SMTL ID : 1xck.3 (2 other biounits)

Crystal structure of apo GroEL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-14-mer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: K.310, D.315 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: G.296, G.297, T.298 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: A.142, Q.145, V.410 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.444, E.447, R.451 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: E.101, R.444 Chain L: A.108 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: V.189, E.190, A.372 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: D.427, R.429 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: E.129, A.132 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: R.451, P.461 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain C: A.142, Q.145 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: D.427, R.429 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: E.101, V.437, R.444 Chain K: A.108 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: R.444, E.447, R.451 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain D: E.101, V.437, V.441, R.444 Chain J: A.108 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain D: A.142, Q.145 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: K.131, A.132, S.134 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain D: Q.504, Y.505 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain D: R.444, E.447, R.451 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain E: R.429, G.430, N.436 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain E: R.444, E.447, R.451 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain F: V.189, E.190, A.372 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain F: R.444, E.447, R.451 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain G: V.188, E.190, A.372 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain G: K.310, D.315 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain G: R.444, E.447, R.451 Ligand excluded by PLIP SO4.52: 5 residues within 4Å: Chain H: V.188, E.190, A.372, G.373, G.374 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain H: V.135, A.142, Q.145, V.146 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain H: R.444, E.447, R.451 Ligand excluded by PLIP SO4.58: 5 residues within 4Å: Chain I: V.135, A.142, Q.145, V.146, I.488 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain I: R.444, E.447, R.451 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain D: A.108 Chain J: E.101, M.110, R.444 Ligand excluded by PLIP SO4.65: 6 residues within 4Å: Chain J: V.135, A.142, Q.145, V.146, V.410, I.488 Ligand excluded by PLIP SO4.66: 5 residues within 4Å: Chain J: D.40, K.41, S.42 Chain K: K.64, N.67 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain J: R.444, E.447, R.451 Ligand excluded by PLIP SO4.70: 4 residues within 4Å: Chain C: A.108 Chain K: E.101, M.110, R.444 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain K: R.444, E.447, R.451 Ligand excluded by PLIP SO4.75: 3 residues within 4Å: Chain L: P.136, Q.145, I.488 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain L: D.489, M.490, G.491 Ligand excluded by PLIP SO4.79: 6 residues within 4Å: Chain M: V.135, P.136, A.142, Q.145, V.146, I.488 Ligand excluded by PLIP SO4.80: 3 residues within 4Å: Chain M: G.109, N.111, D.434 Ligand excluded by PLIP SO4.81: 5 residues within 4Å: Chain A: A.108 Chain M: E.101, M.110, V.437, R.444 Ligand excluded by PLIP SO4.84: 5 residues within 4Å: Chain N: V.188, V.189, E.190, A.372, G.374 Ligand excluded by PLIP SO4.85: 2 residues within 4Å: Chain N: R.444, R.451 Ligand excluded by PLIP

14 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain A: T.29, G.31, K.50 No protein-ligand interaction detected (PLIP) K.13: 3 residues within 4Å: Chain B: T.29, G.31, K.50 No protein-ligand interaction detected (PLIP) K.22: 2 residues within 4Å: Chain C: T.29, G.31 No protein-ligand interaction detected (PLIP) K.29: 3 residues within 4Å: Chain D: T.29, L.30, G.31 No protein-ligand interaction detected (PLIP) K.33: 3 residues within 4Å: Chain E: T.29, G.31, K.50 No protein-ligand interaction detected (PLIP) K.42: 2 residues within 4Å: Chain F: T.29, G.31 No protein-ligand interaction detected (PLIP) K.49: 2 residues within 4Å: Chain G: T.29, G.31 No protein-ligand interaction detected (PLIP) K.55: 2 residues within 4Å: Chain H: T.29, G.31 No protein-ligand interaction detected (PLIP) K.60: 1 residues within 4Å: Chain I: T.29 No protein-ligand interaction detected (PLIP) K.68: 3 residues within 4Å: Chain J: T.29, L.30, G.31 No protein-ligand interaction detected (PLIP) K.72: 2 residues within 4Å: Chain K: T.29, G.31 No protein-ligand interaction detected (PLIP) K.77: 2 residues within 4Å: Chain L: T.29, G.31 No protein-ligand interaction detected (PLIP) K.82: 3 residues within 4Å: Chain M: T.29, L.30, G.31 No protein-ligand interaction detected (PLIP) K.86: 2 residues within 4Å: Chain N: T.29, G.31 No protein-ligand interaction detected (PLIP)

