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(-) Description

Title :  AN ANTIDOTE FOR DABIGATRAN
 
Authors :  F. Schiele, H. Nar
Date :  14 Mar 13  (Deposition) - 27 Mar 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Igg Fragment Binding Dabigatran, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Schiele, J. Van Ryn, K. Canada, C. Newsome, E. Sepulveda, J. Park, H. Nar, T. Litzenburger
A Specific Antidote For Dabigatran: Functional And Structural Characterization.
Blood V. 121 3554 2013
PubMed-ID: 23476049  |  Reference-DOI: 10.1182/BLOOD-2012-11-468207

(-) Compounds

Molecule 1 - ANTI-DABIGATRAN FAB1, HEAVY CHAIN
    Chains: H
    Engineered: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTI-DABIGATRAN FAB1, LIGHT CHAIN
    Chains: L
    Engineered: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE H:34 , ASP H:36 , VAL H:51 , TRP H:53 , GLY H:109 , PHE H:110 , GOL H:302 , HIS L:102 , HOH L:595BINDING SITE FOR RESIDUE GOL H 301
2AC2SOFTWARETYR H:107 , CYS H:226 , GOL H:301 , HOH H:441 , HOH H:453 , TYR L:32 , TYR L:38 , SER L:97 , HOH L:461BINDING SITE FOR RESIDUE GOL H 302
3AC3SOFTWAREGLY H:9 , PRO H:10 , GLY H:11 , VAL H:13 , LEU H:19 , SER H:20 , HOH H:421 , HOH H:504BINDING SITE FOR RESIDUE GOL H 303
4AC4SOFTWARESER H:32 , TYR H:33 , ALA H:54 , LYS H:72 , PHE H:79BINDING SITE FOR RESIDUE GOL H 304
5AC5SOFTWARETYR H:102 , ASN H:106 , GOL H:306 , VAL L:64 , PRO L:65 , ASP L:66 , HOH L:529BINDING SITE FOR RESIDUE GOL H 305
6AC6SOFTWAREASN H:106 , TYR H:107 , GOL H:305 , LYS L:36 , TYR L:38 , TYR L:55 , GOL L:302BINDING SITE FOR RESIDUE GOL H 306
7AC7SOFTWAREPHE H:176 , PRO H:177 , VAL H:179 , SER H:187 , LEU H:188 , SER H:189 , GLN L:166 , SER L:168 , SER L:182 , SER L:183 , THR L:184 , HOH L:439BINDING SITE FOR RESIDUE GOL L 301
8AC8SOFTWARETYR H:102 , ASP H:108 , GOL H:306 , ARG L:52 , TYR L:55 , ASP L:61 , SER L:62 , GLY L:63 , HOH L:584BINDING SITE FOR RESIDUE GOL L 302

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:23 -H:96
2H:150 -H:206
3H:226 -L:220
4L:24 -L:94
5L:140 -L:200

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:156 -Pro H:157
2Glu H:158 -Pro H:159
3Ser L:8 -Pro L:9
4Phe L:100 -Pro L:101
5Tyr L:146 -Pro L:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JN1)

(-) Exons   (0, 0)

(no "Exon" information available for 4JN1)

(-) 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:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.....eeeeeeeee......eeeeee.....eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeeeeeee..ee....ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jn1 H   2 QVQLQESGPGLVKPSETLSLTCTVSGFSLTSYIVDWIRQPPGKGLEWIGVIWAGGSTGYNSALRSRVSITKDTSKNQFSLKLSSVTAADTAVYYCASAAYYSYYNYDGFAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d4jn1l1 L:2-113 automated matches                                                                               d4jn1l2 L:114-220 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jn1 L   2 DVVMTQSPLSLPVTLGQPASISCKSSQSLLYTDGKTYLYWFLQRPGQSPRRLIYLVSKLDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCLQSTHFPHTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   Legend:   → Mismatch (orange background)
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  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 4JN1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JN1)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4JN1)

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  Cis Peptide Bonds
    Glu H:158 - Pro H:159   [ RasMol ]  
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    Tyr L:146 - Pro L:147   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

4jn2