4BZC Hydrolase date Jul 25, 2013
title Crystal Structure Of The Tetrameric Dgtp-Bound Wild Type Samhd1 Catalytic Core
authors X.Ji, H.Yang, Y.Wu, J.Yan, J.Mehrens, M.Delucia, C.Hao, A.M.Gronenb J.Skowronski, J.Ahn, Y.Xiong
compound source
Molecule: Deoxynucleoside Triphosphate Triphosphohydrolase
Chain: A, B, C, D
Fragment: Hd Domain, Residues 113-626
Synonym: Dntpase, Dendritic Cell-Derived Ifng-Induced Prote Dcip, Monocyte Protein 5, Mop-5, Sam Domain And Hd Domain-Containing Protein 1, Samhd1;
Ec: 3.1.5.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta 2
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet28
symmetry Space Group: P 1 21 1
R_factor 0.19032 R_Free 0.24480
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.002 138.727 93.715 90.00 113.56 90.00
method X-Ray Diffractionresolution 2.88 Å
ligand MG, MN, T8T enzyme Hydrolase E.C.3.1.5 BRENDA
Primary referenceMechanism of allosteric activation of SAMHD1 by dGTP., Ji X, Wu Y, Yan J, Mehrens J, Yang H, Delucia M, Hao C, Gronenborn AM, Skowronski J, Ahn J, Xiong Y, Nat Struct Mol Biol. 2013 Oct 20. doi: 10.1038/nsmb.2692. PMID:24141705
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (681 Kb) [Save to disk]
  • Biological Unit Coordinates (4bzc.pdb1.gz) 668 Kb
  • LPC: Ligand-Protein Contacts for 4BZC
  • CSU: Contacts of Structural Units for 4BZC
  • Structure Factors (511 Kb)
  • Retrieve 4BZC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BZC from S2C, [Save to disk]
  • Re-refined 4bzc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BZC 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 4BZC
  • 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 4BZC, from MSDmotif at EBI
  • Fold representative 4bzc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bzc_B] [4bzc_D] [4bzc] [4bzc_C] [4bzc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4BZC: [HDc ] by SMART
  • Other resources with information on 4BZC
  • Community annotation for 4BZC at PDBWiki (http://pdbwiki.org)

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