5MMB Viral Protein date Dec 09, 2016
title Crystal Structure Of The Prototype Foamy Virus (Pfv) Intasom Complex With Magnesium And The Insti Xz434 (Compound 6p)
authors D.P.Maskell, V.E.Pye, P.Cherepanov
compound source
Molecule: Pfv Integrase
Chain: A, B
Synonym: Pr125pol
Ec: 2.7.7.49,2.7.7.7,3.1.26.4,3.4.23.-,2.7.7.-,3.1.-.-
Engineered: Yes
Other_details: G217s, S218g = Natural Variance
Organism_scientific: Human Spumaretrovirus
Organism_common: Sfvcpz(Hu)
Organism_taxid: 11963
Gene: Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Aptptpgptpcpaptpgpgpapaptptptpcpgpcpa)
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Tpgpcpgpapapaptptpcpcpaptpgpapcpa)-3');
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.184 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
160.490 160.490 123.830 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.77 Å
ligand GOL, HEZ, MG, OUY, SO4, ZN enzyme Transferase E.C.2.7.7.49 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors., Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR, J Med Chem. 2017 Jul 24. doi: 10.1021/acs.jmedchem.7b00596. PMID:28737946
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (232 Kb) [Save to disk]
  • Biological Unit Coordinates (5mmb.pdb1.gz) 432 Kb
  • LPC: Ligand-Protein Contacts for 5MMB
  • CSU: Contacts of Structural Units for 5MMB
  • Structure Factors (737 Kb)
  • Retrieve 5MMB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MMB from S2C, [Save to disk]
  • Re-refined 5mmb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5MMB 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 5MMB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5mmb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mmb_D] [5mmb_B] [5mmb_C] [5mmb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5MMB
  • Community annotation for 5MMB at PDBWiki (http://pdbwiki.org)

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