SMTL ID : 6wsi.1

Intact cis-2,3-epoxysuccinic acid bound to Isocitrate Lyase-1 from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.108, D.153 Ligands: GLV.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.153, H2O.1, H2O.1, H2O.3 MG.2: 4 residues within 4Å: Chain A: A.276, A.279, Q.308 Ligands: GOL.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.276, A:A.279, H2O.5, H2O.10 MG.8: 2 residues within 4Å: Chain B: D.153 Ligands: GLV.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.153, H2O.12, H2O.12, H2O.13 MG.9: 4 residues within 4Å: Chain B: A.276, A.279, Q.308 Ligands: GOL.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.276, B:A.279, H2O.16, H2O.21 MG.18: 3 residues within 4Å: Chain C: D.108, D.153 Ligands: GLV.20 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.153, H2O.23, H2O.23, H2O.25 MG.19: 4 residues within 4Å: Chain C: A.276, A.279, Q.308 Ligands: GOL.22 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.276, C:A.279, H2O.27, H2O.33 MG.26: 4 residues within 4Å: Chain D: A.276, A.279, Q.308 Ligands: GOL.30 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.276, D:A.279, H2O.37, H2O.44 MG.27: 2 residues within 4Å: Chain D: D.153 Ligands: GLV.28 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.153, H2O.35, H2O.35, H2O.37

4 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.3: 12 residues within 4Å: Chain A: Y.89, S.91, G.92, W.93, D.108, D.153, H.180, R.228, W.283, T.347 Ligands: MG.1, U9S.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.89, A:G.92, A:W.93, A:D.108, A:R.228 Water bridges: A:K.189, A:K.189 GLV.10: 11 residues within 4Å: Chain B: Y.89, S.91, G.92, W.93, D.153, H.180, R.228, W.283, T.347 Ligands: MG.8, U9S.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.89, B:G.92, B:W.93, B:R.228 Water bridges: B:K.189, B:K.189 GLV.20: 11 residues within 4Å: Chain C: Y.89, S.91, G.92, W.93, D.153, H.180, R.228, W.283, T.347 Ligands: MG.18, U9S.21 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.92, C:W.93, C:R.228 Water bridges: C:K.189, C:K.189, C:K.189 GLV.28: 11 residues within 4Å: Chain D: Y.89, S.91, G.92, W.93, D.153, H.180, R.228, W.283, T.347 Ligands: MG.27, U9S.29 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.92, D:W.93, D:R.228 Water bridges: D:K.189, D:K.189

4 x U9S: (2R,3S)-oxirane-2,3-dicarboxylic acid(Non-covalent)

U9S.4: 13 residues within 4Å: Chain A: W.93, D.108, C.191, G.192, H.193, R.228, E.285, N.313, S.315, S.317, T.347, L.348 Ligands: GLV.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.108, A:G.192, A:N.313, A:S.315, A:S.317, A:T.347, A:T.347 Water bridges: A:R.228 Salt bridges: A:H.193, A:H.193, A:R.228 U9S.11: 13 residues within 4Å: Chain B: W.93, D.108, C.191, G.192, H.193, R.228, E.285, N.313, S.315, S.317, T.347, L.348 Ligands: GLV.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.108, B:G.192, B:N.313, B:S.315, B:S.317 Water bridges: B:R.228 Salt bridges: B:H.193, B:H.193, B:R.228 U9S.21: 13 residues within 4Å: Chain C: W.93, D.108, C.191, G.192, H.193, R.228, E.285, N.313, S.315, S.317, T.347, L.348 Ligands: GLV.20 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.192, C:N.313, C:S.315, C:S.317 Water bridges: C:R.228 Salt bridges: C:H.193, C:H.193, C:R.228 U9S.29: 13 residues within 4Å: Chain D: W.93, D.108, C.191, G.192, H.193, R.228, E.285, N.313, S.315, S.317, T.347, L.348 Ligands: GLV.28 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.192, D:N.313, D:S.315, D:S.317, D:T.347, D:T.347 Water bridges: D:R.228 Salt bridges: D:H.193, D:H.193, D:R.228

