7VA1

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with GDD-04-35

• PDB DOI: https://doi.org/10.2210/pdb7VA1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-27 Released: 2023-03-08 
• Deposition Author(s): Cen, Y., Gao, D., Zhou, J., Tian, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.225 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with GDD-04-35

Cen, Y., Gao, D., Zhou, J., Tian, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.83 kDa 
• Atom Count: 6,295 
• Modelled Residue Count: 765 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase	A [auth B], B [auth A], C, D	214	Homo sapiens	Mutation(s): 0  Gene Names: PHGDH, PGDH3 EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (PDB Primary Data), 1.1.1.37 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43175 (Homo sapiens) Explore O43175  Go to UniProtKB:  O43175
PHAROS:  O43175 GTEx:  ENSG00000092621

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5YP (Subject of Investigation/LOI)	E [auth B], F [auth A], G [auth C], H [auth D]	4-[(3-ethanoylphenyl)sulfamoyl]-~{N}-[4-(3-fluorophenyl)-1,3-thiazol-2-yl]benzamide C24 H18 F N3 O4 S2 VUAMLKVINZWIJR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.225 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.41	α = 90
b = 112.52	β = 92.358
c = 87.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-08 
Deposition Author(s): Cen, Y., Gao, D., Zhou, J., Tian, P.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-03-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description