SMTL ID : 7dkm.1

PHGDH covalently linked to oridonin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

1 x ODN: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one(Covalent)

ODN.1: 5 residues within 4Å: Chain A: C.16, K.19, I.20, D.23, E.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.23

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

NAD.2: 24 residues within 4Å: Chain A: T.76, P.97, N.100, A.104, G.150, G.152, R.153, I.154, Y.172, D.173, P.174, I.175, H.204, T.205, P.206, T.211, C.232, A.233, R.234, D.258, V.259, H.281, G.283, A.284 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:N.100, A:A.104, A:I.154 Hydrogen bonds: A:G.152, A:R.153, A:I.154, A:T.205, A:R.234, A:D.258, A:G.283, A:A.284 Water bridges: A:R.153, A:R.153, A:G.155, A:Y.172 Salt bridges: A:R.153 NAD.5: 24 residues within 4Å: Chain B: T.76, N.100, A.104, G.150, G.152, R.153, I.154, Y.172, D.173, P.174, I.175, I.176, H.204, T.205, P.206, S.210, T.211, C.232, A.233, R.234, D.258, H.281, G.283, A.284 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:T.76, B:N.100, B:A.104, B:I.154 Hydrogen bonds: B:T.76, B:G.152, B:R.153, B:I.154, B:T.205, B:S.210, B:D.258, B:D.258, B:G.283, B:A.284 Water bridges: B:R.153, B:R.153, B:G.155, B:Y.172, B:R.234 Salt bridges: B:R.153

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: P.174 Ligand excluded by PLIP

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

NA.6: 5 residues within 4Å: Chain B: N.100, A.284, A.289, Q.290, C.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.100, B:N.100 Water bridges: B:Q.290

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 2 residues within 4Å: Chain B: K.130, K.135 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.130, B:K.135, B:K.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, Y. et al., Biophysical and biochemical properties of PHGDH revealed by studies on PHGDH inhibitors. Cell.Mol.Life Sci. (2021)

Release Date

2022-02-02

Peptides

D-3-phosphoglycerate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-3-phosphoglycerate dehydrogenase