SMTL ID : 9hra.1 (1 other biounit)

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Products Succinic and Pyruvic Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-tetramer

Ligands

4 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 8 residues within 4Å: Chain A: R.154, E.184, N.206, T.208, R.233, R.237 Chain D: R.266 Ligands: PYR.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.208 Salt bridges: A:R.154, A:R.237, D:R.266 SIN.9: 7 residues within 4Å: Chain B: R.154, E.184, N.206, T.208, R.237 Chain C: R.266 Ligands: PYR.10 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.208 Hydrogen bonds: B:T.208, B:R.237 Water bridges: B:R.233 Salt bridges: B:R.154, C:R.266 SIN.19: 9 residues within 4Å: Chain B: R.266 Chain C: D.56, R.154, E.184, N.206, T.208, P.232, R.237 Ligands: PYR.20 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:T.208 Hydrogen bonds: C:D.56, C:E.184 Water bridges: C:R.237, B:R.266 Salt bridges: C:R.154, C:R.237, B:R.266 SIN.27: 7 residues within 4Å: Chain A: R.266 Chain D: R.154, E.184, N.206, T.208, R.237 Ligands: PYR.28 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:T.208 Hydrogen bonds: D:T.208, D:R.237 Water bridges: D:R.154, D:R.154, D:R.233 Salt bridges: D:R.154, A:R.266

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 12 residues within 4Å: Chain A: Y.42, S.44, G.45, G.46, D.56, D.83, H.110, R.154, L.230, P.232 Ligands: SIN.1, MG.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.230, A:P.232 Hydrogen bonds: A:G.45, A:G.46, A:R.154 PYR.10: 11 residues within 4Å: Chain B: Y.42, S.44, G.45, G.46, D.56, D.83, H.110, R.154, P.232 Ligands: SIN.9, MG.15 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.232 Hydrogen bonds: B:G.45, B:G.46, B:D.56, B:R.154 Water bridges: B:S.44, B:G.47 PYR.20: 11 residues within 4Å: Chain C: Y.42, S.44, G.45, G.46, D.83, R.154, F.182, N.206, P.232 Ligands: SIN.19, MG.22 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.182, C:P.232 Hydrogen bonds: C:Y.42, C:G.45, C:G.46, C:R.154 PYR.28: 10 residues within 4Å: Chain D: Y.42, S.44, G.45, G.46, D.83, H.110, R.154, P.232 Ligands: SIN.27, MG.33 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.232 Hydrogen bonds: D:G.45, D:G.46, D:D.83, D:D.83, D:R.154 Water bridges: D:D.85

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

EDO.3: 6 residues within 4Å: Chain A: E.16, P.18, L.19, Q.20, F.38, K.39 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.16, A:Q.20, A:K.39 EDO.4: 3 residues within 4Å: Chain A: E.102, Q.105 Chain B: Q.105 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.105, A:Q.105 Hydrogen bonds: B:Q.105 EDO.5: 5 residues within 4Å: Chain A: D.56, L.57, G.58, D.85, E.112 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.56, A:D.56, A:D.85, A:E.112 EDO.12: 2 residues within 4Å: Chain B: S.146, N.147 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.147, B:N.147 Water bridges: B:S.146, B:D.148 EDO.13: 3 residues within 4Å: Chain B: D.56, E.112, Q.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.56 EDO.14: 4 residues within 4Å: Chain B: F.210, T.213, P.214, L.215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.210, B:T.213, B:L.215 Water bridges: B:G.211 EDO.21: 4 residues within 4Å: Chain B: A.218, A.219 Chain C: K.252, G.254 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.219 EDO.29: 3 residues within 4Å: Chain D: K.252, H.253, G.254 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.254 EDO.30: 3 residues within 4Å: Chain D: H.17, A.222, K.227 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.227 EDO.31: 1 residues within 4Å: Chain D: F.262 No protein-ligand interaction detected (PLIP) EDO.32: 5 residues within 4Å: Chain D: G.58, E.112, Q.114, V.115, Q.117 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.117

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: D.83, D.85 Ligands: PYR.2 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.83, H2O.1, H2O.1, H2O.1, PYR.2 MG.15: 6 residues within 4Å: Chain B: G.45, G.46, D.56, D.83, D.85 Ligands: PYR.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.83, H2O.3, H2O.3, H2O.3 MG.22: 5 residues within 4Å: Chain C: G.46, D.56, D.83, D.85 Ligands: PYR.20 5 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:D.83, H2O.6, H2O.6, H2O.6, PYR.20 MG.33: 3 residues within 4Å: Chain D: D.83, D.85 Ligands: PYR.28 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.83, H2O.8, H2O.8, H2O.8

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

CL.7: 4 residues within 4Å: Chain A: Y.270, Y.275 Chain D: N.50, D.56 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: N.50, D.56 Chain C: Y.275 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: C.171 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: L.52, G.53, L.54 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain B: Y.270, Y.275 Chain C: N.50, P.55, D.56 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain C: C.171, A.198 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: A.74 Chain C: L.54 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain A: N.50, D.56 Chain D: Y.270, Y.275 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain D: V.174 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain A: L.54 Chain D: A.74 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain D: L.54 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 3 residues within 4Å: Chain B: G.177, A.178, D.179 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.179 DMS.26: 2 residues within 4Å: Chain D: L.215, Q.220 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.220

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
D

D
F

2-methylisocitrate lyase

Related Entries With Identical Sequence