SMTL ID : 9hgq.1

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Substrate 2-MIC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x MIC: ALPHA-METHYLISOCITRIC ACID(Non-covalent)

MIC.1: 15 residues within 4Å: Chain A: Y.62, S.64, G.65, G.66, D.76, D.103, R.174, E.204, N.226, T.228, P.252, R.253, R.257 Chain B: R.286 Ligands: MG.9 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.228, A:P.252, A:P.252 Hydrogen bonds: A:Y.62, A:G.65, A:G.66, A:D.76, A:R.174, A:R.174, A:N.226 Water bridges: A:S.64, A:D.103, A:E.132, A:R.253 Salt bridges: A:R.174, A:R.257, B:R.286 MIC.15: 16 residues within 4Å: Chain A: R.286 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 Ligands: MG.24 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.252, B:P.252 Hydrogen bonds: B:Y.62, B:Y.62, B:G.65, B:G.66, B:G.141, B:R.174, B:R.174, B:N.226 Water bridges: B:S.64, B:G.67, B:D.76, B:D.76, B:D.76, B:K.138, B:R.257, B:R.257 Salt bridges: B:R.174, B:R.257, A:R.286 MIC.28: 15 residues within 4Å: Chain C: Y.62, S.64, G.65, G.66, D.76, D.103, R.174, E.204, N.226, T.228, P.252, R.253, R.257 Chain D: R.286 Ligands: MG.36 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.228, C:P.252, C:P.252 Hydrogen bonds: C:G.65, C:G.66, C:D.76, C:D.103, C:R.174, C:R.174, C:N.226 Water bridges: C:S.64, C:D.103, C:E.132, C:R.253 Salt bridges: C:R.174, C:R.257, D:R.286 MIC.42: 16 residues within 4Å: Chain C: 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.257 Ligands: MG.51 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.252, D:P.252 Hydrogen bonds: D:Y.62, D:G.65, D:G.66, D:D.103, D:D.103, D:G.141, D:R.174, D:R.174, D:N.226, D:T.228 Water bridges: D:S.64, D:G.67, D:D.76, D:R.257, D:R.257 Salt bridges: D:R.174, D:R.257, C:R.286

20 x EOH: ETHANOL(Non-functional Binders)

EOH.2: 5 residues within 4Å: Chain A: G.110, A.111, F.112, T.113 Chain C: C.140 Ligand excluded by PLIP EOH.3: 3 residues within 4Å: Chain A: L.28, Q.31, A.32 Ligand excluded by PLIP EOH.5: 5 residues within 4Å: Chain A: F.112, A.115, R.116, K.119 Chain C: L.74 Ligand excluded by PLIP EOH.6: 4 residues within 4Å: Chain A: E.36, P.38, L.39, Q.40 Ligand excluded by PLIP EOH.7: 6 residues within 4Å: Chain A: G.78, I.79, T.80, F.108 Chain C: F.108, T.113 Ligand excluded by PLIP EOH.8: 8 residues within 4Å: Chain A: I.45, D.256, M.259, S.260 Chain B: N.46, Y.48, C.49, M.259 Ligand excluded by PLIP EOH.16: 5 residues within 4Å: Chain B: F.112, A.115, R.116, K.119 Chain C: Y.298 Ligand excluded by PLIP EOH.17: 2 residues within 4Å: Chain B: L.280, T.285 Ligand excluded by PLIP EOH.18: 3 residues within 4Å: Chain B: E.122 Chain C: Q.125 Ligands: EDO.19 Ligand excluded by PLIP EOH.20: 7 residues within 4Å: Chain B: G.78, I.79, T.80, D.81, F.108 Chain D: F.108 Ligands: EOH.47 Ligand excluded by PLIP EOH.29: 5 residues within 4Å: Chain A: C.140 Chain C: G.110, A.111, F.112, T.113 Ligand excluded by PLIP EOH.30: 3 residues within 4Å: Chain C: L.28, Q.31, A.32 Ligand excluded by PLIP EOH.32: 5 residues within 4Å: Chain A: L.74 Chain C: F.112, A.115, R.116, K.119 Ligand excluded by PLIP EOH.33: 4 residues within 4Å: Chain C: E.36, P.38, L.39, Q.40 Ligand excluded by PLIP EOH.34: 6 residues within 4Å: Chain A: F.108, T.113 Chain C: G.78, I.79, T.80, F.108 Ligand excluded by PLIP EOH.35: 8 residues within 4Å: Chain C: I.45, D.256, M.259, S.260 Chain D: N.46, Y.48, C.49, M.259 Ligand excluded by PLIP EOH.43: 5 residues within 4Å: Chain A: Y.298 Chain D: F.112, A.115, R.116, K.119 Ligand excluded by PLIP EOH.44: 2 residues within 4Å: Chain D: L.280, T.285 Ligand excluded by PLIP EOH.45: 3 residues within 4Å: Chain A: Q.125 Chain D: E.122 Ligands: EDO.46 Ligand excluded by PLIP EOH.47: 7 residues within 4Å: Chain B: F.108 Chain D: G.78, I.79, T.80, D.81, F.108 Ligands: EOH.20 Ligand excluded by PLIP

