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 Diffraction	resolution	3.15 Å
ligand	CAF	enzyme
Gene Ontology	Chain Function Process Component A, B protein binding protein dimerization activit... antigen processing and prese... antigen processing and prese... immune response antigen processing and prese... interaction with host oxidation-reduction process phagosome maturation cytoplasm cytosol membrane phagolysosome NADPH oxidase complex
Primary reference	Full-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 (173 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_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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