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: K.24, D.25, A.279, D.280, D.307, Q.308, M.309 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.25, A:D.280, A:Q.308, A:M.309 GOL.6: 8 residues within 4Å: Chain A: E.16, W.17, W.23, R.28, D.217, D.220, V.221, P.222 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.16, A:R.28, A:D.217, A:D.217, A:V.221 GOL.12: 9 residues within 4Å: Chain A: T.419, G.420 Chain B: G.195, G.196, K.197, A.233, A.234, T.235, L.236 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.196, B:K.197, B:K.197, B:A.233, B:T.235, B:L.236, A:T.419 GOL.13: 8 residues within 4Å: Chain B: K.24, D.25, A.279, D.280, D.307, Q.308, M.309 Ligands: MG.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.25, B:Q.308, B:M.309 GOL.14: 5 residues within 4Å: Chain A: R.123 Chain B: D.98, A.99, N.100, G.103 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.100, B:G.103 Water bridges: B:D.98, A:R.123 GOL.15: 7 residues within 4Å: Chain B: E.16, W.17, W.23, R.28, D.217, V.221, P.222 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.16, B:R.28, B:D.217, B:V.221 GOL.16: 9 residues within 4Å: Chain B: V.78, R.82, A.131, I.134, A.135, W.146, T.389, R.395, E.396 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.82, B:A.131, B:A.135, B:R.395 Water bridges: B:Q.79, B:E.138, B:D.140 GOL.22: 8 residues within 4Å: Chain C: K.24, D.25, A.279, D.280, D.307, Q.308, M.309 Ligands: MG.19 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.25, C:D.25, C:Q.308, C:Q.308, C:M.309 GOL.23: 9 residues within 4Å: Chain C: K.8, E.16, W.17, W.23, R.28, D.217, D.220, V.221, P.222 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.16, C:E.16, C:W.17, C:R.28, C:V.221 GOL.24: 8 residues within 4Å: Chain C: G.195, G.196, K.197, A.233, A.234, T.235, L.236 Chain D: T.419 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:T.419, C:G.196, C:K.197, C:A.233, C:T.235, C:L.236 GOL.30: 7 residues within 4Å: Chain D: K.24, A.279, D.280, D.307, Q.308, M.309 Ligands: MG.26 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.25, D:D.25, D:Q.308, D:Q.308, D:M.309 GOL.31: 7 residues within 4Å: Chain D: G.195, G.196, K.197, A.233, A.234, T.235, L.236 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain D Water bridges: C:T.419 Hydrogen bonds: D:L.194, D:G.196, D:K.197, D:K.197, D:T.235, D:L.236 GOL.32: 9 residues within 4Å: Chain D: E.16, W.17, W.23, R.28, D.217, D.220, V.221, P.222 Ligands: PEG.33 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.16, D:R.28, D:D.217, D:V.221

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

PEG.7: 10 residues within 4Å: Chain A: A.399, F.402, D.403, A.406, T.415, T.416, A.417 Chain B: Q.109, K.190 Chain C: L.162 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.109, A:D.403, A:T.415 Water bridges: A:T.415 PEG.17: 8 residues within 4Å: Chain B: L.199, R.244, D.245, F.248, T.261, P.267, A.270, R.271 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.271 Water bridges: B:D.245, B:T.261, B:A.270 PEG.25: 5 residues within 4Å: Chain A: T.407, T.408, P.411 Chain C: T.29, D.34 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.31 PEG.33: 5 residues within 4Å: Chain D: E.16, N.20, W.23, P.222 Ligands: GOL.32 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.16 PEG.34: 9 residues within 4Å: Chain B: L.162 Chain C: Q.109 Chain D: A.399, F.402, D.403, A.406, T.415, T.416, A.417 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.109

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

2021-03-24

Peptides

Isocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isocitrate lyase

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