3MB3 Signaling Protein date Mar 25, 2010
title Crystal Structure Of The Second Bromodomain Of Pleckstrin Ho Domain Interacting Protein (Phip)
authors P.Filippakopoulos, S.Picaud, T.Keates, E.Ugochukwu, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, S.Knapp, Stru Genomics Consortium (Sgc)
compound source
Molecule: Ph-Interacting Protein
Chain: A
Fragment: Unp Residues 1302-1434
Synonym: Phip, Irs-1 Ph Domain-Binding Protein, Wd Repeat-C Protein 11;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Phip, Wdr11
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-R3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 31 2 1
R_factor 0.206 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.090 92.090 76.120 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.25 Å
ligand MB3 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] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (3mb3.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 3MB3
  • CSU: Contacts of Structural Units for 3MB3
  • Structure Factors (825 Kb)
  • Retrieve 3MB3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MB3 from S2C, [Save to disk]
  • Re-refined 3mb3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MB3 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 3MB3
  • 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 3MB3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1e3mb3, region B:117-269 [Jmol] [rasmolscript] [script source]
        - Domain d1v3mb3, region B:407-496 [Jmol] [rasmolscript] [script source]
  • Fold representative 3mb3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mb3] [3mb3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3MB3: [BROMO ] by SMART
  • Other resources with information on 3MB3
  • Community annotation for 3MB3 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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