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(-) Description

Title :  SH3 DOMAIN OF P40PHOX COMPLEXED WITH C-TERMINAL POLYPROLINE REGION OF P47PHOX
 
Authors :  C. Massenet, S. Chenavas, C. Cohen-Addad, M. -C. Dagher, G. Brandolin, E. Pebay-Peyroula, F. Fieschi
Date :  26 Aug 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Nadph Oxidase, P40Phox, P47Phox, Sh3 Domain, Polyproline (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Massenet, S. Chenavas, C. Cohen-Addad, M. -C. Dagher, G. Brandolin, E. Pebay-Peyroula, F. Fieschi
Effects Of P47Phox C-Terminus Phosphorylation On Binding Interactions With P40Phox And P67Phox: Structural And Functional Comparison Of P40Phox P67Phox Sh3 Domains
J. Biol. Chem. V. 280 13752 2005
PubMed-ID: 15657040  |  Reference-DOI: 10.1074/JBC.M412897200

(-) Compounds

Molecule 1 - NEUTROPHIL CYTOSOL FACTOR 4
    CellNEUTROPHIL
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPIVEX2.4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentSH3 DOMAIN, RESIDUES 174-228
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNCF-4, NEUTROPHIL NADPH OXIDASE FACTOR 4, P40PHOX, P40-PHOX
 
Molecule 2 - NEUTROPHIL CYTOSOL FACTOR 1
    CellNEUTROPHIL
    ChainsC, D
    FragmentPOLYPROLINE MOTIF, RESIDUES 360-372
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNCF-1,NEUTROPHIL NADPH OXIDASE FACTOR 1,47 KDA NEUTROPHIL OXIDASE FACTOR, P47-PHOX
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2SO44Ligand/IonSULFATE ION
3TFA2Ligand/IonTRIFLUOROACETYL GROUP
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SO41Ligand/IonSULFATE ION
3TFA-1Ligand/IonTRIFLUOROACETYL GROUP
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SO43Ligand/IonSULFATE ION
3TFA2Ligand/IonTRIFLUOROACETYL GROUP

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:171 , HIS A:172 , HOH A:2083 , HOH A:2084 , HOH A:2085BINDING SITE FOR RESIDUE SO4 A1229
2AC2SOFTWAREARG B:202 , ASN B:204 , LYS B:205 , HOH B:2081BINDING SITE FOR RESIDUE SO4 B1229
3AC3SOFTWAREILE B:170 , LYS B:171 , HIS B:172 , ARG B:174 , PHE B:198 , HOH B:2045 , HOH B:2082 , HOH B:2083 , HOH B:2084 , HOH B:2086 , HOH B:2087BINDING SITE FOR RESIDUE SO4 B1230
4AC4SOFTWARELYS A:192 , LYS A:205 , ARG B:174 , PHE B:198 , HOH B:2088BINDING SITE FOR RESIDUE SO4 B1231
5AC5SOFTWARELEU A:187 , ILE A:203 , ILE A:218 , LEU B:169 , ILE B:170 , SER B:201 , ARG B:202 , HOH B:2089 , PRO C:369BINDING SITE FOR RESIDUE TFA B1232
6AC6SOFTWAREILE A:170 , ARG A:202 , LEU B:187 , ILE B:218 , HOH B:2090 , PRO D:369 , SER D:370BINDING SITE FOR RESIDUE TFA B1233

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W70)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W70)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009314L147INCF4_HUMANPolymorphism  ---A/BI170I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009314L147INCF4_HUMANPolymorphism  ---AI170I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009314L147INCF4_HUMANPolymorphism  ---BI170I

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NCF4_HUMAN170-229
 
  2A:175-228
B:175-228
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NCF4_HUMAN170-229
 
  1A:175-228
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NCF4_HUMAN170-229
 
  1-
B:175-228

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002488991ENSE00002158629chr22:37257030-37257245216NCF4_HUMAN1-11110--
1.2ENST000002488992ENSE00001766180chr22:37260087-3726017185NCF4_HUMAN11-39290--
1.3ENST000002488993ENSE00001678302chr22:37260961-37261114154NCF4_HUMAN40-91520--
1.4ENST000002488994ENSE00001775431chr22:37263434-3726350471NCF4_HUMAN91-114240--
1.5ENST000002488995ENSE00000880088chr22:37266457-37266584128NCF4_HUMAN115-157432A:169-174
B:169-174
6
6
1.6ENST000002488996ENSE00000880089chr22:37267694-3726775158NCF4_HUMAN157-176202A:175-176
B:175-176
2
2
1.8ENST000002488998ENSE00000653691chr22:37268369-3726846799NCF4_HUMAN177-209332A:177-209
B:177-209
33
33
1.9aENST000002488999aENSE00001270603chr22:37271695-37271825131NCF4_HUMAN210-253442A:210-228
B:210-228
19
19
1.9eENST000002488999eENSE00000653693chr22:37272071-3727213666NCF4_HUMAN253-275230--
1.10bENST0000024889910bENSE00001850230chr22:37273670-37274057388NCF4_HUMAN275-339650--

