SMTL ID : 9hhy.3 (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.7 15 PLIP interactions: 14 interactions with chain A, 1 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:E.204, A:N.226, A:T.228 Water bridges: A:S.64, A:R.257, A:R.257 Salt bridges: A:R.174, A:R.257, D:R.286 ICT.9: 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.11 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.252 Hydrogen bonds: B:Y.62, B:G.65, B:G.66, B:G.141, B:R.174, B:E.204, B:N.226, B:T.228, B:T.228 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.76, D.103, C.140, G.141, H.142, R.174, E.204, N.226, T.228, P.252, R.257 Ligands: MG.16 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.252 Hydrogen bonds: C:Y.62, C:Y.62, C:G.65, C:G.66, C:D.76, C:G.141, C:R.174, C:N.226, C:T.228 Water bridges: C:D.76 Salt bridges: C:R.174, C:R.257, B:R.286 ICT.18: 14 residues within 4Å: Chain A: R.286 Chain D: Y.62, S.64, G.65, G.66, D.103, R.174, E.204, N.226, T.228, P.252, R.253, R.257 Ligands: MG.21 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:P.252 Hydrogen bonds: D:Y.62, D:Y.62, D:G.65, D:G.66, D:R.174, D:N.226, D:T.228, D:T.228 Water bridges: D:S.64, D:R.253, D:R.257 Salt bridges: D:R.174, D:R.257, A:R.286

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

EDO.2: 1 residues within 4Å: Chain A: F.282 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.265, A:S.279 EDO.3: 5 residues within 4Å: Chain A: E.122, R.123, Q.125 Chain B: Q.125 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.125 EDO.4: 3 residues within 4Å: Chain A: V.180, E.181, G.182 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: K.232, T.233, P.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.233 EDO.6: 4 residues within 4Å: Chain A: Q.125 Chain B: E.122, Q.125 Ligands: EDO.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.125, A:Q.125 Water bridges: B:R.123 EDO.10: 4 residues within 4Å: Chain B: E.299, L.302 Chain C: Q.137, R.139 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain C: V.194, A.198 No protein-ligand interaction detected (PLIP) EDO.19: 1 residues within 4Å: Chain D: N.210 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain D: P.213, D.243, H.244 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: 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.11: 6 residues within 4Å: Chain B: G.65, G.66, D.103, D.105, K.138 Ligands: ICT.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.103, H2O.3, H2O.3, H2O.4 MG.16: 6 residues within 4Å: Chain C: G.65, 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.6, H2O.7, H2O.8 MG.21: 4 residues within 4Å: Chain D: G.65, G.66, D.103 Ligands: ICT.18 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.103, H2O.10, H2O.11, H2O.11

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

CL.8: 4 residues within 4Å: Chain A: A.94, A.95, T.96, H.97 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: A.95, T.96, H.97 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: A.94, H.97 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: E.54, N.55 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain D: A.94, H.97 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.15: 4 residues within 4Å: Chain C: E.122, Q.125 Chain D: E.122, Q.125 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.125, D:Q.125

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
G

B
I

C
J

D
L

2-methylisocitrate lyase

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