1YH3 Hydrolase date Jan 06, 2005
title Crystal Structure Of Human Cd38 Extracellular Domain
authors Q.Liu, I.A.Kriksunov, R.Graeff, C.Munshi, H.C.Lee, Q.Hao
compound source
Molecule: Adp-Ribosyl Cyclase 1
Chain: A, B
Fragment: Human Cd38 Extracellular Domain
Synonym: Cyclic Adp-Ribose Hydrolase 1, Cadpr Hydrolase 1, Differentiation Antigen Cd38, T10, Acute Lymphoblastic Leuk Antigen Cd38;
Ec: 3.2.2.5
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd38
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_strain: X-33
symmetry Space Group: P 1
R_factor 0.188 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.839 51.491 66.439 108.27 90.47 97.29
method X-Ray Diffractionresolution 1.91 Å
ligand
enzyme Hydrolase E.C.3.2.2.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of human CD38 extracellular domain., Liu Q, Kriksunov IA, Graeff R, Munshi C, Lee HC, Hao Q, Structure (Camb) 2005 Sep;13(9):1331-9. PMID:16154090
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (1yh3.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (1yh3.pdb2.gz) 44 Kb
  • CSU: Contacts of Structural Units for 1YH3
  • Likely Quarternary Molecular Structure file(s) for 1YH3
  • Structure Factors (313 Kb)
  • Retrieve 1YH3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YH3 from S2C, [Save to disk]
  • Re-refined 1yh3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YH3 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 1YH3
  • 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
  • 3D motif for 1YH3, from MSDmotif at EBI
  • Fold representative 1yh3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yh3] [1yh3_B] [1yh3_A]
  • SWISS-PROT database: [P28907]
  • Domain organization of [CD38_HUMAN] by SWISSPFAM
  • Other resources with information on 1YH3
  • Community annotation for 1YH3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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