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 :  TRAIL-R2 EXTRACELLULAR REGION COMPLEXED TO A FAB FRAGMENT FROM HUMAN AGONIST ANTIBODY KMTR2
 
Authors :  T. Tamada
Date :  20 Jan 15  (Deposition) - 23 Dec 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Trail-R2, Agonist Antibody, Apoptosis-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Tamada, D. Shimmi, E. Mori, Y. Yonezawa, S. Kataoka, K. Motoki, R. Kuroki
Trail-R2 Superoligomerization Induced By Human Monoclonal Agonistic Antibody Kmtr2
Sci Rep 2015
PubMed: search

(-) Compounds

Molecule 1 - HEAVY CHAIN OF KMTR2
    ChainsH
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Taxid10029
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - LIGHT CHAIN OF KMTR2
    ChainsL
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Taxid10029
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 10B
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Taxid10029
    FragmentUNP RESIDUES 54-184
    GeneDR5, KILLER, TNFRSF10B, TRAILR2, TRICK2, UNQ160/PRO186, ZTNFR9
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDEATH RECEPTOR 5, TNF-RELATED APOPTOSIS-INDUCING LIGAND RECEPTOR 2, TRAIL RECEPTOR 2, TRAIL-R2

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN H:73BINDING SITE FOR RESIDUE NAG H 301
2AC2SOFTWARETRP H:47 , HOH H:406 , THR L:97 , PHE L:98BINDING SITE FOR RESIDUE CL H 302
3AC3SOFTWAREVAL H:176 , HIS H:177 , GLU L:165 , GLN L:166 , ASP L:167 , HOH L:481BINDING SITE FOR RESIDUE GOL L 301
4AC4SOFTWAREGLY H:42 , GLN H:43 , ALA L:9 , TYR L:87 , GLY L:100 , GLY L:101BINDING SITE FOR RESIDUE GOL L 302
5AC5SOFTWAREPHE H:179 , PRO H:180 , SER H:190 , LEU H:191 , SER H:192 , SER L:162 , SER L:176 , THR L:178BINDING SITE FOR RESIDUE GOL L 303
6AC6SOFTWARETHR L:5 , ARG L:24 , LYS L:207 , HOH L:422 , HOH L:454BINDING SITE FOR RESIDUE GOL L 304
7AC7SOFTWARESER L:12 , GLU L:105 , TYR L:140 , PRO L:141 , ARG L:142BINDING SITE FOR RESIDUE GOL L 305

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:81 -A:94
2A:97 -A:113
3A:116 -A:129
4A:119 -A:137
5H:22 -H:96
6H:140 -L:214
7H:153 -H:209
8L:23 -L:88
9L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe H:159 -Pro H:160
2Glu H:161 -Pro H:162
3Ser L:7 -Pro L:8
4Trp L:94 -Pro L:95
5Tyr L:140 -Pro L:141
6Thr A:143 -Phe A:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X3F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X3F)

(-) Exons   (0, 0)

(no "Exon" information available for 3X3F)

(-) 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:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee......eee.....ee..........ee.......eeeee........eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 3x3f A  74 SSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTF 144
                                    83        93       103       113       123       133       143 

Chain H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......ee.hhhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee..hhhhh.............eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3x3f H   1 QVQLVQSGAEMKKPGASVKVSCKTSGYTFTNYKINWVRQAPGQGLEWMGWMNPDTDSTGYPQKFQGRVTMTRNTSISTAYMELSSLRSEDTAVYYCARSYGSGSYYRDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPCSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVES 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140||     154       164       174       184       194       204       214       224  
                                                                                                                                                                      141|                                                                                
                                                                                                                                                                       146                                                                                

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x3f L   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    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  (0, 0)

(no "SCOP Domain" information available for 3X3F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X3F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X3F)

(-) Gene Ontology  (30, 30)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    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 ]
 
  Cis Peptide Bonds
    Glu H:161 - Pro H:162   [ RasMol ]  
    Phe H:159 - Pro H:160   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Thr A:143 - Phe A:144   [ RasMol ]  
    Trp L:94 - Pro L:95   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ 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
  3x3f
    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
  TR10B_HUMAN | O14763
    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
  TR10B_HUMAN | O14763
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TR10B_HUMAN | O147631d0g 1d4v 1du3 1za3 2h9g 4i9x 4n90 4od2

(-) Related Entries Specified in the PDB File

3x3g