SMTL ID : 9wbt.1

Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue-3.2A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-14-mer

Ligands

23 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.1: 5 residues within 4Å: Chain A: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.2: 7 residues within 4Å: Chain A: N.82, D.83, A.84, A.85, G.86, N.326, H.401 Ligand excluded by PLIP HEZ.8: 6 residues within 4Å: Chain B: A.84, R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.9: 7 residues within 4Å: Chain A: E.386 Chain B: G.280, F.281, R.284, M.288, K.364, E.367 Ligand excluded by PLIP HEZ.14: 5 residues within 4Å: Chain C: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.15: 7 residues within 4Å: Chain C: K.34, C.458, G.459, E.460, E.483 Chain D: D.115, D.435 Ligand excluded by PLIP HEZ.20: 5 residues within 4Å: Chain D: A.84, R.501, S.502, Q.505, Y.506 Ligand excluded by PLIP HEZ.21: 8 residues within 4Å: Chain D: D.83, A.84, A.85, G.86, H.401, A.405, E.408, K.498 Ligand excluded by PLIP HEZ.25: 5 residues within 4Å: Chain E: K.498, R.501, S.502, Q.505, Y.506 Ligand excluded by PLIP HEZ.26: 8 residues within 4Å: Chain E: V.136, P.137, C.138, Q.146, I.150, V.411, I.489, D.490 Ligand excluded by PLIP HEZ.27: 8 residues within 4Å: Chain E: N.82, D.83, A.84, A.85, G.86, N.326, H.401, A.405 Ligand excluded by PLIP HEZ.33: 5 residues within 4Å: Chain F: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.34: 8 residues within 4Å: Chain F: P.137, C.138, A.143, Q.146, V.147, I.150, I.489, L.494 Ligand excluded by PLIP HEZ.38: 5 residues within 4Å: Chain G: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.44: 5 residues within 4Å: Chain H: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.45: 8 residues within 4Å: Chain H: K.34, C.458, G.459, E.460, E.483 Chain I: G.110, D.115, D.435 Ligand excluded by PLIP HEZ.50: 5 residues within 4Å: Chain I: A.84, R.501, S.502, Q.505, Y.506 Ligand excluded by PLIP HEZ.51: 6 residues within 4Å: Chain I: P.137, A.143, Q.146, I.489, D.490, L.494 Ligand excluded by PLIP HEZ.55: 5 residues within 4Å: Chain J: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.59: 5 residues within 4Å: Chain K: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.61: 5 residues within 4Å: Chain L: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.63: 5 residues within 4Å: Chain M: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP HEZ.65: 5 residues within 4Å: Chain N: R.501, S.502, Q.505, Y.506, S.509 Ligand excluded by PLIP

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: G.86, D.398 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.86, A:D.398, H2O.1, H2O.1 MG.22: 2 residues within 4Å: Chain D: G.86, D.398 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:G.86, H2O.1, H2O.1, H2O.1 MG.28: 3 residues within 4Å: Chain E: G.86, D.87, D.398 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:G.86, E:D.398, H2O.1 MG.35: 2 residues within 4Å: Chain F: G.86, D.398 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:G.86, F:D.398, H2O.2, H2O.2 MG.39: 2 residues within 4Å: Chain G: G.86, D.398 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:G.86, G:D.398, H2O.2, H2O.2 MG.46: 2 residues within 4Å: Chain H: G.86, D.398 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:G.86, H:D.398, H2O.2 MG.66: 2 residues within 4Å: Chain N: G.86, D.398 4 PLIP interactions: 2 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:G.86, N:D.398, H2O.2, H2O.2

