SMTL ID : 3dc2.1

Crystal structure of serine bound D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x SER: SERINE(Non-covalent)

SER.1: 10 residues within 4Å: Chain A: Y.461, D.463, R.464, P.465, G.466, A.467, L.468, L.487 Chain D: N.481, I.482 7 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain D Hydrogen bonds: A:D.463, A:D.463, A:R.464, A:A.467, A:L.468, S.1, D:I.482 SER.3: 11 residues within 4Å: Chain B: Y.461, D.463, R.464, P.465, G.466, A.467, L.468, L.487, A.496 Chain C: N.481, I.482 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.463, B:R.464, B:G.466, C:N.481, C:I.482 SER.6: 10 residues within 4Å: Chain B: N.481, I.482 Chain C: Y.461, D.463, R.464, P.465, G.466, A.467, L.468, L.487 7 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: S.6, C:Y.461, C:D.463, C:R.464, C:A.467, C:L.468, B:I.482 SER.8: 11 residues within 4Å: Chain A: N.481, I.482 Chain D: Y.461, D.463, R.464, P.465, G.466, A.467, L.468, L.487, A.496 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Y.461, D:D.463, D:R.464, D:G.466, A:N.481, A:I.482

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

TLA.2: 8 residues within 4Å: Chain A: G.445, R.446, H.447 Chain D: K.439, D.449, L.450, R.451, R.501 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:H.447, D:K.439, D:D.449, D:R.451 Water bridges: A:H.447, D:K.439 Salt bridges: A:H.447, D:K.439, D:R.501 TLA.4: 9 residues within 4Å: Chain B: R.446, H.447, S.488 Chain C: K.439, D.449, L.450, R.451, A.484, R.501 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:K.439, C:D.449, C:R.451, C:R.451, B:R.446, B:H.447, B:S.488 Salt bridges: C:K.439, C:K.439, C:R.451, C:R.501, B:R.446, B:H.447 TLA.5: 5 residues within 4Å: Chain B: E.360, E.361, V.362, E.363, K.402 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.362, B:E.363 Salt bridges: B:K.402 TLA.7: 8 residues within 4Å: Chain B: K.439, D.449, L.450, R.451, R.501 Chain C: G.445, R.446, H.447 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.439, B:D.449, B:D.449, B:R.451, C:H.447 Water bridges: B:K.439, C:H.447 Salt bridges: B:K.439, B:R.501, C:H.447 TLA.9: 9 residues within 4Å: Chain A: K.439, D.449, L.450, R.451, A.484, R.501 Chain D: R.446, H.447, S.488 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:K.439, A:D.449, A:D.449, A:R.451, A:R.451, D:R.446, D:H.447, D:S.488 Salt bridges: A:K.439, A:K.439, A:R.451, A:R.501, D:R.446, D:H.447 TLA.10: 5 residues within 4Å: Chain D: E.360, E.361, V.362, E.363, K.402 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.362, D:E.363 Salt bridges: D:K.402

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

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