4YVF Hydrolase date Mar 20, 2015
title Structure Of S-Adenosyl-L-Homocysteine Hydrolase
authors K.Akiko
compound source
Molecule: Adenosylhomocysteinase
Chain: A, B
Synonym: Adohcyase,S-Adenosyl-L-Homocysteine Hydrolase
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ahcy, Sahh
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.199 R_Free 0.239
length a length b length c angle alpha angle beta angle gamma
91.528 134.150 185.164 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand NAI, XFA enzyme Hydrolase E.C. BRENDA
A, B

Primary referenceDiscovery and structural analyses of S-adenosyl-L-homocysteine hydrolase inhibitors based on non-adenosine analogs., Nakao A, Suzuki H, Ueno H, Iwasaki H, Setsuta T, Kashima A, Sunada S, Bioorg Med Chem. 2015 Aug 1;23(15):4952-69. doi: 10.1016/j.bmc.2015.05.018. Epub , 2015 May 19. PMID:26037610
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (4yvf.pdb1.gz) 280 Kb
  • LPC: Ligand-Protein Contacts for 4YVF
  • CSU: Contacts of Structural Units for 4YVF
  • Structure Factors (264 Kb)
  • Retrieve 4YVF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YVF from S2C, [Save to disk]
  • Re-refined 4yvf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YVF 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 4YVF
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 4yvf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yvf] [4yvf_A] [4yvf_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YVF: [AdoHcyase] [AdoHcyase_NAD ] by SMART
  • Other resources with information on 4YVF
  • Community annotation for 4YVF at PDBWiki (http://pdbwiki.org)

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