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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 :  1.90
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  H,L  (1x)
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-FAB2A HEAVY CHAIN
    Chains: A, H
    Engineered: YES
    Expression System: CRICETINAE
    Expression System Taxid: 10026
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ADABI-FAB2A LIGHT CHAIN
    Chains: B, L
    Engineered: YES
    Expression System: CRICETINAE
    Expression System Taxid: 10026
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
14CC2Ligand/IonN-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE
Biological Unit 1 (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
Biological Unit 2 (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  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:31 , TYR A:33 , HIS A:35 , GLU A:50 , ARG A:54 , TYR A:103 , ASP A:104 , TYR A:105 , PHE A:106 , HOH A:408 , HOH A:424 , HOH A:437 , HOH A:600 , HOH A:616 , GLU B:39 , PHE B:94 , ALA B:96 , TYR B:101binding site for residue 4CC A 301
2AC2SOFTWAREASP 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:616 , GLU L:39 , PHE L:94 , ALA L:96 , TYR L:101binding site for residue 4CC H 301

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:146 -A:202
3A:222 -B:219
4B:23 -B:93
5B:139 -B:199
6H:22 -H:96
7H:146 -H:202
8H:222 -L:219
9L:23 -L:93
10L:139 -L:199

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe A:152 -Pro A:153
2Glu A:154 -Pro A:155
3Thr B:7 -Pro B:8
4Val B:99 -Pro B:100
5Tyr B:145 -Pro B:146
6Phe H:152 -Pro H:153
7Glu H:154 -Pro H:155
8Thr L:7 -Pro L:8
9Val L:99 -Pro L:100
10Tyr L:145 -Pro L:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YHI)

(-) 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 A 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.......eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yhi A   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 B 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
                 4yhi B   1 DIVMTQTPLSLSVTPGQPASISCRSSQSIVHSDGNIYLEWYLQKPGQSPKLLIYKVSYRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQASHVPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


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.......eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yhi 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
                 4yhi L   1 DIVMTQTPLSLSVTPGQPASISCRSSQSIVHSDGNIYLEWYLQKPGQSPKLLIYKVSYRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQASHVPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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)
  - → 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 4YHI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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