1Q0Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ANTI-MORPHINE ANTIBODY 9B1 COMPLEXED WITH MORPHINE

Authors :   E. Pozharski, M. A. Wilson, A. Hewagama, A. B. Shanafelt, G. Petsko, D. R

Date :   17 Jul 03 (Deposition) - 20 Apr 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : H,L

Keywords :   Anti-Morphine Antibody, Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Pozharski, M. A. Wilson, A. Hewagama, A. B. Shanafelt, G. Petsko, D. Ringe
Anchoring A Cationic Ligand: The Structure Of The Fab Fragment Of The Anti-Morphine Antibody 9B1 And Its Complex With Morphine
J. Mol. Biol. V. 337 691 2004
PubMed-ID: 15019787 | Reference-DOI: 10.1016/J.JMB.2003.12.084

Molecule 1 - FAB 9B1, LIGHT CHAIN
	Chains	:	L
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - FAB 9B1, HEAVY CHAIN
	Chains	:	H
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2
Asymmetric/Biological Unit	:	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	MOI	1	Ligand/Ion	(7R,7AS,12BS)-3-METHYL-2,3,4,4A,7,7A-HEXAHYDRO-1H-4,12-METHANO[1]BENZOFURO[3,2-E]ISOQUINOLINE-7,9-DIOL
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU H:50 , TRP H:95 , LEU H:97 , HOH H:578 , TYR L:32 , TRP L:91	BINDING SITE FOR RESIDUE MOI H 401
2	AC2	SOFTWARE	TYR H:27 , THR H:28 , TYR H:32 , HOH H:590 , GLU L:7 , SER L:8 , HOH L:525	BINDING SITE FOR RESIDUE SO4 H 501
3	AC3	SOFTWARE	THR L:182 , ARG L:184 , ARG L:188 , HOH L:652	BINDING SITE FOR RESIDUE SO4 L 502

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:142	-	H:208
3	L:23	-	L:88
4	L:134	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Tyr L:140	-	Pro L:141
2	Phe H:148	-	Pro H:149
3	Glu H:150	-	Pro H:151
4	Trp H:199	-	Pro H:200

(no "SAP(SNP)/Variant" information available for 1Q0Y)

(no "PROSITE Motif" information available for 1Q0Y)

(no "Exon" information available for 1Q0Y)

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:215
 aligned with Q8VDC9_MOUSE | Q8VDC9 from UniProtKB/TrEMBL  Length:168

    Alignment length:219
                                                                                                                                                                              168                                                                      
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159        |-         -         -         -         -         -         -         
        Q8VDC9_MOUSE     20 QVQLQQSGAELMKPGASVKISCKATGYTFSSYWIDWVKQRPGHGLEWIGEILPGSGRTNYNEKFKGKTTFTADTSSNTAYIQFSSLTSEDSAVYYCANYGSSRWYFDVWGAGTTVTVSSTKTTAPSVYPLAPVCGDTTGSSVTLGCLVK----------------------------------------------------------------------    -
               SCOP domains d1q0yh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1q0yh2 H:114-2    28 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                  SCOP domains
               CATH domains 1q0yH01 H:1-113 Immunoglobulins                                                                                        1q0yH02 H:114-2    27 Immunoglobulins                                                              - CATH domains
               Pfam domains -V-set-1q0yH01 H:2-111                                                                                               ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee....----..eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q0y H    1 EVQLQQSGAELMKPGASVKISCKATGYTFSSYWIEWVKQRPGHGLEWIGEILPGSGDTIFNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARWVLDYYGMDYWGQGTSLTVSSASTTPPSVYPLAPGG----SAMVTLGCLVKGYFPEPVTVVWNKGSLSTGTHTFPAVLAADLYTLSSSVTVSASSWPGQSVTCNVAHPASSTKVDKKIAPS  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124   |   136       146       157 ||    172       184       194  || ||207       217      || 
                                                                              52A                            82A||               100A|                         128  135                 155| ||   170|     180|           197| || ||              224| 
                                                                                                              82B|                100B                                                   157 ||    172      183            199 || ||               227 
                                                                                                               82C                                                                         159|                              201| ||                   
                                                                                                                                                                                            164                               203 ||                   
                                                                                                                                                                                                                                205|                   
                                                                                                                                                                                                                                 207

