SMTL ID : 5j5d.1

Crystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with alpha-ketopimelic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

8 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: P.152, I.153, E.154, P.155, K.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.154, A:E.154 NA.2: 3 residues within 4Å: Chain A: E.154, P.155, D.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.156, A:D.156 NA.4: 5 residues within 4Å: Chain B: P.152, I.153, E.154, P.155, K.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.153, B:E.154 NA.5: 3 residues within 4Å: Chain B: E.154, P.155, D.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.156, B:D.156 NA.7: 5 residues within 4Å: Chain C: P.152, I.153, E.154, P.155, K.174 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.153 Water bridges: C:D.176, C:D.176 NA.8: 3 residues within 4Å: Chain C: E.154, P.155, D.156 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.156, C:D.156 NA.10: 5 residues within 4Å: Chain D: P.152, I.153, E.154, P.155, K.174 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.154 Water bridges: D:D.176, D:D.176 NA.11: 3 residues within 4Å: Chain D: E.154, P.155, D.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.156, D:D.156

4 x 6GT: 2-oxoheptanedioic acid(Non-covalent)

6GT.3: 11 residues within 4Å: Chain A: A.18, G.53, T.54, T.55, Y.143, I.145, R.148, K.171, G.194, I.211, V.213 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.18 Hydrogen bonds: A:T.54, A:T.54, A:T.55, A:T.55, A:T.55, A:Y.143 Water bridges: A:R.148, A:R.148 Salt bridges: A:R.148, A:K.171 6GT.6: 11 residues within 4Å: Chain B: A.18, G.53, T.54, T.55, Y.143, I.145, R.148, K.171, G.194, I.211, V.213 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.18 Hydrogen bonds: B:T.54, B:T.54, B:T.55, B:T.55, B:T.55, B:Y.143 Water bridges: B:R.148, B:R.148 Salt bridges: B:R.148, B:K.171 6GT.9: 11 residues within 4Å: Chain C: A.18, G.53, T.54, T.55, Y.143, I.145, R.148, K.171, G.194, I.211, V.213 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.18 Hydrogen bonds: C:T.54, C:T.55, C:T.55 Water bridges: C:R.148, C:R.148 Salt bridges: C:R.148, C:K.171 6GT.12: 11 residues within 4Å: Chain D: A.18, G.53, T.54, T.55, Y.143, I.145, R.148, K.171, G.194, I.211, V.213 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.18 Hydrogen bonds: D:T.54, D:T.55, D:T.55 Water bridges: D:R.148, D:R.148 Salt bridges: D:R.148, D:K.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shrivastava, P. et al., Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues. Sci Rep (2016)

Release Date

2016-08-17

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

4-hydroxy-tetrahydrodipicolinate synthase