1NJ9 - JenaLib

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Title :   COCAINE HYDROLYTIC ANTIBODY 15A10

Authors :   N. A. Larsen, P. De Prada, S. X. Deng, X. Zhu, D. W. Landry, I. A. Wilson

Date :   30 Dec 02 (Deposition) - 17 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. A. Larsen, P. De Prada, S. X. Deng, A. Mittal, M. Braskett, X. Zhu, I. A. Wilson, D. W. Landry
Crystallographic And Biochemical Analysis Of Cocaine-Degrading Antibody 15A10.
Biochemistry V. 43 8067 2004
PubMed-ID: 15209502 | Reference-DOI: 10.1021/BI049495L
(for further references see the PDB file header)

Molecule 1 - IMMUNOGLOBULIN VARIABLE CHAIN
	Chains	:	L, A
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN
	Chains	:	H, B
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	NA	8	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:28 , TYR A:32 , ALA A:33 , VAL A:50	BINDING SITE FOR RESIDUE NA A 1000
2	AC2	SOFTWARE	ARG L:61	BINDING SITE FOR RESIDUE NA L 1001
3	AC3	SOFTWARE	THR H:203	BINDING SITE FOR RESIDUE NA H 1002
4	AC4	SOFTWARE	LYS L:39 , ASP L:41	BINDING SITE FOR RESIDUE NA L 1003
5	AC5	SOFTWARE	ARG H:212 , HOH H:1017	BINDING SITE FOR RESIDUE NA H 1004
6	AC6	SOFTWARE	THR H:152 , TRP H:153 , GLY H:156 , LEU H:158 , HOH H:1026	BINDING SITE FOR RESIDUE NA H 1005
7	AC7	SOFTWARE	LEU B:158	BINDING SITE FOR RESIDUE NA B 1007

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:135	-	A:194
3	B:22	-	B:92
4	B:139	-	B:194
5	H:22	-	H:92
6	H:139	-	H:194
7	L:23	-	L:88
8	L:135	-	L:194

Asymmetric Unit

No.	Residues
1	Tyr L:141	-	Pro L:142
2	Phe H:145	-	Pro H:146
3	Glu H:147	-	Pro H:148
4	Arg H:187	-	Pro H:188
5	Tyr A:141	-	Pro A:142
6	Phe B:145	-	Pro B:146
7	Glu B:147	-	Pro B:148
8	Arg B:187	-	Pro B:188

(no "SAP(SNP)/Variant" information available for 1NJ9)

(no "PROSITE Motif" information available for 1NJ9)

(no "Exon" information available for 1NJ9)

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:212
                                                                                                                                                                                                                                                    
               SCOP domains d1nj9a1 A:1-108 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d1nj9a2 A:109-210 Immunoglobulin light chain lambda constant domain, CL-lambda                         SCOP domains
               CATH domains 1nj9A01 A:1-109 Immunoglobulins                                                                                1nj9A02 A:110-208 Immunoglobulins                                                                  -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..eeee.....eeeeee......hhhhh.eeeeee...eeeeeee............eeeee...eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee.....hhhhh.eeeeeeeeee.....eeeeee..eee.........ee.....eeeeeeeeehhhhhh...eeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nj9 A   1 QAVVTQESALTTSPGETVTLTCRSSTGTITSDNYANWVQEKPDHLFSGLIGVNNARPPGVPARFSGSLTGDKAVLTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTAREWERHSSYSCQVTHEGHTVEKSLSRA 210
                                    11        21      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
                                    9|              27A||                                                                                                                                                                                       
                                    11               27B|                                                                                                                                                                                       
                                                      27C

Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1nj9b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                      d1nj9b2 B:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1nj9B01 B:1-113 Immunoglobulins                                                                                     1nj9B02 B:114-211 Immunoglobulins                                                                 - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.......eeeee......eee.......eeee......eeeeee...hhhhheeeeeee...........eeeee.......eeeee..........eeeeeeeeeee.....eeee........eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nj9 B   1 EVQLQQSGPELVKPGASVKVSCKASGYSFTDYNMYWVKQNHGESLEWIAYIDPSNGDTFYNQKFQGKATVTLDKSSSTAFMHLNSLTSEDSAVYYCARGGGLFAFWGQGTLVTVSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR 212
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127       137       147       157       167       177       187       197       207     
                                                                              52A                            82A||               99|                                                                                                               
                                                                                                              82B|               101                                                                                                               
                                                                                                               82C

Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1nj9h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                      d1nj9h2 H:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1nj9H01 H:1-113 Immunoglobulins                                                                                     1nj9H02 H:114-212 Immunoglobulins                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...........eeeee.......eeeee..........eeeeeeeeeee.....eeee.........eeeeeee....eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nj9 H   1 EVQLQQSGPELVKPGASVKVSCKASGYSFTDYNMYWVKQNHGESLEWIAYIDPSNGDTFYNQKFQGKATVTLDKSSSTAFMHLNSLTSEDSAVYYCARGGGLFAFWGQGTLVTVSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR 212
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127       137       147       157       167       177       187       197       207     
                                                                              52A                            82A||               99|                                                                                                               
                                                                                                              82B|               101                                                                                                               
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d1nj9l1 L:1-108 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d1nj9l2 L:109-210 Immunoglobulin light chain lambda constant domain, CL-lambda                         SCOP domains
               CATH domains 1nj9L01 L:1-109 Immunoglobulins                                                                                1nj9L02 L:110-208 Immunoglobulins                                                                  -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..eeee...eeeeeeee......hhhhh.eeeeee...eeeeee.............eeeee...eeeeeeeeehhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhh.....eeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeee..hhhhhh...eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nj9 L   1 QAVVTQESALTTSPGETVTLTCRSSTGTITSDNYANWVQEKPDHLFSGLIGVNNARPPGVPARFSGSLTGDKAVLTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTAREWERHSSYSCQVTHEGHTVEKSLSRA 210
                                    11        21      ||28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
                                    9|              27A||                                                                                                                                                                                       
                                    11               27B|                                                                                                                                                                                       
                                                      27C

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		→ 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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	1nj9H02	H:114-212
1b	1nj9B02	B:114-211
1c	1nj9A01	A:1-109
1d	1nj9L01	L:1-109
1e	1nj9B01	B:1-113
1f	1nj9H01	H:1-113
1g	1nj9A02	A:110-208
1h	1nj9L02	L:110-208

(no "Pfam Domain" information available for 1NJ9)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1NJ9)

Asymmetric Unit
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	Cis Peptide Bonds
		Arg B:187 - Pro B:188	[ RasMol ]
		Arg H:187 - Pro H:188	[ RasMol ]
		Glu B:147 - Pro B:148	[ RasMol ]
		Glu H:147 - Pro H:148	[ RasMol ]
		Phe B:145 - Pro B:146	[ RasMol ]
		Phe H:145 - Pro H:146	[ RasMol ]
		Tyr A:141 - Pro A:142	[ RasMol ]
		Tyr L:141 - Pro L:142	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (7, 7)

SS Bonds (8, 8)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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