5N53 Oxidoreductase date Feb 12, 2017
title Crystal Structure Of Human 3-Phosphoglycerate Dehydrogenase With N-(3-Chloro-4-Methoxyphenyl) Acetamide
authors J.E.Unterlass, A.Basle, T.J.Blackburn, J.Tucker, C.Cano, M.E.M.No N.J.Curtin
compound source
Molecule: D-3-Phosphoglycerate Dehydrogenase
Chain: B, A
Synonym: 3-Pgdh
Ec: 1.1.1.95
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Phgdh, Pgdh3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Rosetta (De3)
symmetry Space Group: P 1
R_factor 0.189 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.353 45.323 55.255 97.90 110.06 106.35
method X-Ray Diffractionresolution 1.48 Å
ligand 8NB enzyme Oxidoreductase E.C.1.1.1.95 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceValidating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer., Unterlass JE, Basle A, Blackburn TJ, Tucker J, Cano C, Noble MEM, Curtin NJ, Oncotarget. 2016 Aug 22;9(17):13139-13153. doi: 10.18632/oncotarget.11487., eCollection 2018 Mar 2. PMID:29568346
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (5n53.pdb1.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 5N53
  • CSU: Contacts of Structural Units for 5N53
  • Structure Factors (1531 Kb)
  • Retrieve 5N53 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5N53 from S2C, [Save to disk]
  • Re-refined 5n53 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5N53 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5N53
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5n53_B] [5n53] [5n53_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5N53
  • Community annotation for 5N53 at PDBWiki (http://pdbwiki.org)

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