Macromolecule Content

Total Structure Weight: 72.18 kDa
Atom Count: 3671
Residue Count: 496
Unique protein chains: 1

7CVP

The Crystal Structure of human PHGDH from Biortus.

DOI: 10.2210/pdb7CVP/pdb

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

Deposited: 2020-08-26 Released: 2020-09-09
Deposition Author(s): Wang, F., Lv, Z., Cheng, W., Lin, D., Miao, Q., Huang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.320
R-Value Work: 0.261

wwPDB Validation 3D Report Full Report

Literature

The Crystal Structure of human PHGDH from Biortus.

Wang, F., Lv, Z., Cheng, W., Lin, D., Miao, Q., Huang, Y.

To be published.

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase	A, B	329	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)
Find proteins for O43175 (Homo sapiens) Explore O43175 Go to UniProtKB: O43175
NIH Common Fund Data Resources
PHAROS: O43175 GTEx: ENSG00000092621
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [B] MOL2 format, chain C [A] MOL2 format, chain D [B]	A, B	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.320
R-Value Work: 0.261
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.101	α = 90
b = 121.638	β = 99.974
c = 59.372	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2020-08-26
Released Date: 2020-09-09

Deposition Author(s):

Revision History

Version 1.0: 2020-09-09
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.