5X2L Lyase, Isomerase date Feb 01, 2017
title Crystal Structure Of Human Serine Racemase
authors T.Obita, K.Matsumoto, H.Mori, N.Toyooka, M.Mizuguchi
compound source
Molecule: Serine Racemase
Chain: A, B
Synonym: D-Serine Ammonia-Lyase,D-Serine Dehydratase,L-Seri Ammonia-Lyase,L-Serine Dehydratase;
Ec: 5.1.1.18,4.3.1.18,4.3.1.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Srr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.220 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.120 112.590 88.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.81 Å
ligand MG, PLP enzyme Isomerase E.C.5.1.1.18 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDesign, synthesis, and evaluation of novel inhibitors for wild-type human serine racemase., Takahara S, Nakagawa K, Uchiyama T, Yoshida T, Matsumoto K, Kawasumi Y, Mizuguchi M, Obita T, Watanabe Y, Hayakawa D, Gouda H, Mori H, Toyooka N, Bioorg Med Chem Lett. 2017 Dec 13. pii: S0960-894X(17)31180-0. doi:, 10.1016/j.bmcl.2017.12.021. PMID:29277459
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (208 Kb) [Save to disk]
  • Biological Unit Coordinates (5x2l.pdb1.gz) 194 Kb
  • LPC: Ligand-Protein Contacts for 5X2L
  • CSU: Contacts of Structural Units for 5X2L
  • Structure Factors (3404 Kb)
  • Retrieve 5X2L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5X2L from S2C, [Save to disk]
  • View 5X2L 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 5X2L
  • 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: [5x2l_B] [5x2l_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5X2L
  • Community annotation for 5X2L at PDBWiki (http://pdbwiki.org)

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