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 :  STRUCTURAL BASIS FOR TSLP ANTAGONISM BY THE THERAPEUTIC ANTIBODY TEZEPELUMAB (MEDI9929 / AMG-157)
 
Authors :  K. Verstraete, S. N. Savvides
Date :  28 Mar 16  (Deposition) - 05 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cytokine Inflammation Tslp Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Verstraete, F. Peelman, H. Braun, J. Lopez, D. Van Rompaey, A. Dansercoer, I. Vandenberghe, K. Pauwels, J. Tavernier, B. N. Lambrecht, H. Hammad, H. De Winter, R. Beyaert, G. Lippens, S. N. Savvides
Structure And Antagonism Of The Receptor Complex Mediated B Human Tslp In Allergy And Asthma.
Nat Commun V. 8 14937 2017
PubMed-ID: 28368013  |  Reference-DOI: 10.1038/NCOMMS14937

(-) Compounds

Molecule 1 - THYMIC STROMAL LYMPHOPOIETIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B-HTSLPDELTA127-131
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTSLP
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsBEFORE CRYSTALLISATION, THE N-TERMINAL HIS-TAG (RESIDUES 1 - 17, MGSSHHHHHHSSGLVPR) WAS REMOVED BY THROMBIN CLEAVAGE. RESIDUES 127 TO 131 OF TSLP (127-RRKRK-131) (ACCORDING TO THE REFERENCE SEQUENCE NUMBERING SCHEME FOR TSLP) WERE DELETED IN THE CONSTRUCT USED FOR CRYSTALLIZATION.
 
Molecule 2 - ANTI-TSLP FAB-FRAGMENT, LIGHT CHAIN
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Atcc NumberCRL-3216
    Expression System Cell LineHEK-293T
    Expression System PlasmidPHLSEC
    Expression System StrainHUMAN EMBRYONIC KIDNEY 293
    Expression System Taxid9606
    Expression System VariantHEK-293T
    Expression System Vector TypePLASMID
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHE SIGNAL PEPTIDE (RESIDUES 1 - 28) IS REMOVED FROM THE MATURE PROTEIN.
 
Molecule 3 - ANTI-TSLP FAB-FRAGMENT, HEAVY CHAIN
    ChainsC
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Atcc NumberCRL-3216
    Expression System Cell LineHEK-293T
    Expression System PlasmidPHLSEC
    Expression System StrainHUMAN EMBRYONIC KIDNEY 293
    Expression System Taxid9606
    Expression System VariantHEK-293T
    Expression System Vector TypePLASMID
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHE SIGNAL PEPTIDE (RESIDUES 1 - 28) IS REMOVED FROM THE MATURE PROTEIN.

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:85 , TYR B:145 , LYS B:171 , TYR B:177 , HOH B:415binding site for residue SO4 B 301
2AC2SOFTWARELYS B:134 , HOH B:406 , SER C:132 , PHE C:134 , HOH C:310binding site for residue SO4 B 302
3AC3SOFTWAREGLN B:172 , SER B:173 , HOH B:401 , HOH B:405 , HOH B:408 , HOH B:423 , LYS C:68 , HIS C:176binding site for residue SO4 B 303

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:34 -A:110
2A:69 -A:75
3A:90 -A:137
4B:25 -B:90
5B:139 -B:198
6B:216 -C:139
7C:25 -C:99
8C:152 -C:208

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr B:145 -Pro B:146
2Phe C:158 -Pro C:159
3Glu C:160 -Pro C:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J13)

(-) Exons   (0, 0)

(no "Exon" information available for 5J13)

(-) 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:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5j13 A  28 MYDFTNCDFEKIKAAYLSTISKDLITYMSGTKSTNNTVSCSNRPHCLTEIQSLTFNPTAGCASLAKEMFAMKTKAALAIWCPGYSTTNKCLEQVSQLQGLWRRFNRPLL 156
                                    37        47        57   ||   69        79        89        99       109    || 137       147         
                                                            61|                                               114|                       
                                                             64                                                133                       

Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeeehhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j13 B   4 SYVLTQPPSVSVAPGQTARITCGGNNLGSKSVHWYQQKPGQAPVLVVYDDSDRPSWIPERFSGSNSGNTATLTISRGEAGDEADYYCQVWDSSSDHVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC 216
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   

Chain C from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.ee..ee....ee...eeeee........eeeee.....eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee....eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j13 C   4 QMQLVESGGGVVQPGRSLRLSCAASGFTFRTYGMHWVRQAPGKGLEWVAVIWYDGSNKHYADSVKGRFTITRDNSKNTLNLQMNSLRAEDTAVYYCARAPQWELVHEAFDIWGQGTMVTVSSASTKGPSVFPLAPCSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPQTYTCNVDHKPSNTKVDKTVE 224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      |149       159       169       179       189       205       215         
                                                                                                                                                                  140|                                               197|                    
                                                                                                                                                                   147                                                204                    

   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 5J13)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J13)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J13)

(-) Gene Ontology  (3, 3)

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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu C:160 - Pro C:161   [ RasMol ]  
    Phe C:158 - Pro C:159   [ RasMol ]  
    Tyr B:145 - Pro B:146   [ RasMol ]  
 

(-) 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
  5j13
    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
  TSLP_HUMAN | Q969D9
    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
  TSLP_HUMAN | Q969D9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TSLP_HUMAN | Q969D95j11 5j12

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5J13)