Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF SOLUBLE HUMAN INTERLEUKIN 8 EXPRESSED IN PICHIA PASTORIS
 
Authors :  D. A. Ostrov, Y. A. Pompeu, J. J. Jakoncic
Date :  20 Dec 14  (Deposition) - 23 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytokine, Alpha Beta Protein, Il8 Fold, Chemokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. A. Ostrov, Y. A. Pompeu, J. J. Jakoncic
The Crystal Structure Of Soluble Human Interleukin 8 Expressed In Pichia Pastoris
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INTERLEUKIN-8
    ChainsA
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System Taxid4922
    GeneCXCL8, IL8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-8,C-X-C MOTIF CHEMOKINE 8,CHEMOKINE (C-X-C MOTIF) LIGAND 8,EMOCTAKIN,GRANULOCYTE CHEMOTACTIC PROTEIN 1,GCP-1,MONOCYTE-DERIVED NEUTROPHIL CHEMOTACTIC FACTOR,MDNCF,MONOCYTE-DERIVED NEUTROPHIL- ACTIVATING PEPTIDE,MONAP,NEUTROPHIL-ACTIVATING PROTEIN 1,NAP-1, PROTEIN 3-10C,T-CELL CHEMOTACTIC FACTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4XDX)

(-) Sites  (0, 0)

(no "Site" information available for 4XDX)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:7 -A:34
2A:9 -A:50

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XDX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XDX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XDX)

(-) Exons   (0, 0)

(no "Exon" information available for 4XDX)

(-) Sequences/Alignments

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:70
                                                                                                     
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhh.eeeeeee.........eeeeee....eeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  4xdx A  3 KELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRAENS 72
                                    12        22        32        42        52        62        72

   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 4XDX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XDX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XDX)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

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
(no "Ligands, Modified Residues, Ions" information available for 4xdx)
 
  Sites
(no "Sites" information available for 4xdx)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xdx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4xdx
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IL8_HUMAN | P10145
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  IL8_HUMAN | P10145
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IL8_HUMAN | P101451icw 1ikl 1ikm 1il8 1ilp 1ilq 1qe6 1rod 2il8 3il8 5d14

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4XDX)