SMTL ID : 3ddn.1

Crystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

6 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 8 residues within 4Å: Chain A: R.445, H.446 Chain D: K.438, D.448, L.449, R.450, A.483, R.500 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:H.446, D:K.438, D:D.448, D:D.448, D:R.450 Water bridges: A:H.446, A:S.487, D:K.438 Salt bridges: A:R.445, A:H.446, D:K.438, D:R.500 TLA.2: 10 residues within 4Å: Chain B: R.445, H.446, S.487, E.488 Chain C: K.438, D.448, L.449, R.450, A.483, R.500 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:K.438, C:D.448, C:D.448, C:R.450, C:R.450, B:H.446, B:S.487, B:E.488 Salt bridges: C:K.438, C:R.450, C:R.500, B:R.445, B:H.446 TLA.3: 5 residues within 4Å: Chain B: E.359, E.360, V.361, E.362, K.401 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.361, B:E.362 Water bridges: B:V.363 Salt bridges: B:K.401 TLA.5: 8 residues within 4Å: Chain B: K.438, D.448, L.449, R.450, A.483, R.500 Chain C: R.445, H.446 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:H.446, B:K.438, B:D.448, B:R.450 Water bridges: C:H.446, C:S.487, B:K.438 Salt bridges: C:R.445, C:H.446, B:K.438, B:R.500 TLA.6: 10 residues within 4Å: Chain A: K.438, D.448, L.449, R.450, A.483, R.500 Chain D: R.445, H.446, S.487, E.488 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:K.438, A:D.448, A:R.450, A:R.450, D:H.446, D:S.487, D:E.488 Salt bridges: A:K.438, A:R.450, A:R.500, D:R.445, D:H.446 TLA.7: 5 residues within 4Å: Chain D: E.359, E.360, V.361, E.362, K.401 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.361, D:E.362 Water bridges: D:V.363 Salt bridges: D:K.401

2 x HPV: 2-oxo-3-(phosphonooxy)propanoic acid(Non-covalent)

HPV.4: 12 residues within 4Å: Chain A: R.131 Chain B: R.50, S.51, R.71, A.72, G.73, V.74, G.75, N.98, A.282, S.283, Q.288 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Salt bridges: A:R.131, B:R.50, B:R.71 Hydrogen bonds: B:S.51, B:R.71, B:R.71, B:V.74, B:G.75, B:N.98 HPV.8: 12 residues within 4Å: Chain C: R.131 Chain D: R.50, S.51, R.71, A.72, G.73, V.74, G.75, N.98, A.282, S.283, Q.288 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.51, D:R.71, D:R.71, D:V.74, D:G.75, D:N.98 Salt bridges: D:R.50, D:R.71, C:R.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dey, S. et al., Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase. Biochemistry (2008)

Release Date

2008-07-22

Peptides

D-3-phosphoglycerate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

D-3-phosphoglycerate dehydrogenase