SMTL ID : 7rb1.1

Isocitrate Lyase-1 from Mycobacterium tuberculosis covalently modified by 5-descarboxy-5-nitro-D-isocitric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

3 x 48J: dihydroxyacetic acid(Non-covalent)

48J.1: 13 residues within 4Å: Chain A: Y.89, S.91, G.92, W.93, D.108, D.153, H.180, R.228, W.283, N.313, T.347 Ligands: MG.2, 54I.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.92, A:W.93 Water bridges: A:K.189, A:K.189, A:K.189, A:K.189, A:K.189, A:R.228 Salt bridges: A:H.180, A:R.228 48J.8: 12 residues within 4Å: Chain B: Y.89, S.91, G.92, W.93, D.153, H.180, R.228, W.283, T.347, L.348 Ligands: MG.9, 54I.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.92, B:W.93, B:D.153 Water bridges: B:K.189, B:K.189, B:R.228, B:R.228 Salt bridges: B:H.180, B:R.228 48J.14: 13 residues within 4Å: Chain C: Y.89, S.91, G.92, W.93, D.108, D.153, H.180, R.228, W.283, N.313, T.347 Ligands: MG.15, 54I.17 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.92, C:W.93, C:D.153 Water bridges: C:K.189, C:K.189, C:R.228, C:R.228 Salt bridges: C:H.180, C:R.228

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.108, D.153, K.189 Ligands: 48J.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.153, H2O.1, H2O.1, H2O.1 MG.3: 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.6, H2O.7 MG.9: 4 residues within 4Å: Chain B: D.108, D.153, K.189 Ligands: 48J.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.153, H2O.9, H2O.9, H2O.11 MG.10: 4 residues within 4Å: Chain B: A.276, A.279, Q.308 Ligands: GOL.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.276, B:A.279, H2O.11, H2O.15 MG.15: 4 residues within 4Å: Chain C: D.108, D.153, K.189 Ligands: 48J.14 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.153, H2O.17, H2O.17, H2O.18 MG.16: 4 residues within 4Å: Chain C: A.276, A.279, Q.308 Ligands: GOL.18 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.276, C:A.279, H2O.18, H2O.22 MG.21: 4 residues within 4Å: Chain D: D.108, D.153, K.189 Ligands: GLV.20 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.153, H2O.24, H2O.24, H2O.25 MG.22: 4 residues within 4Å: Chain D: A.276, A.279, Q.308 Ligands: GOL.24 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.276, D:A.279, H2O.27, H2O.30

4 x 54I: (3E)-3-(hydroxyimino)propanoic acid(Covalent)(Non-covalent)

54I.4: 12 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 Ligands: 48J.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.108, A:G.192, A:R.228, A:R.228, A:N.313, A:S.315, A:S.317, A:T.347, A:T.347 Water bridges: A:K.189 Salt bridges: A:H.193 54I.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: 48J.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.348 Hydrogen bonds: B:G.192, B:R.228, B:R.228, B:E.285, B:N.313, B:S.315, B:S.317 Salt bridges: B:H.193 54I.17: 12 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 Ligands: 48J.14 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.93 Hydrogen bonds: C:G.192, C:R.228, C:R.228, C:N.313, C:S.315, C:S.317, C:T.347, C:T.347 Salt bridges: C:H.193 54I.23: 12 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 Ligands: GLV.20 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.93 Hydrogen bonds: D:G.192, D:R.228, D:R.228, D:N.313, D:S.315, D:S.317 Salt bridges: D:H.193

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: D.25, A.279, D.280, D.307, Q.308, M.309 Ligands: MG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.280, A:Q.308, A:M.309 Water bridges: A:D.25 GOL.6: 9 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:E.16, A:R.28, A:D.217, A:D.217, A:V.221 GOL.7: 9 residues within 4Å: Chain A: V.78, R.82, A.131, I.134, A.135, W.146, T.389, R.395, E.396 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.82, A:A.135, A:T.389, A:E.396 Water bridges: A:Q.79, A:R.395 GOL.12: 7 residues within 4Å: Chain B: K.24, A.279, D.280, D.307, Q.308, M.309 Ligands: MG.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:M.309 Water bridges: B:D.25, B:D.25, B:A.276, B:A.276, B:A.279 GOL.13: 7 residues within 4Å: Chain B: E.16, W.17, W.23, D.217, D.220, V.221, P.222 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.16, B:D.220, B:V.221 GOL.18: 8 residues within 4Å: Chain C: K.24, D.25, A.279, D.280, D.307, Q.308, M.309 Ligands: MG.16 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.25, C:Q.308, C:M.309 Water bridges: C:D.25, C:D.25, C:A.276, C:A.276 GOL.19: 8 residues within 4Å: Chain C: 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:W.17, C:R.28 Water bridges: C:E.16, C:D.217, C:D.220 GOL.24: 7 residues within 4Å: Chain D: D.25, A.279, D.280, D.307, Q.308, M.309 Ligands: MG.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.25, D:Q.308, D:M.309 Water bridges: D:D.307

1 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.20: 11 residues within 4Å: Chain D: Y.89, S.91, G.92, W.93, D.153, H.180, R.228, T.347, L.348 Ligands: MG.21, 54I.23 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Y.89, D:G.92, D:W.93, D:R.228 Water bridges: D:D.108, D:D.108, D:K.189, D:K.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mellott, D.M. et al., Mechanism-Based Inactivation of Mycobacterium tuberculosis Isocitrate Lyase 1 by (2 R ,3 S )-2-Hydroxy-3-(nitromethyl)succinic acid. J.Am.Chem.Soc. (2021)

Release Date

2021-12-01

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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