3HMF Transcription date May 29, 2009
title Crystal Structure Of The Second Bromodomain Of Human Poly-Br Containing Protein 1 (Pb1)
authors P.Filippakopoulos, S.Picaud, T.Keates, J.Muniz, F.Von Delft, C.H.Arrowsmith, A.Edwards, J.Weigelt, C.Bountra, S.Knapp, Struct Genomics Consortium (Sgc)
compound source
Molecule: Protein Polybromo-1
Chain: A
Fragment: Bromodomain, Unp Residues 178-291
Synonym: Pb1, Hpb1, Polybromo-1d, Brg1-Associated Factor 18
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pb1, Pbrm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-R3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: C 1 2 1
R_factor 0.171 R_Free 0.199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.810 49.360 33.610 90.00 97.91 90.00
method X-Ray Diffractionresolution 1.63 Å
ligand CL, EDO, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceHistone recognition and large-scale structural analysis of the human bromodomain family., Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP, Barsyte-Lovejoy D, Felletar I, Volkmer R, Muller S, Pawson T, Gingras AC, Arrowsmith CH, Knapp S, Cell. 2012 Mar 30;149(1):214-31. PMID:22464331
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (3hmf.pdb1.gz) 43 Kb
  • Biological Unit Coordinates (3hmf.pdb2.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 3HMF
  • CSU: Contacts of Structural Units for 3HMF
  • Likely Quarternary Molecular Structure file(s) for 3HMF
  • Structure Factors (806 Kb)
  • Retrieve 3HMF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HMF from S2C, [Save to disk]
  • Re-refined 3hmf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HMF 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 3HMF
  • 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
  • 3D motif for 3HMF, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hmf_A] [3hmf]
  • SWISS-PROT database: [Q86U86]
  • Domain organization of [PB1_HUMAN] by SWISSPFAM
  • Domain found in 3HMF: [BROMO ] by SMART
  • Other resources with information on 3HMF
  • Community annotation for 3HMF 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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