4CC9 Protein Binding date Oct 19, 2013
title Crystal Structure Of Human Samhd1 (Amino Acid Residues 582-6 To Vpx Isolated From Sooty Mangabey And Human Dcaf1 (Amino Residues 1058-1396)
authors D.Schwefel, H.C.T.Groom, V.C.Boucherit, E.Christodoulou, P.A.Wal J.P.Stoye, K.N.Bishop, I.A.Taylor
compound source
Molecule: Protein Vprbp
Chain: A
Fragment: Residues 1058-1396
Synonym: Ddb1- And Cul4-Associated Factor 1, Hiv-1 Vpr-Bind In, Vprbp, Vpr-Interacting Protein, Dcaf1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Ptriex-6

Molecule: Protein Vpx
Chain: B
Synonym: Viral Protein X, X Orf Protein, Vpx
Engineered: Yes

Organism_scientific: Simian Immunodeficiency Virus
Organism_taxid: 11723
Strain: Sooty Mangabey
Variant: Isolate Pbj14bcl-3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet49b

Molecule: Deoxynucleoside Triphosphate Triphosphohydrolase
Chain: C
Fragment: Residues 582-626
Synonym: Dntpase, Dendritic Cell-Derived Ifng-Induced Prote Monocyte Protein 5, Mop-5, Sam Domain And Hd Domain-Contain Otein 1, Samhd1;
Ec: 3.1.5.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet52b
symmetry Space Group: P 21 21 21
R_factor 0.176 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.250 82.881 115.561 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.47 Å
ligand PG4, ZN enzyme Hydrolase E.C.3.1.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural basis of lentiviral subversion of a cellular protein degradation pathway., Schwefel D, Groom HC, Boucherit VC, Christodoulou E, Walker PA, Stoye JP, Bishop KN, Taylor IA, Nature. 2013 Dec 15. doi: 10.1038/nature12815. PMID:24336198
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (4cc9.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 4CC9
  • CSU: Contacts of Structural Units for 4CC9
  • Structure Factors (228 Kb)
  • Retrieve 4CC9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4CC9 from S2C, [Save to disk]
  • Re-refined 4cc9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4CC9 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 4CC9
  • 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 4CC9, from MSDmotif at EBI
  • Fold representative 4cc9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4cc9] [4cc9_B] [4cc9_A] [4cc9_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4CC9
  • Community annotation for 4CC9 at PDBWiki (http://pdbwiki.org)

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