SMTL ID : 9hhy.2 (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: 17 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.3 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:P.252 Hydrogen bonds: A:Y.62, A:Y.62, A:G.65, A:G.66, A:G.141, A:R.174, A:N.226, A:T.228 Water bridges: A:G.67, A:D.76, A:R.174 Salt bridges: A:H.142, A:R.174, A:R.257, D:R.286 ICT.5: 17 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.253, R.257 Chain C: R.286 Ligands: MG.9 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.62, B:G.65, B:G.66, B:G.141, B:R.174, B:N.226, B:T.228 Water bridges: B:E.132, B:K.138, C:R.286 Salt bridges: B:R.174, B:R.257, C:R.286 ICT.11: 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.17 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.252 Hydrogen bonds: C:Y.62, C:G.65, C:G.66, C:D.103, C:D.103, C:G.141, C:R.174, C:N.226, C:T.228, C:T.228, C:R.253 Salt bridges: C:R.174, C:R.257, B:R.286 ICT.19: 18 residues within 4Å: Chain A: R.286 Chain D: Y.62, S.64, G.65, G.66, D.76, D.103, C.140, G.141, H.142, R.174, E.204, N.226, T.228, P.252, R.253, R.257 Ligands: MG.21 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.62, D:Y.62, D:G.65, D:G.66, D:G.141, D:R.174, D:N.226, D:T.228 Salt bridges: D:H.142, D:R.174, D:R.253, D:R.257, A:R.286

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

PEG.2: 4 residues within 4Å: Chain A: D.156, K.159, A.160 Chain B: R.308 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.160

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: 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.1, H2O.1 MG.9: 6 residues within 4Å: Chain B: G.65, G.66, D.103, D.105, K.138 Ligands: ICT.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.103, H2O.1, H2O.2, H2O.2 MG.17: 5 residues within 4Å: Chain C: G.66, D.103, D.105, K.138 Ligands: ICT.11 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.103, H2O.4, H2O.4, H2O.5 MG.21: 4 residues within 4Å: Chain D: D.103, D.105, K.138 Ligands: ICT.19 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.103, H2O.5, H2O.5, H2O.6

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

CL.4: 2 residues within 4Å: Chain A: A.94, H.97 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: A.94, A.95, H.97 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: A.94, A.95, T.96, H.97 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: A.94, H.97 Ligand excluded by PLIP

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

EDO.6: 2 residues within 4Å: Chain B: V.194, A.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.194 EDO.7: 3 residues within 4Å: Chain B: P.213, D.243, H.244 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain B: K.271, K.272, H.273, G.274 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.272, C:A.239 EDO.12: 3 residues within 4Å: Chain C: V.194, G.197, A.198 No protein-ligand interaction detected (PLIP) EDO.13: 3 residues within 4Å: Chain C: P.213, D.243, H.244 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain C: A.297, Y.298, K.301 Chain D: F.112 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain C: Q.125 Chain D: E.122, Q.125 Ligands: EDO.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.125, C:Q.125 EDO.16: 4 residues within 4Å: Chain C: E.122, Q.125 Chain D: Q.125 Ligands: EDO.15 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.125, D:Q.125 EDO.20: 2 residues within 4Å: Chain D: A.265, F.282 No protein-ligand interaction detected (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
E

B
F

C
H

D
K

2-methylisocitrate lyase

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