(-) Sequences/Alignments

Asymmetric 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:60
 aligned with NCF4_HUMAN | Q15080 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:83
                                   155       165       175       185       195       205       215       225   
           NCF4_HUMAN   146 ALRRLRPRTRKVKSVSPQGNSVDRMAAPRAEALFDFTGNSKLELNFKAGDVIFLLSRINKDWLEGTVRGATGIFPLSFVKILK 228
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains 1w70A0                       0 A:169-228 SH3 Domains                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....e-----------------------eee..................eeeeeee....eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -I--------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SH3  PDB: A:175-228 UniProt: 170-229                        PROSITE
           Transcript 1 (1) Exon 1.5    -------------------Exon 1.8  PDB: A:177-209         Exon 1.9a           Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.6            ---------------------------------------------------- Transcript 1 (2)
                 1w70 A 169 LIKHMR-----------------------AEALFDFTGNSKLELNFKAGDVIFLLSRINKDWLEGTVRGATGIFPLSFVKILK 228
                                 |   -         -       175       185       195       205       215       225   
                               174                     175                                                     

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with NCF4_HUMAN | Q15080 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:83
                                   155       165       175       185       195       205       215       225   
           NCF4_HUMAN   146 ALRRLRPRTRKVKSVSPQGNSVDRMAAPRAEALFDFTGNSKLELNFKAGDVIFLLSRINKDWLEGTVRGATGIFPLSFVKILK 228
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains 1w70B0                       0 B:169-228 SH3 Domains                                CATH domains
           Pfam domains (1) ------------------------------SH3_1-1w70B01 B:176-221                       ------- Pfam domains (1)
           Pfam domains (2) ------------------------------SH3_1-1w70B02 B:176-221                       ------- Pfam domains (2)
         Sec.struct. author .....e-----------------------eee...ee.......ee....eeeeeee....eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -I--------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SH3  PDB: B:175-228 UniProt: 170-229                        PROSITE
           Transcript 1 (1) Exon 1.5    -------------------Exon 1.8  PDB: B:177-209         Exon 1.9a           Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.6            ---------------------------------------------------- Transcript 1 (2)
                 1w70 B 169 LIKHMR-----------------------AEALFDFTGNSKLELNFKAGDVIFLLSRINKDWLEGTVRGATGIFPLSFVKILK 228
                                 |   -         -       175       185       195       205       215       225   
                               174                     175                                                     

Chain C from PDB  Type:PROTEIN  Length:14
 aligned with NCF1_HUMAN | P14598 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:14
                                   368    
           NCF1_HUMAN   359 SKPQPAVPPRPSAD 372
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 1w70 C 359 xKPQPAVPPRPSAD 372
                            |      368    
                            |             
                          359-ACE         

Chain D from PDB  Type:PROTEIN  Length:12
 aligned with NCF1_HUMAN | P14598 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:12
                                   368  
           NCF1_HUMAN   359 SKPQPAVPPRPS 370
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 1w70 D 359 xKPQPAVPPRPS 370
                            |      368  
                          359-ACE       

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1W70)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: SH3 (175)
(-)
Family: SH3_1 (141)
1aSH3_1-1w70B01B:176-221
1bSH3_1-1w70B02B:176-221

(-) Gene Ontology  (30, 42)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

Chain C,D   (NCF1_HUMAN | P14598)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    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:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    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:0016175    superoxide-generating NADPH oxidase activity    Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-.
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:0006968    cellular defense response    A defense response that is mediated by cells.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0045730    respiratory burst    A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0042554    superoxide anion generation    The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways.
    GO:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
    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:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NCF1_HUMAN | P145981gd5 1k4u 1kq6 1ng2 1o7k 1ov3 1uec 1wlp
        NCF4_HUMAN | Q150801h6h 1oey 1w6x 1z9q 2dyb

(-) Related Entries Specified in the PDB File

1gd5 SOLUTION STRUCTURE OF THE PX DOMAIN FROM HUMAN P47PHOXNADPH OXIDASE
1h6h STRUCTURE OF THE PX DOMAIN FROM P40PHOX BOUND TO PHOSPHATIDYLINOSITOL 3-PHOSPHATE
1k4u SOLUTION STRUCTURE OF THE C-TERMINAL SH3 DOMAIN OF P67PHOXCOMPLEXED WITH THE C- TERMINAL TAIL REGION OF P47PHOX
1kq6 P47PHOX PX DOMAIN
1ng2 STRUCTURE OF AUTOINHIBITED P47PHOX
1o7k HUMAN P47 PX DOMAIN COMPLEX WITH SULPHATES
1oey HETERODIMER OF P40PHOX AND P67PHOX PB1 DOMAINS FROM HUMAN NADPH OXIDASE
1ov3 STRUCTURE OF THE P22PHOX-P47PHOX COMPLEX
1uec CRYSTAL STRUCTURE OF AUTOINHIBITED FORM OF TANDEM SH3DOMAIN OF P47PHOX
1w6x SH3 DOMAIN OF P40PHOX, COMPONENT OF THE NADPH OXIDASE