SMTL ID : 9hra.2 (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: 7 residues within 4Å: Chain A: R.154, E.184, N.206, T.208, R.237 Chain D: R.266 Ligands: PYR.2 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A Salt bridges: D:R.266, A:R.154, A:R.237 Hydrophobic interactions: A:T.208 Hydrogen bonds: A:T.208 SIN.14: 8 residues within 4Å: Chain B: R.154, E.184, N.206, T.208, P.232 Chain C: R.266 Ligands: PYR.15, EDO.16 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.184 Salt bridges: B:R.154, B:R.237, C:R.266 SIN.22: 8 residues within 4Å: Chain B: R.266 Chain C: R.154, E.184, N.206, T.208, R.233, R.237 Ligands: PYR.23 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.206 Water bridges: C:R.233, C:R.233 Salt bridges: C:K.126, C:R.154, C:R.233, C:R.237, B:R.266 SIN.31: 8 residues within 4Å: Chain A: R.266 Chain D: R.154, E.184, N.206, T.208, P.232, R.237 Ligands: PYR.32 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:T.208 Water bridges: D:R.237, A:R.266 Salt bridges: D:R.154, D:R.237, A:R.266

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 9 residues within 4Å: Chain A: Y.42, S.44, G.45, G.46, D.83, R.154, P.232 Ligands: SIN.1, MG.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.232 Hydrogen bonds: A:G.45, A:G.46, A:D.56, A:R.154 PYR.15: 10 residues within 4Å: Chain B: Y.42, S.44, G.45, G.46, D.83, H.110, R.154, P.232 Ligands: SIN.14, MG.19 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.232 Hydrogen bonds: B:Y.42, B:G.45, B:G.46, B:R.154 PYR.23: 11 residues within 4Å: Chain C: Y.42, S.44, G.45, G.46, D.83, H.110, R.154, N.206, P.232 Ligands: SIN.22, MG.28 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:P.232 Hydrogen bonds: C:Y.42, C:G.45, C:G.46, C:R.154 Water bridges: C:D.56, C:D.56, C:D.56, C:D.83 PYR.32: 11 residues within 4Å: Chain D: Y.42, S.44, G.45, G.46, D.56, D.83, H.110, R.154, P.232 Ligands: SIN.31, MG.37 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:P.232 Hydrogen bonds: D:Y.42, D:G.45, D:G.46, D:R.154 Water bridges: D:G.45, D:D.56

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

EDO.3: 2 residues within 4Å: Chain A: V.174, E.175 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: D.56, D.85, E.112, Q.114 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.56, A:D.56, A:D.85, A:D.85, A:E.112 EDO.6: 3 residues within 4Å: Chain A: E.102, Q.105 Chain B: Q.105 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.105, A:Q.105 EDO.7: 4 residues within 4Å: Chain A: T.257 Chain D: L.215, Y.216, T.217 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.220 EDO.16: 8 residues within 4Å: Chain B: N.50, P.55, D.56, R.233 Chain C: Y.270, L.273, Y.275 Ligands: SIN.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.50, B:N.50, B:D.56, B:R.233 EDO.17: 5 residues within 4Å: Chain B: D.56, G.58, D.85, E.112 Ligands: MG.19 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.112 Water bridges: B:D.56, B:D.56, B:D.56, B:D.85, B:D.85, B:E.112 EDO.18: 4 residues within 4Å: Chain B: N.35, A.268, E.271 Chain C: L.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.271 Water bridges: B:Q.264 EDO.25: 7 residues within 4Å: Chain A: L.57, G.58, Q.117 Chain C: G.90, A.91, F.92, T.93 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.90, C:A.91, C:F.92, C:T.93, A:G.58, A:Q.117 EDO.26: 4 residues within 4Å: Chain C: K.126, E.127, L.128, V.160 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.126, C:L.128 EDO.27: 4 residues within 4Å: Chain C: D.56, L.57, G.58, E.112 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.56 Water bridges: C:D.85 EDO.34: 1 residues within 4Å: Chain D: R.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.10 EDO.35: 5 residues within 4Å: Chain D: D.56, D.85, E.112, Q.114, Q.117 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.56, D:Q.114, D:V.115 Water bridges: D:D.85 EDO.36: 2 residues within 4Å: Chain D: H.17, K.227 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.17

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

PGE.4: 4 residues within 4Å: Chain A: A.219, Q.220, D.223, H.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.220, A:D.223, A:H.224

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: D.83, D.85 Ligands: PYR.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.83, H2O.1, H2O.1, H2O.1 MG.19: 7 residues within 4Å: Chain B: G.45, G.46, D.56, D.83, D.85 Ligands: PYR.15, EDO.17 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.83, H2O.4, H2O.4, H2O.4 MG.28: 3 residues within 4Å: Chain C: D.83, D.85 Ligands: PYR.23 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.83, H2O.6, H2O.7, H2O.7 MG.37: 3 residues within 4Å: Chain D: D.83, D.85 Ligands: PYR.32 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.83, H2O.9, H2O.9, H2O.10

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

CL.9: 4 residues within 4Å: Chain A: N.50, D.56 Chain D: Y.270, Y.275 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: Y.270, Y.275 Chain D: D.56 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: D.223 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: L.54 Chain D: A.74 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: Y.270, Y.275 Chain C: N.50, D.56 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: A.74 Chain C: L.52, L.54 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain C: C.171 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: L.54 Chain C: A.74 Ligand excluded by PLIP CL.38: 1 residues within 4Å: Chain D: K.200 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain A: A.74 Chain D: L.54 Ligand excluded by PLIP

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

PEG.24: 2 residues within 4Å: Chain C: T.194, A.198 No protein-ligand interaction detected (PLIP) PEG.33: 3 residues within 4Å: Chain D: A.245, A.258, F.262 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
G

B
I

C
J

D
L

2-methylisocitrate lyase

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