7CVP | pdb_00007cvp

The Crystal Structure of human PHGDH from Biortus.

• PDB DOI: https://doi.org/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.320 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.270 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of human PHGDH from Biortus.

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 72.18 kDa 
• Atom Count: 3,671 
• Modeled Residue Count: 496 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

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)
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
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.320 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.270 (DCC) 

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

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description