5OFM

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole

• PDB DOI: https://doi.org/10.2210/pdb5OFM/pdb

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


• Deposited: 2017-07-11 Released: 2017-08-16 
• Deposition Author(s): Unterlass, J.E., Basle, A., Blackburn, T.J., Tucker, J., Cano, C., Noble, M.E.M., Curtin, N.J.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.249 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole

Unterlass, J.E., Curtin, N.J.

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)

Macromolecule Content

• Total Structure Weight: 48.16 kDa 
• Atom Count: 3,416 
• Modelled Residue Count: 390 
• Deposited Residue Count: 446 
• 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]	223	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
9TT	C [auth B], D [auth A]	1-methylindol-5-amine C9 H10 N2 PGTSGPCXPIFQEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.249 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.342	α = 97.91
b = 45.86	β = 110.74
c = 56.175	γ = 106.39

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Unterlass, J.E., Basle, A., Blackburn, T.J., Tucker, J., Cano, C., Noble, M.E.M., Curtin, N.J.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C2115/A21421

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references