SMTL ID : 1psd.1

THE ALLOSTERIC LIGAND SITE IN THE VMAX-TYPE COOPERATIVE ENZYME PHOSPHOGLYCERATE DEHYDROGENASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: F.105, N.107, V.111, G.157, Y.158, G.159, H.160, I.161, Y.179, D.180, I.181, K.184, H.209, V.210, P.211, S.215, T.216, M.219, A.237, S.238, R.239, D.263, V.264, H.291, I.292 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.111 Hydrogen bonds: A:Y.158, A:H.160, A:H.160, A:I.161, A:I.181, A:K.184, A:E.212, A:S.215, A:D.263, A:D.263 Water bridges: A:G.159, A:G.162, A:R.239, A:S.295 NAD.3: 24 residues within 4Å: Chain B: F.105, N.107, V.111, G.157, Y.158, G.159, H.160, I.161, Y.179, D.180, I.181, K.184, H.209, V.210, P.211, T.216, A.237, S.238, R.239, D.263, V.264, H.291, I.292, G.294 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.111 Hydrogen bonds: B:Y.158, B:H.160, B:I.161, B:I.181, B:K.184, B:V.210, B:D.263, B:G.294 Water bridges: B:G.159, B:G.162 NAD.5: 25 residues within 4Å: Chain C: F.105, N.107, V.111, G.157, Y.158, G.159, H.160, I.161, Y.179, D.180, I.181, K.184, H.209, V.210, P.211, S.215, T.216, M.219, A.237, S.238, R.239, D.263, V.264, H.291, I.292 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:V.111 Hydrogen bonds: C:Y.158, C:H.160, C:H.160, C:I.161, C:I.181, C:K.184, C:E.212, C:S.215, C:D.263, C:D.263 Water bridges: C:G.159, C:G.162, C:R.239, C:S.295 NAD.7: 24 residues within 4Å: Chain D: F.105, N.107, V.111, G.157, Y.158, G.159, H.160, I.161, Y.179, D.180, I.181, K.184, H.209, V.210, P.211, T.216, A.237, S.238, R.239, D.263, V.264, H.291, I.292, G.294 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.111 Hydrogen bonds: D:Y.158, D:H.160, D:I.161, D:I.181, D:K.184, D:V.210, D:D.263, D:G.294 Water bridges: D:G.159, D:G.162

4 x SER: SERINE(Non-covalent)

SER.2: 11 residues within 4Å: Chain A: H.343, E.344, N.345, R.346, P.347, G.348, V.349, L.350, L.369 Chain D: N.363, I.364 8 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: A:N.345, A:N.345, A:R.346, A:G.348, S.2, D:N.363, D:I.364 Salt bridges: A:H.343 SER.4: 11 residues within 4Å: Chain B: H.343, E.344, N.345, R.346, P.347, G.348, V.349, L.350, L.369 Chain C: N.363, I.364 8 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: B:N.345, B:R.346, B:R.346, B:G.348, S.4, C:N.363, C:I.364 Salt bridges: B:H.343 SER.6: 11 residues within 4Å: Chain B: N.363, I.364 Chain C: H.343, E.344, N.345, R.346, P.347, G.348, V.349, L.350, L.369 8 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: C:N.345, C:N.345, C:R.346, C:G.348, S.6, B:N.363, B:I.364 Salt bridges: C:H.343 SER.8: 11 residues within 4Å: Chain A: N.363, I.364 Chain D: H.343, E.344, N.345, R.346, P.347, G.348, V.349, L.350, L.369 8 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain D, 2 interactions with chain A Hydrogen bonds: S.8, D:N.345, D:R.346, D:R.346, D:G.348, A:N.363, A:I.364 Salt bridges: D:H.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schuller, D.J. et al., The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Nat.Struct.Biol. (1995)

Release Date

1995-07-31

Peptides

D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)