Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  TRUNCATED HUMAN GROB[5-73], NMR, 20 STRUCTURES
 
Authors :  Y. Q. Qian, K. Johanson, P. Mcdevitt
Date :  18 Oct 99  (Deposition) - 04 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Chemokine, Chemokine 15-O, Human Chemokine Grob[5-73], Cxc Chemokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Q. Qian, K. Johanson, P. Mcdevitt
Nuclear Magnetic Resonance Solution Structure Of Truncated Human Grobeta [5-73] And Its Structural Comparison With Cxc Chemokine Family Members Groalpha And Il-8.
J. Mol. Biol. V. 294 1065 1999
PubMed-ID: 10600366  |  Reference-DOI: 10.1006/JMBI.1999.3333
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GROB[5-73]
    Cellular LocationBLOOD
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Strain(LW 14)
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Strain(LW 14)

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1QNK)

(-) Sites  (0, 0)

(no "Site" information available for 1QNK)

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:9 -A:35
2A:11 -A:51
3B:9 -B:35
4B:11 -B:51

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QNK)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SMALL_CYTOKINES_CXCPS00471 Small cytokines (intercrine/chemokine) C-x-C subfamily signature.CXCL2_HUMAN43-87
 
  2A:9-53
B:9-53

(-) Exons   (0, 0)

(no "Exon" information available for 1QNK)

(-) Sequences/Alignments

NMR Structure
   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:69
 aligned with CXCL2_HUMAN | P19875 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:69
                                    48        58        68        78        88        98         
          CXCL2_HUMAN    39 TELRCQCLQTLQGIHLKNIQSVKVKSPGPHCAQTEVIATLKNGQKACLNPASPMVKKIIEKMLKNGKSN 107
               SCOP domains d1qnka_ A: Gro beta                                                   SCOP domains
               CATH domains 1qnkA00 A:5-73  [code=2.40.50.40, no name defined]                    CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeee.........eeeeee....eeee.....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SMALL_CYTOKINES_CXC  PDB: A:9-53             -------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1qnk A   5 TELRCQCLQTLQGIHLKNIQSVKVKSPGPHCAQTEVIATLKNGQKACLNPASPMVKKIIEKMLKNGKSN  73
                                    14        24        34        44        54        64         

Chain B from PDB  Type:PROTEIN  Length:69
 aligned with CXCL2_HUMAN | P19875 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:69
                                    48        58        68        78        88        98         
          CXCL2_HUMAN    39 TELRCQCLQTLQGIHLKNIQSVKVKSPGPHCAQTEVIATLKNGQKACLNPASPMVKKIIEKMLKNGKSN 107
               SCOP domains d1qnkb_ B: Gro beta                                                   SCOP domains
               CATH domains 1qnkB00 B:5-73  [code=2.40.50.40, no name defined]                    CATH domains
           Pfam domains (1) IL8-1qnkB01 B:5-67                                             ------ Pfam domains (1)
           Pfam domains (2) IL8-1qnkB02 B:5-67                                             ------ Pfam domains (2)
         Sec.struct. author ....................eeeee.........eeeeee....eeee.....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SMALL_CYTOKINES_CXC  PDB: B:9-53             -------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1qnk B   5 TELRCQCLQTLQGIHLKNIQSVKVKSPGPHCAQTEVIATLKNGQKACLNPASPMVKKIIEKMLKNGKSN  73
                                    14        24        34        44        54        64         

   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  (1, 2)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

NMR Structure

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A,B   (CXCL2_HUMAN | P19875)
molecular function
    GO:0045236    CXCR chemokine receptor binding    Interacting selectively and non-covalently with a chemokine receptor in the CXCR family.
    GO:0008009    chemokine activity    The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    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).
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0070098    chemokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0090023    positive regulation of neutrophil chemotaxis    Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0002237    response to molecule of bacterial origin    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

 Visualization

(-) Interactive Views

NMR Structure
  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 1qnk)
 
  Sites
(no "Sites" information available for 1qnk)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qnk)
 

(-) 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
  1qnk
    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
  CXCL2_HUMAN | P19875
    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
  CXCL2_HUMAN | P19875
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1QNK)

(-) Related Entries Specified in the PDB File

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