SMTL ID : 1f8i.1

CRYSTAL STRUCTURE OF ISOCITRATE LYASE:NITROPROPIONATE:GLYOXYLATE COMPLEX FROM MYCOBACTERIUM TUBERCULOSIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.109, D.154 Ligands: GLV.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.154, H2O.1, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain B: W.94, D.109, D.154 Ligands: GLV.5, SIN.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.154, H2O.11, H2O.11, H2O.11 MG.7: 3 residues within 4Å: Chain C: D.109, D.154 Ligands: GLV.8 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.154, H2O.22, H2O.22, H2O.22 MG.10: 3 residues within 4Å: Chain D: D.109, D.154 Ligands: GLV.11 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.154, H2O.32, H2O.33, H2O.33

4 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.2: 12 residues within 4Å: Chain A: Y.90, S.92, G.93, W.94, D.109, D.154, H.181, R.229, W.284, T.348 Ligands: MG.1, SIN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.93, A:W.94, A:R.229 Water bridges: A:R.229 GLV.5: 12 residues within 4Å: Chain B: Y.90, S.92, G.93, W.94, D.109, D.154, H.181, R.229, W.284, T.348 Ligands: MG.4, SIN.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.93, B:W.94, B:D.154, B:R.229 Water bridges: B:R.229 GLV.8: 12 residues within 4Å: Chain C: Y.90, S.92, G.93, W.94, D.109, D.154, H.181, R.229, W.284, T.348 Ligands: MG.7, SIN.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.90, C:G.93, C:W.94, C:D.154, C:R.229 Water bridges: C:G.193 GLV.11: 12 residues within 4Å: Chain D: Y.90, S.92, G.93, W.94, D.109, D.154, H.181, R.229, W.284, T.348 Ligands: MG.10, SIN.12 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Y.90, D:Y.90, D:G.93, D:W.94, D:R.229 Water bridges: D:K.190, D:K.190, D:K.190, D:R.229

4 x SIN: SUCCINIC ACID(Non-covalent)

SIN.3: 12 residues within 4Å: Chain A: W.94, D.109, S.192, G.193, H.194, R.229, E.286, N.314, S.316, S.318, T.348 Ligands: GLV.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.348 Hydrogen bonds: A:D.109, A:G.193, A:N.314, A:S.316, A:S.318, A:T.348, A:T.348 Water bridges: A:H.194, A:R.229 Salt bridges: A:H.194, A:H.194, A:R.229 SIN.6: 14 residues within 4Å: Chain B: W.94, D.109, S.192, G.193, H.194, R.229, E.286, N.314, S.316, S.318, T.348, L.349 Ligands: MG.4, GLV.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.349 Hydrogen bonds: B:D.109, B:G.193, B:N.314, B:S.316, B:S.318, B:T.348 Water bridges: B:H.194, B:R.229 Salt bridges: B:H.194, B:H.194, B:R.229 SIN.9: 11 residues within 4Å: Chain C: D.109, S.192, G.193, H.194, R.229, E.286, N.314, S.316, S.318, T.348 Ligands: GLV.8 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:D.109, C:G.193, C:E.286, C:N.314, C:N.314, C:S.316, C:S.318, C:T.348 Water bridges: C:H.194, C:R.229 Salt bridges: C:H.194, C:H.194, C:R.229 SIN.12: 12 residues within 4Å: Chain D: W.94, D.109, S.192, G.193, H.194, R.229, E.286, N.314, S.316, S.318, T.348 Ligands: GLV.11 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.109, D:D.109, D:S.192, D:G.193, D:N.314, D:N.314, D:S.316, D:S.318 Water bridges: D:R.229 Salt bridges: D:H.194, D:H.194, D:R.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, V. et al., Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat.Struct.Biol. (2000)

Release Date

2000-12-30

Peptides

ISOCITRATE LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ISOCITRATE LYASE