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

MPD.6: 4 residues within 4Å: Chain A: R.500, Q.504, Y.505, S.508 Ligand excluded by PLIP MPD.7: 4 residues within 4Å: Chain A: R.35, L.455, N.456 Chain B: E.517 Ligand excluded by PLIP MPD.14: 7 residues within 4Å: Chain B: N.9, V.13, L.16, T.100, L.103, K.104, A.107 Ligand excluded by PLIP MPD.15: 5 residues within 4Å: Chain B: V.28, Q.452, L.455, N.456 Chain C: E.517 Ligand excluded by PLIP MPD.16: 3 residues within 4Å: Chain B: Q.504, Y.505, S.508 Ligand excluded by PLIP MPD.17: 5 residues within 4Å: Chain B: V.135, A.142, Q.145, V.146, I.488 Ligand excluded by PLIP MPD.23: 6 residues within 4Å: Chain C: V.28, R.35, Q.452, L.455, N.456 Chain D: E.517 Ligand excluded by PLIP MPD.30: 5 residues within 4Å: Chain D: G.296, L.313, E.314, L.316, Q.318 Ligand excluded by PLIP MPD.34: 6 residues within 4Å: Chain E: V.188, E.190, E.338, A.372, G.373, G.374 Ligand excluded by PLIP MPD.35: 6 residues within 4Å: Chain E: V.135, P.136, A.142, Q.145, I.488, L.493 Ligand excluded by PLIP MPD.36: 5 residues within 4Å: Chain D: R.35, Q.452, L.455, N.456 Chain E: E.517 Ligand excluded by PLIP MPD.37: 3 residues within 4Å: Chain E: D.166, K.167, G.169 Ligand excluded by PLIP MPD.38: 4 residues within 4Å: Chain E: Q.452, L.455, N.456 Chain F: E.517 Ligand excluded by PLIP MPD.43: 4 residues within 4Å: Chain F: P.136, A.142, Q.145, I.488 Ligand excluded by PLIP MPD.44: 5 residues within 4Å: Chain F: R.35, Q.452, L.455, N.456 Chain G: E.517 Ligand excluded by PLIP MPD.45: 5 residues within 4Å: Chain F: N.9, V.13, T.100, L.103, K.104 Ligand excluded by PLIP MPD.50: 6 residues within 4Å: Chain G: P.136, A.142, Q.145, V.146, I.149, I.488 Ligand excluded by PLIP MPD.51: 3 residues within 4Å: Chain A: E.517 Chain G: R.35, N.456 Ligand excluded by PLIP MPD.56: 6 residues within 4Å: Chain H: V.28, R.35, Q.452, L.455, N.456 Chain I: E.517 Ligand excluded by PLIP MPD.57: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP MPD.61: 2 residues within 4Å: Chain I: Q.504, Y.505 Ligand excluded by PLIP MPD.62: 4 residues within 4Å: Chain I: V.189, E.190, Q.342, A.372 Ligand excluded by PLIP MPD.63: 6 residues within 4Å: Chain I: V.28, R.35, Q.452, L.455, N.456 Chain J: E.517 Ligand excluded by PLIP MPD.69: 5 residues within 4Å: Chain J: V.28, R.35, L.455, N.456 Chain K: E.517 Ligand excluded by PLIP MPD.73: 5 residues within 4Å: Chain K: V.28, Q.452, L.455, N.456 Chain L: E.517 Ligand excluded by PLIP MPD.74: 2 residues within 4Å: Chain K: E.459, E.482 Ligand excluded by PLIP MPD.78: 5 residues within 4Å: Chain L: R.35, Q.452, L.455, N.456 Chain M: E.517 Ligand excluded by PLIP MPD.83: 5 residues within 4Å: Chain M: V.28, Q.452, L.455, N.456 Chain N: E.517 Ligand excluded by PLIP MPD.87: 6 residues within 4Å: Chain G: A.108 Chain N: E.101, K.104, V.437, V.441, R.444 Ligand excluded by PLIP MPD.88: 5 residues within 4Å: Chain H: E.517 Chain N: V.28, R.35, L.455, N.456 Ligand excluded by PLIP MPD.89: 3 residues within 4Å: Chain H: F.7 Chain N: R.17, D.24 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.39: 5 residues within 4Å: Chain E: E.101, R.444 Chain I: A.108, G.109, D.434 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain E Hydrogen bonds: I:D.434, E:R.444, E:R.444

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: 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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