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

(-) Description

Title :  CRYSTAL STRUCTURE OF ECTODOMAIN 3 OF THE IL-13 RECEPTOR ALPHA1 IN COMPLEX WITH A HUMAN NEUTRALIZING MONOCLONAL ANTIBODY FRAGMENT
 
Authors :  Y. Xu
Date :  07 Nov 12  (Deposition) - 27 Feb 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fab, Fniii, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. T. Redpath, Y. Xu, N. J. Wilson, L. J. Fabri, M. Baca, A. E. Andrews, H. Braley, P. Lu, C. Ireland, R. E. Ernst, A. Woods, G. Forrest, Z. An, D. M. Zaller, W. R. Strohl, C. S. Luo, P. E. Czabotar, T. P. Garrett, D. J. Hilton, A. D. Nash, J. G. Zhang, N. A. Nicola
Crystal Structure Of Ectodomain 3 Of The Il-13 Receptor Alpha1 In Complex With A Human Neutralizing Monoclonal Antibody Fragment
Biochem. J. V. 451 165 2013
PubMed-ID: 23384096  |  Reference-DOI: 10.1042/BJ20121819

(-) Compounds

Molecule 1 - FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: LIGHT CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG H:60 , PRO H:63 , GLN H:66 , HOH H:427 , HOH L:425BINDING SITE FOR RESIDUE SO4 H 301
02AC2SOFTWARESER H:8 , GLY H:9 , SER H:121 , THR H:122 , HOH H:507BINDING SITE FOR RESIDUE SO4 H 302
03AC3SOFTWARELYS H:20 , GLN H:83 , HOH H:536BINDING SITE FOR RESIDUE SO4 H 303
04AC4SOFTWARETYR H:28 , SER H:29 , TYR H:33 , GLY H:55 , LYS H:75BINDING SITE FOR RESIDUE GOL H 304
05AC5SOFTWARETRP H:34 , ASP H:56 , TRP H:103BINDING SITE FOR RESIDUE GOL H 305
06AC6SOFTWARETRP H:34 , MET H:100 , HOH H:513BINDING SITE FOR RESIDUE GOL H 306
07AC7SOFTWARELYS H:88 , ALA H:89 , SER H:90BINDING SITE FOR RESIDUE GOL H 307
08AC8SOFTWAREASN H:161 , GLN H:198 , HOH H:407 , HOH H:408 , HOH H:532BINDING SITE FOR RESIDUE GOL H 308
09AC9SOFTWARELYS H:44 , GLY H:45 , GLU H:47 , GLN L:97 , GOL L:303BINDING SITE FOR RESIDUE GOL H 309
10BC1SOFTWAREARG L:105 , SER L:111 , ASN L:135BINDING SITE FOR RESIDUE SO4 L 301
11BC2SOFTWAREASP H:56 , TRP H:103 , ASP H:107 , HOH H:490 , HOH H:511 , TYR L:50 , ALA L:56 , THR L:57 , HOH L:439BINDING SITE FOR RESIDUE GOL L 302
12BC3SOFTWARELEU H:46 , TRP H:48 , GOL H:309 , GLU L:93 , THR L:94 , PHE L:95BINDING SITE FOR RESIDUE GOL L 303
13BC4SOFTWAREPRO L:8 , GLY L:9 , THR L:10 , HOH L:482BINDING SITE FOR RESIDUE GOL L 304
14BC5SOFTWAREPHE H:172 , PRO H:173 , VAL H:175 , SER H:183 , LEU H:184 , SER H:185 , GLN L:157 , SER L:173 , SER L:174 , THR L:175BINDING SITE FOR RESIDUE GOL L 305

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:23 -H:97
2H:146 -H:202
3L:23 -L:89
4L:131 -L:191

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:152 -Pro H:153
2Glu H:154 -Pro H:155
3Ser L:7 -Pro L:8
4Tyr L:137 -Pro L:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HWE)

(-) 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 H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee........eeeeehhh.eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hwe H   2 EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGVIYPGDSYTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARMPNWGSFDYWGQGTLVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131||     147       157       167       177       187       197       207       217   
                                                                                                                                                            132|                                                                                 
                                                                                                                                                             139                                                                                 


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d4hwel1 L:1-104 automated matches                                                                       d4hwel2 L:105-210 automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeeehhhhheeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hwe L   1 EVVLTQSPGTLSLSPGERATLSCRASQSISSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYETFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4HWE)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:154 - Pro H:155   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:137 - Pro L:138   [ RasMol ]  
 

(-) 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 | Asym./Biol. Unit - sites 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
  4hwe
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4HWE)

(-) Related Entries Specified in the PDB File

4hwb