4JN2 - JenaLib

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Title :   AN ANTIDOTE FOR DABIGATRAN

Authors :   F. Schiele, H. Nar

Date :   14 Mar 13 (Deposition) - 27 Mar 13 (Release) - 11 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.71

Chains :   Asym. Unit : A,B,H,L
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: H,L  (1x)

Keywords :   Igg Fragment Binding Dabigatran, Dabigatran, Immune System-Inhibitor Complex (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

Molecule 1 - ANTI DABIGATRAN FAB
	Chains	:	A, L
	Engineered	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ANTI DABIGATRAN FAB
	Chains	:	B, H
	Engineered	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	4CC	2	Ligand/Ion	N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE
2	GOL	8	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	4CC	1	Ligand/Ion	N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE
2	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	4CC	1	Ligand/Ion	N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE
2	GOL	4	Ligand/Ion	GLYCEROL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:32 , TYR A:38 , TYR A:40 , SER A:97 , THR A:98 , PHE A:100 , HIS A:102 , GOL A:302 , HOH A:692 , HOH A:738 , ILE B:34 , ASP B:36 , VAL B:51 , TRP B:53 , SER B:57 , THR B:58 , TYR B:107 , ASP B:108 , GLY B:109 , LYS B:216 , HOH B:452	BINDING SITE FOR RESIDUE 4CC A 301
02	AC2	SOFTWARE	PHE A:100 , 4CC A:301 , HOH A:624 , GLY B:59 , HOH B:472	BINDING SITE FOR RESIDUE GOL A 302
03	AC3	SOFTWARE	HOH A:636 , HOH A:642 , HOH A:747 , HOH A:750 , GLY H:59 , HOH H:500 , PHE L:100 , 4CC L:301 , HOH L:519	BINDING SITE FOR RESIDUE GOL A 303
04	AC4	SOFTWARE	SER A:120 , VAL A:121 , PHE A:122 , HOH A:650 , HOH A:730 , THR B:145	BINDING SITE FOR RESIDUE GOL A 304
05	AC5	SOFTWARE	GLN A:28 , HIS A:99 , PHE A:100 , HOH A:532 , HOH A:736	BINDING SITE FOR RESIDUE GOL A 305
06	AC6	SOFTWARE	VAL H:3 , PHE H:28 , ALA H:100 , TYR H:112 , HOH H:420 , HOH H:587 , HOH H:730	BINDING SITE FOR RESIDUE GOL H 301
07	AC7	SOFTWARE	HOH B:549 , GLN H:2 , HOH H:731 , HOH H:737	BINDING SITE FOR RESIDUE GOL H 302
08	AC8	SOFTWARE	GOL A:303 , HOH A:730 , GLY B:144 , THR B:145 , HOH B:492 , ILE H:34 , ASP H:36 , VAL H:51 , TRP H:53 , SER H:57 , TYR H:107 , ASP H:108 , GLY H:109 , HOH H:410 , HOH H:416 , HOH H:440 , TYR L:32 , TYR L:38 , TYR L:40 , SER L:97 , THR L:98 , PHE L:100 , HIS L:102 , HOH L:513 , HOH L:721	BINDING SITE FOR RESIDUE 4CC L 301
09	AC9	SOFTWARE	HIS H:174 , THR L:170 , GLU L:171 , GLN L:172 , ASP L:173 , HOH L:420 , HOH L:497	BINDING SITE FOR RESIDUE GOL L 302
10	BC1	SOFTWARE	SER H:138 , THR H:141 , VAL L:116 , ALA L:118 , GLY L:206 , LYS L:213 , HOH L:631 , HOH L:685	BINDING SITE FOR RESIDUE GOL L 303

Asymmetric Unit

No.	Residues
1	A:24	-	A:94
2	A:140	-	A:200
3	A:220	-	B:226
4	B:23	-	B:96
5	B:150	-	B:206
6	H:23	-	H:96
7	H:150	-	H:206
8	H:226	-	L:220
9	L:24	-	L:94
10	L:140	-	L:200

Asymmetric Unit

No.	Residues
1	Ser A:8	-	Pro A:9
2	Phe A:100	-	Pro A:101
3	Tyr A:146	-	Pro A:147
4	Thr B:31	-	Ser B:32
5	Gly B:143	-	Gly B:144
6	Phe B:156	-	Pro B:157
7	Glu B:158	-	Pro B:159
8	Phe H:156	-	Pro H:157
9	Glu H:158	-	Pro H:159
10	Ser L:8	-	Pro L:9
11	Phe L:100	-	Pro L:101
12	Tyr L:146	-	Pro L:147

(no "SAP(SNP)/Variant" information available for 4JN2)

(no "PROSITE Motif" information available for 4JN2)

(no "Exon" information available for 4JN2)

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:219
                                                                                                                                                                                                                                                           
               SCOP domains d4jn2a1 A:2-113 automated matches                                                                               d4jn2a2 A:114-220 automated matches                                                                         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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jn2 A   2 DVVMTQSPLSLPVTLGQPASISCKSSQSLLYTDGKTYLYWFLQRPGQSPRRLIYLVSKLDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCLQSTHFPHTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee.....eeeeeee...eeeeeeee......eeeeee.....eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeeeeeee..ee....ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jn2 B   3 VQLQESGPGLVKPSETLSLTCTVSTSYIVDWIRQPPGKGLEWIGVIWAGGSTGYNSALRSRVSITKDTSKNQFSLKLSSVTAADTAVYYCASAAYYSYYNYDGFAYWGQGTLVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 226
                                    12        22   ||   36        46        56        66        76        86        96       106       116       126       136|      152       162       172       182       192       202       212       222    
                                                  26|                                                                                                      136|                                                                                   
                                                   31                                                                                                       143

Chain H from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.....eeeeeeeee......eeeeee.....eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeeeeeee..ee....ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jn2 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 d4jn2l1 L:2-113 automated matches                                                                               d4jn2l2 L:114-220 automated matches                                                                         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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jn2 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)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

1a	d4jn2a1	A:2-113
1b	d4jn2l1	L:2-113

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

2a	d4jn2a2	A:114-220
2b	d4jn2l2	L:114-220

(no "CATH Domain" information available for 4JN2)

(no "Pfam Domain" information available for 4JN2)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4JN2)

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		Glu H:158 - Pro H:159	[ RasMol ]
		Gly B:143 - Gly B:144	[ RasMol ]
		Phe A:100 - Pro A:101	[ RasMol ]
		Phe B:156 - Pro B:157	[ RasMol ]
		Phe H:156 - Pro H:157	[ RasMol ]
		Phe L:100 - Pro L:101	[ RasMol ]
		Ser A:8 - Pro A:9	[ RasMol ]
		Ser L:8 - Pro L:9	[ RasMol ]
		Thr B:31 - Ser B:32	[ RasMol ]
		Tyr A:146 - Pro A:147	[ RasMol ]
		Tyr L:146 - Pro L:147	[ RasMol ]

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	4jn2
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Description

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Ligands, Modified Residues, Ions (2, 10)

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SS Bonds (10, 10)

Cis Peptide Bonds (12, 12)

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