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(-) Description

Title :  REVERSAL AGENT FOR DABIGATRAN
 
Authors :  F. Schiele, H. Nar
Date :  27 Feb 15  (Deposition) - 13 Jan 16  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Antibody, Dabigatran, Pradaxa, Antidote, Reversal Agent, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Schiele, J. Van Ryn, T. Litzenburger, M. Ritter, D. Seeliger, H. Na
Structure-Guided Residence Time Optimization Of A Dabigatra Reversal Agent.
Mabs V. 7 871 2015
PubMed-ID: 26047352  |  Reference-DOI: 10.1080/19420862.2015.1057364

(-) Compounds

Molecule 1 - ADABI-FAB2B HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: CRICETINAE
    Expression System Taxid: 10026
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ADABI-FAB2B LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: CRICETINAE
    Expression System Taxid: 10026
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
14CC1Ligand/IonN-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR H:30 , ASP H:31 , TYR H:33 , HIS H:35 , GLU H:50 , ASN H:52 , ARG H:54 , GLY H:102 , TYR H:103 , ASP H:104 , TYR H:105 , PHE H:106 , HOH H:549 , HOH H:551 , GLU L:39 , PHE L:94 , ALA L:96binding site for residue 4CC H 301

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:146 -H:202
3H:222 -L:219
4L:23 -L:93
5L:139 -L:199

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:152 -Pro H:153
2Glu H:154 -Pro H:155
3Thr L:7 -Pro L:8
4Val L:99 -Pro L:100
5Tyr L:145 -Pro L:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YHM)

(-) 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:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yhm H   1 QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYYMHWVRQAPGQGLEWMGETNPRNGGTTYNEKFKGKATMTRDTSTSTAYMELSSLRSEDTAVYYCTIGTSGYDYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhm L   1 DIVMTQTPLSLSVTPGQPASISCRSSQSIVHSDGNIYLEWYLQKPGQSPKLLIYKVSYRFSGVPDRFSGSGSGTGFTLKISRVEAEDVGVYYCFQASHVPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 219
                                    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)
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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  (0, 0)

(no "SCOP Domain" information available for 4YHM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  4yhm
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