7EWH

Crystal structure of human PHGDH in complex with Homoharringtonine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of human PHGDH in complex with Homoharringtonine

Hsieh, C.H.Cheng, Y.S.Lee, Y.S.Huang, H.C.Juan, H.F.

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
302Homo 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
PHAROS:  O43175
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
HMT (Subject of Investigation/LOI)
Query on HMT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
C29 H39 N O9
HYFHYPWGAURHIV-JFIAXGOJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.165α = 90
b = 120.639β = 100.72
c = 59.48γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST-109-2320-B-002-017-MY3
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST-109-2221-E-002-161-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description