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Title :   CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXNERI Y LIPOPOLYSACCHARIDE COMPLEXED WITH A PENTASACCHARIDE

Authors :   N. K. Vyas, M. N. Vyas, M. C. Chervenak, M. A. Johnson, B. M. Pinto, D. R. Bu F. A. Quiocho

Date :   19 Jul 02 (Deposition) - 22 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Fab-Carbohydrate Interactions; Shigella O-Antigen; And Anti- Carbohydrate Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. K. Vyas, M. N. Vyas, M. C. Chervenak, M. A. Johnson, B. M. Pinto, D. R. Bundle, F. A. Quiocho
Molecular Recognition Of Oligosaccharide Epitopes By A Monoclonal Fab Specific For Shigella Flexneri Y Lipopolysaccharide: X-Ray Structures And Thermodynamics
Biochemistry V. 41 13575 2002
PubMed-ID: 12427018 | Reference-DOI: 10.1021/BI0261387
(for further references see the PDB file header)

Molecule 1 - LIGHT CHAIN OF THE MONOCLONAL ANTIBODY FAB SYA/J6
	Cell	:	PLASMACYTOMA CELL
	Cell Line	:	SYA/J6 HYBRIDOMA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organ	:	SPLEEN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 2 - HEAVY CHAIN OF THE MONOCLONAL ANTIBODY FAB SYA/J6
	Cell	:	PLASMACYTOMA CELL
	Cell Line	:	SYA/J6 HYBRIDOMA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organ	:	SPLEEN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	RAM	3	Ligand/Ion	ALPHA-L-RHAMNOSE
3	RAO	1	Ligand/Ion	1-O-METHYL-ALPHA-RHAMNOSE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:185 , ARG A:188 , RAM A:213 , HOH A:217 , TRP B:33 , GLY B:95 , GLY B:96 , ALA B:97	BINDING SITE FOR RESIDUE RAM A 212
2	AC2	SOFTWARE	TYR A:32 , RAM A:212 , RAM A:214 , NAG A:215 , ALA B:97	BINDING SITE FOR RESIDUE RAM A 213
3	AC3	SOFTWARE	TYR A:32 , THR A:91 , RAM A:213 , NAG A:215 , GLY B:96 , GLY B:99	BINDING SITE FOR RESIDUE RAM A 214
4	AC4	SOFTWARE	THR A:91 , RAM A:213 , RAM A:214 , RAO A:216 , HOH A:218 , GLU B:50	BINDING SITE FOR RESIDUE NAG A 215
5	AC5	SOFTWARE	HIS A:27D , THR A:92 , HIS A:93 , NAG A:215 , HOH A:218	BINDING SITE FOR RESIDUE RAO A 216

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:140	-	B:195

Asymmetric/Biological Unit

No.	Residues
1	Thr A:7	-	Pro A:8
2	Tyr A:140	-	Pro A:141
3	Phe B:146	-	Pro B:147
4	Glu B:148	-	Pro B:149
5	Trp B:188	-	Pro B:189

(no "SAP(SNP)/Variant" information available for 1M7I)

(no "PROSITE Motif" information available for 1M7I)

(no "Exon" information available for 1M7I)

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
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Chain A from PDB  Type:PROTEIN  Length:215
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
        A2NHM3_MOUSE      1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  216
               SCOP domains d1m7ia1 A:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1m7ia2 A:109-211 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 1m7iA01 A:1-108 Immunoglobulins                                                                                  -1m7iA02 A:110-209 Immunoglobulins                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....-ee...eeeeee......eeeee.....hhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1m7i A    1 DVVLTQTPLSLPVRLGDQASISCRSSQSLLHSDGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQTTHVP-TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C||      35        45        55        65        75        85        95 |     105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                  95 |                                                                                                                  
                                                      27B|||                                                                    97                                                                                                                  
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with HVM32_MOUSE | P01801 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:220
                                                                                                                              101   102          115                                                                                                    
                                    10        20        30        40        50        60        70        80        90       100|     |105       115         -         -         -         -         -         -         -         -         -         -
         HVM32_MOUSE      1 EVKLEESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTTG-----FAYWGQGTLVTVSA----------------------------------------------------------------------------------------------------    -
               SCOP domains d1m7ib1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1m7ib2 B:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1m7iB01 B:1-113 Immunoglobulins                                                                                         1m7iB02 B:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee........eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeee...........eeeeehhhheeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1m7i B    1 EVKVEESGGGLVQPGGSMKLSCVASGFTFSNYWMEWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTRGGAVGAMDYWGQGTSVTVSSATTTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTVICNVAHPASKVDLIKEPSGP  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |103       113       123       133       143       153       163       173       183       193       203       213
                                                                              52A||                            82A||               100A                                                                                                                 
                                                                               52B|                             82B|                                                                                                                                    
                                                                                52C                              82C

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/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	1m7iA02	A:110-209
1b	1m7iB02	B:114-212
1c	1m7iA01	A:1-108
1d	1m7iB01	B:1-113

(no "Pfam Domain" information available for 1M7I)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (A2NHM3_MOUSE | A2NHM3)

Chain B (HVM32_MOUSE | P01801)

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 B:148 - Pro B:149	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Thr A:7 - Pro A:8	[ RasMol ]
		Trp B:188 - Pro B:189	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]

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1m71	CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXNERI Y LIPOPOLYSACCHARIDE COMPLEXED WITH A PENTASACCHARIDE
1m7d	CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXNERI Y LIPOPOLYSACCHARIDE COMPLEXED WITH A TRISACCHARIDE
1mcp	PHOSPHOCHOLINE BINDING IMMUNOGLOBULIN FAB MCPC603. AN X-RAY DIFFRACTION STUDY AT 2.7 A

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Ligands, Modified Residues, Ions (3, 5)

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SS Bonds (4, 4)

Cis Peptide Bonds (5, 5)

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