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(-) Description

Title :  HUMAN TWEAK IN COMPLEX WITH THE FAB FRAGMENT OF A NEUTRALIZING ANTIBODY
 
Authors :  A. Lammens
Date :  31 Oct 12  (Deposition) - 12 Jun 13  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  H,L,T
Biol. Unit 1:  H,L,T  (3x)
Keywords :  Antibody Fab, Tnf Homology Domain, Cytokine, Tweak Receptor, Membrane Bound, Extracellular Thd Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Lammens, M. Baehner, U. Kohnert, J. Niewoehner, L. Von Proff, M. Schraeml, K. Lammens, K. P. Hopfner
Crystal Structure Of Human Tweak In Complex With The Fab Fragment Of A Neutralizing Antibody Reveals Insights Into Receptor Binding.
Plos One V. 8 62697 2013
PubMed-ID: 23667509  |  Reference-DOI: 10.1371/JOURNAL.PONE.0062697

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 12
    Chains: T
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APO3 LIGAND, TNF-RELATED WEAK INDUCER OF APOPTOSIS, TWEAK, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 12, MEMBRANE FORM, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 12, SECRETED FORM
 
Molecule 2 - CHIMERIC ANTIBODY FAB
    Chains: H
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Other Details: CHIMERIC ANTIBODY
 
Molecule 3 - CHIMERIC ANTIBODY FAB
    Chains: L
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Other Details: CHIMERIC ANTIBODY

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : HLT
Biological Unit 1 (3x): HLT

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4HT1)

(-) Sites  (0, 0)

(no "Site" information available for 4HT1)

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:147 -H:203
3L:23 -L:88
4L:138 -L:198
5T:96 -T:115

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ile T:55 -Gly T:56
2Gly T:109 -Pro T:110
3Gly H:9 -Gly H:10
4Phe H:153 -Pro H:154
5Glu H:155 -Pro H:156
6Lys H:208 -Pro H:209
7Thr L:7 -Pro L:8
8Ser L:76 -Gly L:77
9Asn L:141 -Asn L:142
10Tyr L:144 -Pro L:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HT1)

(-) Exons   (0, 0)

(no "Exon" information available for 4HT1)

(-) 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 H from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhh.eeeeeee......eeeeeee.....eee.hhhh..eeee......eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee.....eeeeeeeeee....eeeee.hhh.....ee...ee.....eeeeeeeee......eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ht1 H   1 QEQLVESGGGLVQPGGSLTLSCKASGFDFSTYYMSWVRQAPGKGLEWIGTVYVRQGTTYYASWLNGRFTISSDNAQNTVDLKMNSLTAADTATYFCAKGGYNYDDAFVIWGPGTLVTVSFASTKGPSVFPLAPSSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSTQTYICNVNHKPSNTKVDKKVEP 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 146       156       166       176       186      |200       210       220
                                                                                                                                                                135|                                                193|                      
                                                                                                                                                                 142                                                 198                      


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d4ht1l1 L:1-111 automated matches                                                                              d4ht1l2 L:112-217 automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee........eeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..........ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ht1 L   1 AIEMTQTPFSVSAAVGGTVTINCQASQNIYSNLAWYQQKPGQPPKLLMYTASYLASGVPSRFKGSGSRTEYTLTISGVQCADAATYYCQTAYYNSRPDTVAFGGGTEVVVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain T from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..ee.........eee........eee......eee...eeeeeeeeeeeee.....eeeeeee..eeeeeeee....eeeeeeeeeeeee....eeeee.....ee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ht1 T  10 RAIAAHYEVHGAQAGVDGTVSGWEEARINSSSPLRYNRQIGEFIVTRAGLYYLYCQVHFDEGKAVYLKLDLLVDGVLALRCLEELGPQLRLCQVSGLLALRPGSSLRIRTLPWAHLKAAPFLTYFGLFQVH 154
                                    19|       35        45        55        65        75        85        95   ||  113       123       133       143       153 
                                    19|                                                                       99|                                              
                                     26                                                                       108
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HT1)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn L:141 - Asn L:142   [ RasMol ]  
    Glu H:155 - Pro H:156   [ RasMol ]  
    Gly H:9 - Gly H:10   [ RasMol ]  
    Gly T:109 - Pro T:110   [ RasMol ]  
    Ile T:55 - Gly T:56   [ RasMol ]  
    Lys H:208 - Pro H:209   [ RasMol ]  
    Phe H:153 - Pro H:154   [ RasMol ]  
    Ser L:76 - Gly L:77   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Tyr L:144 - Pro L:145   [ RasMol ]  
 
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