7CVP

The Crystal Structure of human PHGDH from Biortus.


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


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-3-phosphoglycerate dehydrogenase
A, B
329Homo sapiensMutation(s): 0 
Gene Names: PHGDHPGDH3
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
GTEx:  ENSG00000092621 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43175
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.101α = 90
b = 121.638β = 99.974
c = 59.372γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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