66 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.86 MG.74: 2 residues within 4Å: Chain N: D.86 Ligands: AGS.71 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiser, P.D. et al., Use of thallium to identify monovalent cation binding sites in GroEL. Acta Crystallogr.,Sect.F (2009)

Release Date

2009-08-25

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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