1YBA	Oxidoreductase	date	Dec 20, 2004
title	The Active Form Of Phosphoglycerate Dehydrogenase
authors	J.R.Thompson, L.J.Banaszak
compound		source
Molecule: D-3-Phosphoglycerate Dehydrogenase Chain: A, B, C, D Synonym: Pgdh Ec: 1.1.1.95 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Sera Expression_system: Escherichia Coli K12 Expression_system_taxid: 83333 Expression_system_strain: K12 Expression_system_vector_type: Plasmid Expression_system_plasmid: Psawt
symmetry	Space Group: P 43	R_factor 0.186 R_Free 0.235
crystal cell	length a length b length c angle alpha angle beta angle gamma 76.159 76.159 354.144 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.24 Å
ligand	AKG, MSE, NAD, PO4, UNL	enzyme	Oxidoreductase E.C.1.1.1.95 BRENDA
related structures	by homologous chain: 1PSD, 1SC6
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	V(m)(ax) Regulation through Domain and Subunit Changes. The Active Form of Phosphoglycerate Dehydrogenase(,)., Thompson JR, Bell JK, Bratt J, Grant GA, Banaszak LJ, Biochemistry 2005 Apr 19;44(15):5763-5773. PMID:15823035

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (291 Kb) [Save to disk] Biological Unit Coordinates (1yba.pdb1.gz) 279 Kb LPC: Ligand-Protein Contacts for 1YBA CSU: Contacts of Structural Units for 1YBA Likely Quarternary Molecular Structure file(s) for 1YBA Structure Factors (1095 Kb) Retrieve 1YBA in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YBA from S2C, [Save to disk] Re-refined 1yba structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YBA 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 1YBA

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 3D motif for 1YBA, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1yba_B] [1yba_A] [1yba_D] [1yba_C] [1yba] SWISS-PROT database: [P0A9T0] Domain organization of [SERA_ECOLI] by SWISSPFAM

Other resources with information on 1YBA

Community annotation for 1YBA at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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