1H6H - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF THE PX DOMAIN FROM P40PHOX BOUND TO PHOSPHATIDYLINOSITOL 3-PHOSPHATE

Authors :   D. Karathanassis, J. Bravo, M. Pacold, O. Perisic, R. L. Williams

Date :   15 Jun 01 (Deposition) - 01 Nov 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

Keywords :   Px Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Bravo, D. Karathanassis, C. M. Pacold, M. E. Pacold, C. D. Ellson, K. E. Anderson, J. G. Butler, I. Lavenir, O. Perisic, P. T. Hawkins, L. Stephens, R. L. Williams
The Crystal Structure Of The Px Domain From P40Phox Bound To Phosphatidylinositol 3-Phosphate
Mol. Cell V. 8 829 2001
PubMed-ID: 11684018 | Reference-DOI: 10.1016/S1097-2765(01)00372-0
(for further references see the PDB file header)

Molecule 1 - NEUTROPHIL CYTOSOL FACTOR 4
	Cell	:	NEUTROPHIL
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Variant	:	DE3
	Fragment	:	PX DOMAIN RESIDUES 2-144
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NCF-4, NEUTROPHIL NADPH OXIDASE FACTOR 4, P40-PHOX, P40PHOX

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	PIB	1	Ligand/Ion	2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:26 , ALA A:27 , ARG A:58 , TYR A:59 , ARG A:60 , LYS A:92 , VAL A:93 , TYR A:94 , ARG A:105 , HOH A:2057 , HOH A:2170 , HOH A:2171 , HOH A:2172 , HOH A:2173 , HOH A:2174 , HOH A:2175 , HOH A:2176 , HOH A:2177 , HOH A:2178 , HOH A:2179 , HOH A:2180	BINDING SITE FOR RESIDUE PIB A 150
2	AC2	SOFTWARE	ILE A:29 , GLU A:30 , GLU A:31 , GLN A:99 , HOH A:2038 , HOH A:2041 , HOH A:2181	BINDING SITE FOR RESIDUE GOL A 151

(no "SS Bond" information available for 1H6H)

(no "Cis Peptide Bond" information available for 1H6H)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_065949	R	105	Q	NCF4_HUMAN	Disease (CGD3)	387906808	A	R	105	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PX	PS50195	PX domain profile.	NCF4_HUMAN	19-140	1	A:19-140

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000248899	1	ENSE00002158629	chr22:37257030-37257245	216	NCF4_HUMAN	1-11	11	1	A:2-11	10
1.2	ENST00000248899	2	ENSE00001766180	chr22:37260087-37260171	85	NCF4_HUMAN	11-39	29	1	A:11-39	29
1.3	ENST00000248899	3	ENSE00001678302	chr22:37260961-37261114	154	NCF4_HUMAN	40-91	52	1	A:40-91	52
1.4	ENST00000248899	4	ENSE00001775431	chr22:37263434-37263504	71	NCF4_HUMAN	91-114	24	1	A:91-114	24
1.5	ENST00000248899	5	ENSE00000880088	chr22:37266457-37266584	128	NCF4_HUMAN	115-157	43	1	A:115-144	30
1.6	ENST00000248899	6	ENSE00000880089	chr22:37267694-37267751	58	NCF4_HUMAN	157-176	20	0	-	-
1.8	ENST00000248899	8	ENSE00000653691	chr22:37268369-37268467	99	NCF4_HUMAN	177-209	33	0	-	-
1.9a	ENST00000248899	9a	ENSE00001270603	chr22:37271695-37271825	131	NCF4_HUMAN	210-253	44	0	-	-
1.9e	ENST00000248899	9e	ENSE00000653693	chr22:37272071-37272136	66	NCF4_HUMAN	253-275	23	0	-	-
1.10b	ENST00000248899	10b	ENSE00001850230	chr22:37273670-37274057	388	NCF4_HUMAN	275-339	65	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:143
 aligned with NCF4_HUMAN | Q15080 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   
           NCF4_HUMAN     2 AVAQQLRAESDFEQLPDDVAISANIADIEEKRGFTSHFVFVIEVKTKGGSKYLIYRRYRQFHALQSKLEERFGPDSKSSALACTLPTLPAKVYVGVKQEIAEMRIPALNAYMKSLLSLPVWVLMDEDVRIFFYQSPYDSEQVP 144
               SCOP domains d1h6ha_ A: p40phox NADPH oxidase                                                                                                                SCOP domains
               CATH domains 1h6hA00 A:2-144 PX Domain                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeeeeeeeeeee.....eeeeeeeeee....eeeeeeehhhhhhhhhhhhhhhh....hhhhh.............hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------Q--------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PX  PDB: A:19-140 UniProt: 19-140                                                                                         ---- PROSITE
           Transcript 1 (1) Exon 1.1  ----------------------------Exon 1.3  PDB: A:40-91 UniProt: 40-91               -----------------------Exon 1.5  PDB: A:115-144       Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.2  PDB: A:11-39       ---------------------------------------------------Exon 1.4  PDB: A:91-114 ------------------------------ Transcript 1 (2)
                 1h6h A   2 AVAQQLRAESDFEQLPDDVAISANIADIEEKRGFTSHFVFVIEVKTKGGSKYLIYRRYRQFHALQSKLEERFGPDSKSSALACTLPTLPAKVYVGVKQEIAEMRIPALNAYMKSLLSLPVWVLMDEDVRIFFYQSPYDSEQVP 144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: PX domain (23)

Superfamily: PX domain (23)

Family: PX domain (9)

Protein domain: p40phox NADPH oxidase (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1h6ha_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: PX Domain (10)

Homologous Superfamily: PX Domain (10)

Human (Homo sapiens) (5)

1h6hA00

A:2-144

(no "Pfam Domain" information available for 1H6H)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NCF4_HUMAN | Q15080)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0035091	phosphatidylinositol binding	Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	GO:0032266	phosphatidylinositol-3-phosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0016176	superoxide-generating NADPH oxidase activator activity	Increases the activity of the enzyme superoxide-generating NADPH oxidase.
biological process
	GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0048010	vascular endothelial growth factor receptor signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0043020	NADPH oxidase complex	A enzyme complex of which the core is a heterodimer composed of a light (alpha) and heavy (beta) chain, and requires several other water-soluble proteins of cytosolic origin for activity. Functions in superoxide generation by the NADPH-dependent reduction of O2.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0032010	phagolysosome	A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PIB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1h6h)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1h6h
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NCF4_HUMAN \| Q15080
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	613960
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NCF4_HUMAN \| Q15080
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NCF4_HUMAN \| Q15080	:	1oey 1w6x 1w70 1z9q 2dyb

(no "Related Entries Specified in the PDB File" available for 1H6H)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (5, 5)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (19, 19)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File