2DYB Oxidoreductase date Sep 08, 2006
title The Crystal Structure Of Human P40(Phox)
authors K.Honbou
compound source
Molecule: Neutrophil Cytosol Factor 4
Chain: A, B
Synonym: Ncf-4, Neutrophil Nadph Oxidase Factor 4, P40- Phox, P40phox;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproex Htb
symmetry Space Group: C 2 2 21
R_factor 0.263 R_Free 0.302
crystal
cell
length a length b length c angle alpha angle beta angle gamma
146.273 189.813 79.883 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.15 Å
ligand CAF enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceFull-length p40phox structure suggests a basis for regulation mechanism of its membrane binding., Honbou K, Minakami R, Yuzawa S, Takeya R, Suzuki NN, Kamakura S, Sumimoto H, Inagaki F, EMBO J. 2007 Feb 21;26(4):1176-86. Epub 2007 Feb 8. PMID:17290225
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (2dyb.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (2dyb.pdb2.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 2DYB
  • CSU: Contacts of Structural Units for 2DYB
  • Likely Quarternary Molecular Structure file(s) for 2DYB
  • Structure Factors (171 Kb)
  • Retrieve 2DYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DYB from S2C, [Save to disk]
  • Re-refined 2dyb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DYB 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 2DYB
  • 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 2DYB, from MSDmotif at EBI
  • Fold representative 2dyb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dyb] [2dyb_A] [2dyb_B]
  • SWISS-PROT database: [Q15080]
  • Domain organization of [NCF4_HUMAN] by SWISSPFAM
  • Domains found in 2DYB: [PB1] [PX] [SH3 ] by SMART
  • Alignments of the sequence of 2DYB with the sequences similar proteins can be viewed for 2DYB's classification [NCF4_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [NCF4_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2DYB
  • Community annotation for 2DYB 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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