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

EDO.4: 3 residues within 4Å: Chain A: I.209, N.210, H.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.210, A:N.210 EDO.19: 4 residues within 4Å: Chain B: Q.125 Chain C: E.122, Q.125 Ligands: EOH.18 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.125, B:Q.125 EDO.21: 3 residues within 4Å: Chain B: F.230, T.233, L.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.230 Water bridges: B:G.231 EDO.22: 2 residues within 4Å: Chain B: P.281, F.282 No protein-ligand interaction detected (PLIP) EDO.23: 2 residues within 4Å: Chain B: A.265, F.282 No protein-ligand interaction detected (PLIP) EDO.31: 3 residues within 4Å: Chain C: I.209, N.210, H.244 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.210, C:N.210 EDO.46: 4 residues within 4Å: Chain A: E.122, Q.125 Chain D: Q.125 Ligands: EOH.45 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.125, A:Q.125 EDO.48: 3 residues within 4Å: Chain D: F.230, T.233, L.235 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.230 Water bridges: D:G.231 EDO.49: 2 residues within 4Å: Chain D: P.281, F.282 No protein-ligand interaction detected (PLIP) EDO.50: 2 residues within 4Å: Chain D: A.265, F.282 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 5 residues within 4Å: Chain A: G.65, G.66, D.103, D.105 Ligands: MIC.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.103, H2O.1, H2O.1, H2O.3 MG.24: 6 residues within 4Å: Chain B: G.65, G.66, D.76, D.103, D.105 Ligands: MIC.15 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.103, H2O.7, H2O.8, H2O.9 MG.36: 5 residues within 4Å: Chain C: G.65, G.66, D.103, D.105 Ligands: MIC.28 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.103, H2O.11, H2O.12, H2O.14 MG.51: 6 residues within 4Å: Chain D: G.65, G.66, D.76, D.103, D.105 Ligands: MIC.42 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.103, H2O.17, H2O.18, H2O.19

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

CL.10: 2 residues within 4Å: Chain A: N.70, D.76 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: Y.290, Y.295 Chain B: N.70, D.76 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: A.218, V.219 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: A.94, H.97 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: R.90, R.123 Chain D: R.123 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain B: Y.298 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: A.94, H.97 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: A.198 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain C: N.70, D.76 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain C: Y.290, Y.295 Chain D: N.70, D.76 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain C: A.218, V.219 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain C: A.94, H.97 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain B: R.123 Chain C: R.90, R.123 Ligand excluded by PLIP CL.52: 1 residues within 4Å: Chain D: Y.298 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain D: A.94, H.97 Ligand excluded by PLIP CL.54: 1 residues within 4Å: Chain D: A.198 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
A

D
B

2-methylisocitrate lyase

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