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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF AN ANTI-DR5 ANTIBODY BOUND TO DR5
 
Authors :  S. G. Hymowitz, D. Compaan
Date :  09 Jan 14  (Deposition) - 05 Feb 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,S
Keywords :  Igg, Fab Fragment, Crd, Tnfsf, Apoptosis-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Adams, K. Totpal, D. Lawrence, S. Marsters, R. Pitti, S. Yee, S. Ross L. Deforge, H. Koeppen, M. Sagolla, D. Compaan, H. Lowman, S. Hymowitz A. Ashkenazi
Structural And Functional Analysis Of The Interaction Between The Agonistic Monoclonal Antibody Apomab And The Proapoptotic Receptor Dr5.
Cell Death Differ. V. 15 751 2008
PubMed-ID: 18219321  |  Reference-DOI: 10.1038/SJ.CDD.4402306

(-) Compounds

Molecule 1 - FAB FRAGMENT OF DROZITUMAB, LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB FRAGMENT OF DROZITUMAB, HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 10B
    Chains: S
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Strain: HI5 CELLS
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS TRANSFER VECTOR
    Fragment: UNP RESIDUES 73-183
    Gene: DEATH RECEPTOR 5, DR5, KILLER, TNFRSF10B, TRAILR2, TRICK2, UNQ160/PRO186, ZTNFR9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEATH RECEPTOR 5, TNF-RELATED APOPTOSIS-INDUCING LIGAND RECEPTOR 2, TRAIL RECEPTOR 2, TRAIL-R2

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABS

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4OD2)

(-) Sites  (0, 0)

(no "Site" information available for 4OD2)

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:86
2A:135 -A:194
3B:22 -B:96
4B:148 -B:204
5S:28 -S:41
6S:44 -S:60
7S:63 -S:76
8S:66 -S:84
9S:86 -S:100
10S:103 -S:117
11S:107 -S:125

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:141 -Pro A:142
2Phe B:154 -Pro B:155
3Glu B:156 -Pro B:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OD2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OD2)

(-) Exons   (0, 0)

(no "Exon" information available for 4OD2)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeeeee..........eeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee......eee...eeeeee.......eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od2 A   1 SELTQDPAVSVALGQTVRITCSGDSLRSYYASWYQQKPGQAPVLVIYGANNRPSGIPDRFSGSSSGNTASLTITGAQAEDEADYYCNSADSSGNHVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAP 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeeee..eeeeeeeee......eee.......eeeeee....eeeeee........eeeeeeee........eeee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhhh....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4od2 B   1 EVQLVQSGGGVERPGGSLRLSCAASGFTFDDYAMSWVRQAPGKGLEWVSGINWQGGSTGYADSVKGRVTISRDNAKNSLYLQMNSLRAEDTAVYYCAKILGAGRGWYFDYWGKGTTVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  148       158       168       178       188       198       208       218    
                                                                                                                                                               134|                                                                               
                                                                                                                                                                143                                                                               


Chain S from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....eee......eee.....ee..........ee.......eeeee........eeee...ee.....ee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4od2 S  21 SSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFRPEMCRKCRTGCPRGMDCTPWSDIEC 125
                                    30        40        50        60        70        80        90 ||    104      |118       
                                                                                                  92|           111|         
                                                                                                   97            116
   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 4OD2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OD2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OD2)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu B:156 - Pro B:157   [ RasMol ]  
    Phe B:154 - Pro B:155   [ RasMol ]  
    Tyr A:141 - Pro A:142   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        TR10B_HUMAN | O14763: 1d0g 1d4v 1du3 1za3 2h9g 3x3f 4i9x 4n90

(-) Related Entries Specified in the PDB File

1d0g CRYSTAL STRUCTURE OF DR5 BOUND TO APO2L/TRAIL