SMTL ID : 9hhy.1 (2 other biounits)

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Inhibitor Isocitric Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

4 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.1: 18 residues within 4Å: Chain A: Y.62, S.64, G.65, G.66, D.103, C.140, G.141, H.142, R.174, E.204, N.226, T.228, P.252, R.253, R.257 Chain D: R.286 Ligands: MG.4, EDO.24 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:P.252 Hydrogen bonds: A:Y.62, A:G.65, A:G.66, A:G.141, A:R.174, A:N.226, A:T.228, A:T.228 Water bridges: A:S.64, A:G.67, A:D.76, A:R.257, D:R.286 Salt bridges: A:R.174, A:R.257, D:R.286 ICT.6: 16 residues within 4Å: Chain B: Y.62, S.64, G.65, G.66, D.103, C.140, G.141, H.142, R.174, E.204, N.226, T.228, P.252, R.257 Chain C: R.286 Ligands: MG.11 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.252 Hydrogen bonds: B:Y.62, B:Y.62, B:G.65, B:G.66, B:G.141, B:R.174, B:E.204, B:N.226, B:T.228 Water bridges: B:S.64, B:S.64 Salt bridges: B:R.174, B:R.257, C:R.286 ICT.13: 17 residues within 4Å: Chain B: R.286 Chain C: Y.62, S.64, G.65, G.66, D.103, C.140, G.141, H.142, R.174, E.204, N.226, T.228, P.252, R.253, R.257 Ligands: MG.15 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.62, C:Y.62, C:G.65, C:G.66, C:G.141, C:R.174, C:E.204, C:N.226, C:T.228 Salt bridges: C:R.174, C:R.257, B:R.286 ICT.18: 17 residues within 4Å: Chain A: R.286 Chain D: Y.62, S.64, G.65, G.66, D.103, C.140, G.141, H.142, R.174, E.204, N.226, T.228, P.252, R.253, R.257 Ligands: MG.25 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:P.252 Hydrogen bonds: D:Y.62, D:G.65, D:G.66, D:G.141, D:R.174, D:N.226, D:T.228, D:T.228 Water bridges: D:S.64, D:S.64, D:R.174, D:R.257, D:R.257 Salt bridges: D:R.174, D:R.257, A:R.286

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

EDO.2: 3 residues within 4Å: Chain A: Y.298, K.301 Chain B: F.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.301 EDO.3: 4 residues within 4Å: Chain A: E.122, Q.125 Chain B: Q.125 Ligands: EDO.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.125, A:Q.125 EDO.7: 4 residues within 4Å: Chain A: Q.125 Chain B: E.122, Q.125 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.125, B:Q.125 EDO.8: 2 residues within 4Å: Chain B: E.195, A.196 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain B: P.213, D.243, H.244 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain B: K.272, G.274 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.272 EDO.14: 3 residues within 4Å: Chain C: A.297, D.300, K.301 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain C: E.122, Q.125 Chain D: Q.125 Ligands: EDO.20 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.125, D:Q.125 EDO.19: 4 residues within 4Å: Chain C: L.305 Chain D: A.111, D.156, R.157 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.111 EDO.20: 4 residues within 4Å: Chain C: Q.125 Chain D: E.122, Q.125 Ligands: EDO.17 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.125, D:S.166, D:S.166, C:Q.125, C:Q.125 EDO.21: 4 residues within 4Å: Chain D: A.34, N.35, E.36, H.37 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.35 EDO.22: 4 residues within 4Å: Chain D: G.231, K.232, T.233, P.234 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.232 EDO.23: 4 residues within 4Å: Chain D: E.287, Y.290, E.291, H.296 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.287, D:E.291 EDO.24: 6 residues within 4Å: Chain A: N.70, D.76, C.140 Chain D: Y.290, Y.295 Ligands: ICT.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.70, A:D.76, A:D.76, D:R.286, D:Y.290 Water bridges: A:R.253

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: G.65, G.66, D.103, D.105, K.138 Ligands: ICT.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.103, H2O.1, H2O.2, H2O.2 MG.11: 4 residues within 4Å: Chain B: D.103, D.105, K.138 Ligands: ICT.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.103, H2O.5, H2O.5, H2O.6 MG.15: 5 residues within 4Å: Chain C: G.66, D.103, D.105, K.138 Ligands: ICT.13 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.103, H2O.8, H2O.8, H2O.9 MG.25: 5 residues within 4Å: Chain D: G.66, D.103, D.105, K.138 Ligands: ICT.18 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.103, H2O.11, H2O.12, H2O.12

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

CL.5: 2 residues within 4Å: Chain A: A.94, H.97 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: A.94, H.97 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: A.94, A.95, H.97 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain D: A.94 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
C

D
D

2-methylisocitrate lyase

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