SMTL ID : 1xck.2 (2 other biounits)

Crystal structure of apo GroEL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-heptamer

Ligands

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: V.188, E.190, A.372, G.373, G.374 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: V.135, A.142, Q.145, V.146 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: R.444, E.447, R.451 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain B: V.135, A.142, Q.145, V.146, I.488 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: R.444, E.447, R.451 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: E.101, M.110, R.444 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain C: V.135, A.142, Q.145, V.146, V.410, I.488 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain C: D.40, K.41, S.42 Chain D: K.64, N.67 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain C: R.444, E.447, R.451 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain D: E.101, M.110, R.444 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain D: R.444, E.447, R.451 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: P.136, Q.145, I.488 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain E: D.489, M.490, G.491 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain F: V.135, P.136, A.142, Q.145, V.146, I.488 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain F: G.109, N.111, D.434 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain F: E.101, M.110, V.437, R.444 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain G: V.188, V.189, E.190, A.372, G.374 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain G: R.444, R.451 Ligand excluded by PLIP

7 x K: POTASSIUM ION(Non-covalent)

K.4: 2 residues within 4Å: Chain A: T.29, G.31 No protein-ligand interaction detected (PLIP) K.9: 1 residues within 4Å: Chain B: T.29 No protein-ligand interaction detected (PLIP) K.17: 3 residues within 4Å: Chain C: T.29, L.30, G.31 No protein-ligand interaction detected (PLIP) K.21: 2 residues within 4Å: Chain D: T.29, G.31 No protein-ligand interaction detected (PLIP) K.26: 2 residues within 4Å: Chain E: T.29, G.31 No protein-ligand interaction detected (PLIP) K.31: 3 residues within 4Å: Chain F: T.29, L.30, G.31 No protein-ligand interaction detected (PLIP) K.35: 2 residues within 4Å: Chain G: T.29, G.31 No protein-ligand interaction detected (PLIP)

13 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 6 residues within 4Å: Chain A: V.28, R.35, Q.452, L.455, N.456 Chain B: E.517 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.35, A:L.455, B:E.517 MPD.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPD.10: 2 residues within 4Å: Chain B: Q.504, Y.505 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.505 MPD.11: 4 residues within 4Å: Chain B: V.189, E.190, Q.342, A.372 No protein-ligand interaction detected (PLIP) MPD.12: 6 residues within 4Å: Chain B: V.28, R.35, Q.452, L.455, N.456 Chain C: E.517 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:E.517, B:V.28, B:L.455 Hydrogen bonds: C:E.517, B:N.456 MPD.18: 5 residues within 4Å: Chain C: V.28, R.35, L.455, N.456 Chain D: E.517 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.28, C:L.455 Hydrogen bonds: C:R.35 MPD.22: 5 residues within 4Å: Chain D: V.28, Q.452, L.455, N.456 Chain E: E.517 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.28, D:L.455 MPD.23: 2 residues within 4Å: Chain D: E.459, E.482 No protein-ligand interaction detected (PLIP) MPD.27: 5 residues within 4Å: Chain E: R.35, Q.452, L.455, N.456 Chain F: E.517 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:E.517, E:L.455, E:L.455 Hydrogen bonds: F:E.517 MPD.32: 5 residues within 4Å: Chain F: V.28, Q.452, L.455, N.456 Chain G: E.517 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:V.28, F:L.455, F:L.455 MPD.36: 5 residues within 4Å: Chain G: E.101, K.104, V.437, V.441, R.444 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:K.104, G:V.437, G:V.441 MPD.37: 5 residues within 4Å: Chain A: E.517 Chain G: V.28, R.35, L.455, N.456 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:V.28, G:R.35, G:L.455, A:E.517 Hydrogen bonds: G:R.35, G:R.35 MPD.38: 3 residues within 4Å: Chain A: F.7 Chain G: R.17, D.24 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:D.24 Hydrophobic interactions: A:F.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bartolucci, C. et al., Crystal structure of wild-type chaperonin GroEL. J.Mol.Biol. (2005)

Release Date

2005-10-25

Peptides

60 kDa chaperonin: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

E
L

F
M

G
N

60 kDa chaperonin

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