Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  IL-18 RECEPTOR COMPLEX
 
Authors :  H. Wei, X. Wang
Date :  26 Aug 14  (Deposition) - 15 Oct 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A,D  (1x)
Keywords :  Beta-Trefoil Fold, Ig-Like Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wei, D. Wang, Y. Qian, X. Liu, S. Fan, H. S. Yin, X. Wang
Structural Basis For The Specific Recognition Of Il-18 By Its Alpha Receptor.
Febs Lett. V. 588 3838 2014
PubMed-ID: 25261253  |  Reference-DOI: 10.1016/J.FEBSLET.2014.09.019

(-) Compounds

Molecule 1 - INTERLEUKIN-18 RECEPTOR 1
    Chains: C, A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: IL18R1, IL1RRP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-18R-1, IL-18R1, CD218 ANTIGEN-LIKE FAMILY MEMBER A, CDW218A, IL1 RECEPTOR-RELATED PROTEIN, IL-1RRP, IL1R-RP
 
Molecule 2 - INTERLEUKIN-18
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IL18, IGIF, IL1F4
    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 Unit : ABCD
Biological Unit 1 (1x):  BC 
Biological Unit 2 (1x): A  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:114 , ASN C:197 , GLU C:289 , LEU C:292 , ARG C:315BINDING SITE FOR RESIDUE NAG C 801
2AC2SOFTWAREGLU C:122 , TYR C:182 , ASN C:203BINDING SITE FOR RESIDUE NAG C 802
3AC3SOFTWAREASN C:236 , SER C:238 , HIS C:277BINDING SITE FOR RESIDUE NAG C 803
4AC4SOFTWARELEU C:295 , ASN C:297BINDING SITE FOR RESIDUE NAG C 804
5AC5SOFTWAREARG A:114 , PHE A:188 , ASN A:197 , GLU A:289 , LEU A:292 , ARG A:315BINDING SITE FOR RESIDUE NAG A 401
6AC6SOFTWAREGLU A:122 , VAL A:125 , TYR A:182 , ASN A:203BINDING SITE FOR RESIDUE NAG A 402
7AC7SOFTWAREASN A:236 , SER A:238 , HIS A:277 , SER A:279 , VAL A:281BINDING SITE FOR RESIDUE NAG A 403
8AC8SOFTWARELEU A:295 , ASN A:297BINDING SITE FOR RESIDUE NAG A 404

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:22 -A:41
2A:43 -A:81
3A:119 -A:158
4A:140 -A:185
5A:237 -A:298
6C:22 -C:41
7C:43 -C:81
8C:119 -C:158
9C:140 -C:185
10C:237 -C:298

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp C:86 -Pro C:87
2Trp A:86 -Pro A:87
3Ala B:42 -Pro B:43
4Ala D:42 -Pro D:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R6U)

(-) Exons   (0, 0)

(no "Exon" information available for 4R6U)

(-) 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeee.......eeeee......ee.....eeee..eeee...hhhhheeeeee....eeeeeeeee........hhh.eeeeeee...eeeee.....hhh.eeeeeeee..ee..eeeee.hhhhheeeeeeeeeee..eeeeeeeeeeeeee........ee....eeeee......eeeeeeeee....eeeee.....ee...eeee.....eeeeeeeee...........eeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6u A  21 SCTSRPHITVVEGEPFYLKHCSCTTKSWYKSSGSQEHVELNPRRIALHDCVLEFWPVELNDTGSYFFQMKNYTQKWKLNVIRRNKHSCFTERQVTSKIVEVKKFFQITCENSYYQTLVNSTSLYKNCKKLPTIKKNAEFEDQGYYSCVHFLHHNGKLFNITKTFNITIVEDRSNIVPVLLGPKLNHVAVELGKNVRLNCSALLNEEDVIYWMFGENIHEEKEMRIMTPEGKWHASKVLRIENIGESNLNVLYNCTVASTGGTDTKSFILVRKAD 318
                                    30        40  ||    58        68  ||    81        91       101       111       121       131       141       151       161|      178       188       198       208       218       228       238       248    || 264       274       284       294       304       314    
                                                 43|                 71|                                                                                   161|                                                                                 253|                                                          
                                                  52                  75                                                                                    169                                                                                  260                                                          


Chain B from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeee.....eeee..hhhhhhhh.....eeeeeeee.....eeeeeeee...eeeeehhhhh.eee......ee........eeeeee..eeeeeeeee.....eeeeeeee..eeeeeeee.....hhhhheeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6u B   1 YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDSRDNAPRTIFIISMYKDSQPRGMAVTISVKSEKISTLSSENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLASEKERDLFKLILKKEDELGDRSIMFTVQN 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     


Chain C from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeee........eeeee......ee.....eeee..eeee...hhhhheeeeeee..eeeeeeeeee........hhh.eeeeeee...eeeee.....hhh.eeeeeeee..ee..eeeee.hhhhheeeeeeeeeee..eeeeeeeeeeeeee........ee....eeeee......eeeeeeeee....eeeee.....ee..eeeee.....eeeeeeeee...........eeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6u C  21 SCTSRPHITVVEGEPFYLKHCSCTTTKSWYKSSGSQEHVELNPRRIALHDCVLEFWPVELNDTGSYFFQMKNYTQKWKLNVIRRNKHSCFTERQVTSKIVEVKKFFQITCENSYYQTLVNSTSLYKNCKKLPTIKKNAEFEDQGYYSCVHFLHHNGKLFNITKTFNITIVEDRSNIVPVLLGPKLNHVAVELGKNVRLNCSALLNEEDVIYWMFGENIHEEKEMRIMTPEGKWHASKVLRIENIGESNLNVLYNCTVASTGGTDTKSFILVRKAD 318
                                    30        40  ||    57        67   ||   80        90       100       110       120       130       140       150       160||     177       187       197       207       217       227       237       247     ||263       273       283       293       303       313     
                                                 43|                  71|                                                                                   161|                                                                                 253|                                                          
                                                  51                   75                                                                                    169                                                                                  260                                                          


Chain D from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeee.....eeee..hhhhhhhh.....eeeeeeee.....eeeeeeee...eeeeehhhhh.eee......ee........eeeeee..eeeeeeeee.....eeeeeeee..eeeeeeee.....hhhhheeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6u D   1 YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDSRDNAPRTIFIISMYKDSQPRGMAVTISVKSEKISTLSSENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSYEGYFLASEKERDLFKLILKKEDELGDRSIMFTVQN 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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 4R6U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R6U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R6U)

(-) Gene Ontology  (43, 48)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala B:42 - Pro B:43   [ RasMol ]  
    Ala D:42 - Pro D:43   [ RasMol ]  
    Trp A:86 - Pro A:87   [ RasMol ]  
    Trp C:86 - Pro C:87   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4r6u
    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
  IL18R_HUMAN | Q13478
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  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
 
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
  IL18R_HUMAN | Q13478
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  IL18_HUMAN | Q14116
    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
        IL18R_HUMAN | Q13478: 3wo3 3wo4
        IL18_HUMAN | Q14116: 1j0s 2vxt 3f62 3wo2 3wo3 3wo4 4eee 4ekx 4hjj 4xfs 4xft 4xfu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4R6U)