3LYI Transcription date Feb 26, 2010
title Pwwp Domain Of Human Bromodomain-Containing Protein 1
authors R.Lam, H.Zeng, S.Ni, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edw A.Bochkarev, J.Min, H.Wu, Structural Genomics Consortium (Sgc)
compound source
Molecule: Bromodomain-Containing Protein 1
Chain: A, B
Fragment: Pwwp Domain, Residues 925-1049
Synonym: Br140-Like Protein
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Brd1, Brl, Brpf2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-(De3)-V2r-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.276
length a length b length c angle alpha angle beta angle gamma
45.029 46.085 130.712 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand OCS enzyme
note 3LYI is a representative structure
Primary referenceStructural and Histone Binding Ability Characterizations of Human PWWP Domains., Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J, PLoS One. 2011;6(6):e18919. Epub 2011 Jun 20. PMID:21720545
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (3lyi.pdb1.gz) 43 Kb
  • Biological Unit Coordinates (3lyi.pdb2.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 3LYI
  • CSU: Contacts of Structural Units for 3LYI
  • Structure Factors (239 Kb)
  • Retrieve 3LYI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LYI from S2C, [Save to disk]
  • Re-refined 3lyi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LYI 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 3LYI
  • 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 3LYI, from MSDmotif at EBI
  • Fold representative 3lyi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lyi_A] [3lyi] [3lyi_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LYI: [PWWP ] by SMART
  • Other resources with information on 3LYI
  • Community annotation for 3LYI 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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