35 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 3 residues within 4Å: Chain A: M.307, K.311, D.316 Ligand excluded by PLIP BME.5: 3 residues within 4Å: Chain A: Q.146, I.489, L.494 Ligand excluded by PLIP BME.6: 5 residues within 4Å: Chain A: V.29, R.36, Q.453, L.456, N.457 Ligand excluded by PLIP BME.7: 1 residues within 4Å: Chain A: D.25 Ligand excluded by PLIP BME.10: 6 residues within 4Å: Chain B: P.137, A.143, Q.146, V.147, V.411, I.489 Ligand excluded by PLIP BME.11: 2 residues within 4Å: Chain B: R.36, N.457 Ligand excluded by PLIP BME.12: 3 residues within 4Å: Chain B: M.307, K.311, D.316 Ligand excluded by PLIP BME.13: 4 residues within 4Å: Chain B: N.10, V.14, L.17, K.105 Ligand excluded by PLIP BME.16: 3 residues within 4Å: Chain C: K.132, A.133, S.135 Ligand excluded by PLIP BME.17: 3 residues within 4Å: Chain C: R.36, N.457 Chain D: E.518 Ligand excluded by PLIP BME.18: 4 residues within 4Å: Chain C: R.445, E.448, A.449, R.452 Ligand excluded by PLIP BME.19: 3 residues within 4Å: Chain C: A.126, E.129, E.130 Ligand excluded by PLIP BME.23: 6 residues within 4Å: Chain D: P.137, C.138, A.143, Q.146, V.147, V.411 Ligand excluded by PLIP BME.24: 4 residues within 4Å: Chain D: R.445, E.448, A.449, R.452 Ligand excluded by PLIP BME.29: 4 residues within 4Å: Chain E: V.189, V.190, E.191, A.373 Ligand excluded by PLIP BME.30: 5 residues within 4Å: Chain E: K.132, A.133, S.135, V.136, P.137 Ligand excluded by PLIP BME.31: 5 residues within 4Å: Chain E: V.29, R.36, Q.453, N.457 Chain F: E.518 Ligand excluded by PLIP BME.32: 5 residues within 4Å: Chain E: V.136, N.475, N.487, I.489, D.490 Ligand excluded by PLIP BME.36: 6 residues within 4Å: Chain F: V.29, R.36, Q.453, L.456, N.457 Chain G: E.518 Ligand excluded by PLIP BME.40: 4 residues within 4Å: Chain G: P.137, Q.146, V.147, I.489 Ligand excluded by PLIP BME.41: 4 residues within 4Å: Chain A: E.518 Chain G: V.29, R.36, N.457 Ligand excluded by PLIP BME.42: 3 residues within 4Å: Chain G: N.82, D.83, H.401 Ligand excluded by PLIP BME.43: 6 residues within 4Å: Chain G: R.421, S.424, K.425, K.470, G.472, D.473 Ligand excluded by PLIP BME.47: 4 residues within 4Å: Chain H: V.29, R.36, Q.453, N.457 Ligand excluded by PLIP BME.48: 3 residues within 4Å: Chain H: K.132, A.133, S.135 Ligand excluded by PLIP BME.52: 4 residues within 4Å: Chain I: K.470, G.471, G.472, D.473 Ligand excluded by PLIP BME.53: 2 residues within 4Å: Chain I: D.25, K.28 Ligand excluded by PLIP BME.56: 1 residues within 4Å: Chain J: N.457 Ligand excluded by PLIP BME.57: 3 residues within 4Å: Chain J: E.102, K.441, R.445 Ligand excluded by PLIP BME.58: 7 residues within 4Å: Chain J: T.91, G.415, G.416, L.419, P.450, D.495, T.500 Ligand excluded by PLIP BME.60: 3 residues within 4Å: Chain K: V.29, N.457 Chain L: E.518 Ligand excluded by PLIP BME.62: 4 residues within 4Å: Chain L: V.29, R.36, N.457 Chain M: E.518 Ligand excluded by PLIP BME.64: 5 residues within 4Å: Chain M: V.29, R.36, Q.453, N.457 Chain N: E.518 Ligand excluded by PLIP BME.67: 2 residues within 4Å: Chain N: D.25, K.28 Ligand excluded by PLIP BME.68: 2 residues within 4Å: Chain N: R.36, N.457 Ligand excluded by PLIP

3 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.37: 5 residues within 4Å: Chain G: N.21, D.25, K.28, Q.97, T.101 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:T.101 Hydrogen bonds: G:D.25, G:K.28 TAM.49: 4 residues within 4Å: Chain I: V.29, R.36, N.457 Chain J: E.518 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:E.518, I:R.36 TAM.54: 8 residues within 4Å: Chain J: C.458, G.459, E.460, E.483 Chain K: N.112, D.115, N.433, D.435 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:D.115, J:G.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue. To Be Published

Release Date

2025-09-03

Peptides

Chaperonin GroEL: 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

Chaperonin GroEL

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