SMTL ID : 6vb9.1

Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lyase-1 from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.111, D.156, K.192 Ligands: OXD.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.156, H2O.1, H2O.1, H2O.2 MG.2: 3 residues within 4Å: Chain A: A.279, A.282, Q.311 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.279, A:A.282, H2O.7, H2O.9, H2O.9 MG.6: 3 residues within 4Å: Chain B: D.111, D.156 Ligands: OXD.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.156, H2O.10, H2O.11, H2O.12 MG.12: 5 residues within 4Å: Chain C: W.96, D.111, D.156, K.192 Ligands: OXD.15 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.156, H2O.20, H2O.21, H2O.21 MG.13: 3 residues within 4Å: Chain C: A.279, A.282, Q.311 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.279, C:A.282, H2O.21, H2O.28, H2O.28 MG.17: 3 residues within 4Å: Chain D: A.279, A.282, Q.311 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:A.279, D:A.282, H2O.34, H2O.35, H2O.37 MG.18: 5 residues within 4Å: Chain D: G.95, W.96, D.111, D.156 Ligands: OXD.19 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.156, H2O.30, H2O.30, H2O.31

4 x OXD: OXALIC ACID(Non-covalent)

OXD.3: 12 residues within 4Å: Chain A: Y.92, S.94, G.95, W.96, D.156, H.183, C.194, R.231, W.286, N.316, T.350 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.92, A:G.95, A:W.96, A:D.111 Water bridges: A:R.231, A:R.231 Salt bridges: A:H.183, A:R.231 OXD.8: 13 residues within 4Å: Chain B: Y.92, S.94, G.95, W.96, D.111, D.156, H.183, C.194, R.231, W.286, N.316, T.350 Ligands: MG.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.92, B:G.95, B:W.96, B:D.111 Water bridges: B:R.231, B:R.231 Salt bridges: B:H.183, B:R.231 OXD.15: 12 residues within 4Å: Chain C: Y.92, S.94, G.95, W.96, D.111, D.156, H.183, C.194, R.231, W.286, T.350 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.92, C:G.95, C:W.96, C:D.156 Water bridges: C:K.192, C:K.192, C:K.192, C:R.231 Salt bridges: C:H.183, C:R.231 OXD.19: 12 residues within 4Å: Chain D: Y.92, S.94, G.95, W.96, D.111, D.156, H.183, C.194, R.231, W.286, T.350 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.95, D:W.96, D:D.156 Water bridges: D:K.192, D:K.192, D:R.231, D:R.231 Salt bridges: D:H.183, D:R.231

9 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 1 residues within 4Å: Chain A: W.68 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.70, A:N.70 ACY.5: 4 residues within 4Å: Chain A: P.24, R.25, W.60, E.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.61 Salt bridges: A:H.64 ACY.9: 6 residues within 4Å: Chain B: I.16, W.20, W.26, R.31, D.220, D.223 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.31, B:A.219 Salt bridges: B:R.31 ACY.10: 4 residues within 4Å: Chain B: Q.206, Q.207, R.210 Chain D: D.413 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.210 ACY.11: 1 residues within 4Å: Chain B: W.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.68, B:W.68 ACY.16: 2 residues within 4Å: Chain C: W.68, N.70 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:W.68, C:W.68, D:Q.372 Water bridges: C:N.70 ACY.20: 8 residues within 4Å: Chain D: E.19, W.20, W.26, R.31, D.220, D.223, V.224, P.225 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.26 Hydrogen bonds: D:D.223 Salt bridges: D:K.11 ACY.21: 6 residues within 4Å: Chain D: P.10, K.11, I.16, Q.42, V.46, D.223 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.11, D:V.46 Hydrogen bonds: D:K.11, D:Q.42, D:D.223 Salt bridges: D:K.11 ACY.22: 2 residues within 4Å: Chain D: E.67, W.68 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:E.67, D:W.68 Water bridges: D:N.70, C:Q.372

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

PEG.7: 5 residues within 4Å: Chain B: I.203, P.204, Q.207, T.241 Chain C: L.188 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:T.241 Hydrogen bonds: B:T.241, B:T.241 PEG.14: 10 residues within 4Å: Chain C: V.81, Q.82, R.85, A.134, I.137, A.138, W.149, T.392, R.398, E.399 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.82, C:Q.82, C:R.85, C:A.134, C:A.138, C:R.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pham, T.V. et al., Covalent Inactivation of Mycobacterium tuberculosis Isocitrate Lyase by cis -2,3-Epoxy-Succinic Acid. Acs Chem.Biol. (2021)

Release Date

2020-12-30

Peptides

Isocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isocitrate lyase