SMTL ID : 5n6c.1

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-Tartrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

TLA.1: 11 residues within 4Å: Chain A: R.48, S.49, R.69, T.72, N.96, R.230, H.277, A.280, Q.286 Chain B: R.129 Ligands: NAD.2 16 PLIP interactions: 2 interactions with chain B, 14 interactions with chain A Water bridges: B:R.129, A:R.48 Salt bridges: B:R.129, A:R.48, A:R.69, A:R.230, A:H.277 Hydrogen bonds: A:S.49, A:S.49, A:S.49, A:R.69, A:R.69, A:T.72, A:N.96, A:A.280, A:Q.286

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

NAD.2: 22 residues within 4Å: Chain A: T.72, A.100, G.146, G.148, R.149, I.150, Y.168, D.169, P.170, I.171, H.200, T.201, P.202, T.207, C.228, A.229, R.230, D.254, H.277, G.279, A.280 Ligands: TLA.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.100 Hydrogen bonds: A:G.148, A:R.149, A:I.150, A:T.201, A:D.254, A:G.279, A:A.280 Water bridges: A:G.151, A:S.206 Salt bridges: A:R.149 NAD.3: 22 residues within 4Å: Chain B: N.96, A.100, G.146, G.148, R.149, I.150, Y.168, D.169, P.170, I.171, I.172, H.200, T.201, P.202, T.207, C.228, A.229, R.230, D.254, H.277, G.279, A.280 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.96, B:A.100 Hydrogen bonds: B:G.148, B:R.149, B:I.150, B:I.171, B:T.201, B:D.254, B:D.254, B:G.279, B:A.280 Salt bridges: B:R.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unterlass, J.E. et al., Structural insights into the enzymatic activity and potential substrate promiscuity of human 3-phosphoglycerate dehydrogenase (PHGDH). Oncotarget (2017)

Release Date

2017-11-22

Peptides

D-3-phosphoglycerate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-3-phosphoglycerate dehydrogenase