5PPC Gene Regulation date Feb 07, 2017
title Pandda Analysis Group Deposition -- Crystal Structure Of Brd Initial Refinement With No Ligand Modelled (Structure 12)
authors N.M.Pearce, T.Krojer, R.Talon, A.R.Bradley, M.Fairhead, R.Sethi, N E.Maclean, P.Collins, J.Brandao-Neto, A.Douangamath, Z.Renjie, A J.Ng, P.E.Brennan, O.Cox, C.Bountra, C.H.Arrowsmith, A.Edwards, F Delft
compound source
Molecule: Bromodomain-Containing Protein 1
Chain: A, B
Synonym: Br140-Like Protein,Bromodomain And Phd Finger-Cont Protein 2;
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Brd1, Brl, Brpf2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.178 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.793 56.128 101.480 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.61 Å
ligand EDO, NA enzyme
Primary referenceA multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density., Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F, Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123. PMID:28436492
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (5ppc.pdb1.gz) 24 Kb
  • Biological Unit Coordinates (5ppc.pdb2.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 5PPC
  • CSU: Contacts of Structural Units for 5PPC
  • Structure Factors (1664 Kb)
  • Retrieve 5PPC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5PPC from S2C, [Save to disk]
  • Re-refined 5ppc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5PPC 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 5PPC
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ppc] [5ppc_A] [5ppc_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5PPC
  • Community annotation for 5PPC at PDBWiki (http://pdbwiki.org)

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