Chain H from PDB  Type:PROTEIN  Length:215
 aligned with Q9D9B8_MOUSE | Q9D9B8 from UniProtKB/TrEMBL  Length:111

    Alignment length:215
                                                                                                                           104            105   111                                                                                                
                                    16        26        36        46        56        66        76        86        96       | -         -  |     |-         -         -         -         -         -         -         -         -         -     
        Q9D9B8_MOUSE      7 QVQLQQSGPELVKPGASVKISCKASGYAFSSSWMNWVKQRPGKGLEWIGRIYPGDGDTNYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAR--------------HSVTTTS------------------------------------------------------------------------------------------------    -
               SCOP domains d1q0yh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1q0yh2 H:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                  SCOP domains
               CATH domains 1q0yH01 H:1-113 Immunoglobulins                                                                                        1q0yH02 H:114-227 Immunoglobulins                                                              - CATH domains
               Pfam domains -V-set-1q0yH01 H:2-111                                                                                               -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q0y H    1 EVQLQQSGAELMKPGASVKISCKATGYTFSSYWIEWVKQRPGHGLEWIGEILPGSGDTIFNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARWVLDYYGMDYWGQGTSLTVSSASTTPPSVYPLAPGGSAMVTLGCLVKGYFPEPVTVVWNKGSLSTGTHTFPAVLAADLYTLSSSVTVSASSWPGQSVTCNVAHPASSTKVDKKIAPS  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124   ||  140       150    || 165    || 176   ||  188       199 || || 211       221  || 
                                                                              52A                            82A||               100A|                         128|                 155| ||   170|     180|           197| || ||              224| 
                                                                                                              82B|                100B                          135                  157 ||    172      183            199 || ||               227 
                                                                                                               82C                                                                     159|                              201| ||                   
                                                                                                                                                                                        164                               203 ||                   
                                                                                                                                                                                                                            205|                   
                                                                                                                                                                                                                             207

Chain L from PDB  Type:PROTEIN  Length:212
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:212
                                                                                                                                       129                                                                                                      
                                    29        39        49        59        69        79        89        99       109       119       129         -         -         -         -         -         -         -         -         -         -  
          LV1B_MOUSE     20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLG------------------------------------------------------------------------------------------------------    -
               SCOP domains d1q0yl1 L:1-107 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d1q0yl2 L:108-212 Immunoglobulin light chain lambda constant domain, CL-lambda                         SCOP domains
               CATH domains 1q0yL01 L:1-107 Immunoglobulins                                                                               1q0yL02 L:108-210 Immunoglobulins                                                                   -- CATH domains
               Pfam domains -V-set-1q0yL01 L:2-106                                                                                      -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee.....eeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeeehhhhh...eeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q0y L    1 DAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWSNNKLVFGGGTKLTVLGQPKSSPTVTLFPPSSEELSTAKATLVCTITDFYPGVVTVDWKVDGTPVTAGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHSSNKTLSRA  212
                                    11        21      ||28        38        48        58        68        78        88        98       107       117       127       137       147       157       167  ||   178       188       198     ||210  
                                    9|              27A||                                                                            106A                                                             170|                             204|     
                                    11               27B|                                                                                                                                              172                              207     
                                                      27C

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 '\|'

Asymmetric/Biological 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	1q0yH01	H:1-113
1b	1q0yH02	H:114-227
1c	1q0yL01	L:1-107
1d	1q0yL02	L:108-210

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: V-set (144)

Mus musculus (Mouse) (63)

1a	V-set-1q0yL01	L:2-106
1b	V-set-1q0yH01	H:2-111

Asymmetric/Biological Unit(hide GO term definitions)

Chain H (Q8VDC9_MOUSE | Q8VDC9)

Chain H (Q9D9B8_MOUSE | Q9D9B8)

Chain L (LV1B_MOUSE | P01724)

molecular function
	GO:0003823		antigen binding		Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:150 - Pro H:151	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Trp H:199 - Pro H:200	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	Q9D9B8_MOUSE \| Q9D9B8	:	1q0x

1q0x	UNLIGANDED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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