SMTL ID : 9hgk.1

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 8 residues within 4Å: Chain A: Y.62, S.64, G.65, G.66, D.76, D.103, D.105, R.174 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.62 Hydrogen bonds: A:G.66, A:D.105 Water bridges: A:S.64, A:R.174, A:R.174 Salt bridges: A:R.174 EPE.6: 10 residues within 4Å: Chain B: Y.62, S.64, G.65, G.66, D.76, D.103, D.105, R.174, P.252 Ligands: PEG.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.62, B:P.252 Hydrogen bonds: B:G.66, B:D.103 Water bridges: B:R.174, B:R.174 Salt bridges: B:R.174 EPE.10: 8 residues within 4Å: Chain C: Y.62, S.64, G.65, G.66, D.76, D.103, D.105, R.174 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.62 Hydrogen bonds: C:G.66, C:D.105 Water bridges: C:S.64, C:R.174, C:R.174 Salt bridges: C:R.174 EPE.15: 10 residues within 4Å: Chain D: Y.62, S.64, G.65, G.66, D.76, D.103, D.105, R.174, P.252 Ligands: PEG.4 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.62, D:P.252 Hydrogen bonds: D:G.66, D:D.103 Water bridges: D:R.174, D:R.174 Salt bridges: D:R.174

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: L.77 Chain C: G.110, A.111, F.112, T.113 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.110, C:F.112, C:T.113, C:T.113, C:T.113 Water bridges: C:A.111 EDO.3: 5 residues within 4Å: Chain A: L.51, E.54, A.95, T.96, H.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.97 EDO.7: 6 residues within 4Å: Chain B: Y.290, L.293, Y.295 Chain C: N.70, P.75, D.76 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.70, C:N.70, C:D.76 EDO.8: 1 residues within 4Å: Chain B: A.297 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.297 EDO.9: 6 residues within 4Å: Chain A: H.83 Chain B: E.87, R.91 Chain C: L.72, D.84, E.87 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 interactions with chain B Water bridges: A:R.116 Hydrogen bonds: C:D.84, B:E.87, B:E.87, B:R.91 EDO.11: 5 residues within 4Å: Chain A: G.110, A.111, F.112, T.113 Chain C: L.77 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.110, A:F.112, A:T.113, A:T.113 Water bridges: A:A.111 EDO.12: 5 residues within 4Å: Chain C: L.51, E.54, A.95, T.96, H.97 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.96, C:H.97 EDO.16: 6 residues within 4Å: Chain A: N.70, P.75, D.76 Chain D: Y.290, L.293, Y.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.70, A:N.70, A:D.76 EDO.17: 1 residues within 4Å: Chain D: A.297 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.297 EDO.18: 6 residues within 4Å: Chain A: L.72, D.84, E.87 Chain C: H.83 Chain D: E.87, R.91 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:E.87, D:R.91, A:D.84, A:D.84 Water bridges: C:R.116

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

PEG.4: 8 residues within 4Å: Chain A: Y.290, L.293, Y.295 Chain D: G.66, N.70, D.76, R.253 Ligands: EPE.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.64, D:D.76, D:R.253 Water bridges: D:R.257 PEG.13: 8 residues within 4Å: Chain B: G.66, N.70, D.76, R.253 Chain C: Y.290, L.293, Y.295 Ligands: EPE.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.64, B:D.76, B:D.76, B:R.253 Water bridges: B:R.257

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: T.15, N.17 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: T.15, N.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stuart, W.S. et al., Structure and catalytic mechanism of methylisocitrate lyase, a potential drug target against Coxiella burnetii. J.Biol.Chem. (2025)

Release Date

2025-08-13

Peptides

2-methylisocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-methylisocitrate lyase

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