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 :  CRYSTAL STRUCTURE OF YLDV 14L IL-18 BINDING PROTEIN IN COMPLEX WITH HUMAN IL-18
 
Authors :  B. E. Krumm, Y. Xiang, J. Deng
Date :  28 Mar 12  (Deposition) - 26 Sep 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Interleukin-18 Binding Protein, Beta Trefoil, Immunoglobulin Fold, Yaba, Yldv, Cytokine Signaling, Cytokine-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Krumm, X. Meng, Z. Wang, Y. Xiang, J. Deng
A Unique Bivalent Binding And Inhibition Mechanism By The Yatapoxvirus Interleukin 18 Binding Protein.
Plos Pathog. V. 8 02876 2012
PubMed-ID: 22927815  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002876

(-) Compounds

Molecule 1 - 14L PROTEIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB3
    Expression System Strain: ROSETTA-GAMI 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 14L
    Organism Common: YLDV
    Organism Scientific: YABA-LIKE DISEASE VIRUS
    Organism Taxid: 132475
 
Molecule 2 - INTERLEUKIN-18
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IGIF, IL-18, IL18, IL1F4
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-18, IBOCTADEKIN, INTERFERON GAMMA-INDUCING FACTOR, IFN- GAMMA-INDUCING FACTOR, INTERLEUKIN-1 GAMMA, IL-1 GAMMA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4EEE)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:87
2A:43 -A:111
3A:132 -C:132
4C:21 -C:87
5C:43 -C:111

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EEE)

(-) 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:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....eeeeeeeeee......eeeeee...ee.hhh.....eeeee.............eeeeeee..hhhhhhh.eeeeee.....eeeeehhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4eee A  20 ECVKTRSVNIHVPVKETSKVVLECRGDSYFRHFSYVYWIIGKNKTVDQLPPNSGYRERIYLFKKPHRCENRPRADLILTNITDEMRNEKLTCVLIDPKDPLKESVILSKIWNCVY 134
                                    29        39        49        59        69        79        89        99       109       119       129     


Chain B from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains d4eeeb_ B: automated matches                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeee.....eeee.......eeeeeeee......eeeeee......eeehhhhh.eee......ee........eeeeee..eeeeeeeee.....eeeeeeee..eeeeeeee.....hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eee B   1 YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDNAPRTIFIISMYKDSQPRGMAVTISVASAAASTLSSENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLASEKERDLFKLILKKEDELGDRSIMFTVQN 155
                                    10        20        30 ||     48        58        68        78        88        98       108       118       128       138       148       
                                                          32|                                                                                                                  
                                                           41                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.....eeeeeeeeee......eeeeee...ee.hhh.....eeeee.............eeeeeee..hhhhhhh.eeeeee.....eeeeehhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4eee C  19 MECVKTRSVNIHVPVKETSKVVLECRGDSYFRHFSYVYWIIGKNKTVDQLPPNSGYRERIYLFKKPHRCENRPRADLILTNITDEMRNEKLTCVLIDPKDPLKESVILSKIWNCV 133
                                    28        38        48        58        68        78        88        98       108       118       128     


Chain D from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains d4eeed_ D: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee....eeee.....eeee...eeeeeeee......eeeeee......eeehhhhh.eee......ee........eeeeee..eeeeeeeee......eeeeee....eeeeee...hhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eee D   1 YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDTIFIISMYKDSQPRGMAVTISVASAAASTLSSENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLASEKERDLFKLILKKLGDRSIMFTVQNE 156
                                    10        20        30 ||     52        62        72        82        92       102       112       122       132       145       155 
                                                          32|                                                                                            140|            
                                                           45                                                                                             144
   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)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

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 4eee)
 
  Sites
(no "Sites" information available for 4eee)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4eee)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4eee
    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
  IL18_HUMAN | Q14116
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q9DHU8_YLDV | Q9DHU8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

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
  IL18_HUMAN | Q14116
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9DHU8_YLDV | Q9DHU8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IL18_HUMAN | Q14116: 1j0s 2vxt 3f62 3wo2 3wo3 3wo4 4ekx 4hjj 4r6u 4xfs 4xft 4xfu
UniProtKB/TrEMBL
        Q9DHU8_YLDV | Q9DHU8: 4ekx

(-) Related Entries Specified in the PDB File

4ekx