1MH5 - JenaLib

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Title :   THE STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF THE ESTEROLYTIC ANTIBODY MS6-164 AND A TRANSITION-STATE ANALOG

Authors :   S. N. Ruzheinikov, T. A. Muranova, S. E. Sedelnikova, L. J. Partridge, G. M. Blackburn, I. A. Murray, H. Kakinuma, N. Takashi, K. Shimazaki, J Y. Nishi, D. W. Rice

Date :   19 Aug 02 (Deposition) - 23 Sep 03 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Catalytic Antibody, Ester Hydrolysis, Esterolytic, Fab, Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. N. Ruzheinikov, T. A. Muranova, S. E. Sedelnikova, L. J. Partridge, G. M. Blackburn, I. A. Murray, H. Kakinuma, N. Takashi, K. Shimazaki, J. Sun, Y. Nishi, D. W. Rice
High-Resolution Crystal Structure Of The Fab-Fragments Of A Family Of Mouse Catalytic Antibodies With Esterase Activity
J. Mol. Biol. V. 332 423 2003
PubMed-ID: 12948492 | Reference-DOI: 10.1016/S0022-2836(03)00902-1
(for further references see the PDB file header)

Molecule 1 - IMMUNOGLOBULIN MS6-164
	Cell Line	:	HYBRIDOMA
	Chains	:	A, L
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Fragment	:	FAB FRAGMENT, LIGHT CHAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	FUSING OF MOUSE SPLENOCYTES WITH MYELOMA CELL

Molecule 2 - IMMUNOGLOBULIN MS6-164
	Cell Line	:	HYBRIDOMA
	Chains	:	B, H
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Fragment	:	FAB FRAGMENT, HEAVY CHAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	FUSING OF MOUSE SPLENOCYTES WITH MYELOMA CELL

		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, 4)

No.	Name	Count	Type	Full Name
1	HAL	2	Ligand/Ion	N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HAL	1	Ligand/Ion	N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HAL	1	Ligand/Ion	N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG H:56 , HOH H:808 , LYS L:147 , LYS L:149 , GLU L:195	BINDING SITE FOR RESIDUE SO4 H 703
2	AC2	SOFTWARE	LYS A:149 , GLU A:195 , ARG B:56 , HOH B:823	BINDING SITE FOR RESIDUE SO4 B 704
3	AC3	SOFTWARE	HIS A:27D , TYR A:32 , PHE A:36 , LEU A:89 , HIS A:91 , LEU A:92 , TYR A:94 , PHE A:96 , TRP B:33 , ASN B:35 , ASN B:50 , LYS B:95 , VAL B:101 , HOH B:744	BINDING SITE FOR RESIDUE HAL B 601
4	AC4	SOFTWARE	TRP H:33 , ASN H:35 , ASN H:50 , LYS H:95 , TRP H:103 , HOH H:741 , HOH H:770 , TYR L:32 , PHE L:36 , HIS L:91 , LEU L:92 , TYR L:94 , PHE L:96	BINDING SITE FOR RESIDUE HAL H 602

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	H:22	-	H:92
5	H:142	-	H:208
6	L:23	-	L:88
7	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Tyr A:94	-	Pro A:95
2	Tyr A:140	-	Pro A:141
3	Phe B:148	-	Pro B:149
4	Glu B:150	-	Pro B:151
5	Tyr L:94	-	Pro L:95
6	Tyr L:140	-	Pro L:141
7	Phe H:148	-	Pro H:149
8	Glu H:150	-	Pro H:151

(no "SAP(SNP)/Variant" information available for 1MH5)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	2	A:192-197 L:192-197

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	A:192-197 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	- L:192-197

(no "Exon" information available for 1MH5)

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:197
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:206
                                1        11        12       21                                                                                          22                                                                                
                                |    6    |    -    |   17   |     -         -         -         -         -         -         -         -         -     |  26        36        46        56        66        76        86        96      
          IGKC_MOUSE      - ----ADAAPTVSIFP---------PSSEQLTSGG-------------------------------------------------------------------------------------------ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFN  102
               SCOP domains d1mh5a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1mh5a2 A:108-210 Immunoglobulin light chain kappa constant domain,     CL-kappa               SCOP domains
               CATH domains 1mh5A01 A:1-108 Immunoglobulins                                                                                  1mh5A02 A:109-207 Immunoglobulins                                                         --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee...eeeeeeeee.......eeee........eeeee.........eeeeeeee...----....eeee..-----...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mh5 A    1 DIVMTQAAPSVSVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCLQHLEYPFTFGAGTKLELKRADAAPTVSIFPPASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTK----RHNSYTCEAT-----SPIVKSFN  210
                                    10        20       27C||      35        45        55        65        75        85        95       105       115    || 134       144       154       164       174        |-   |   194  |    204      
                                                     27A||||                                                                                          120|                                                  183  188      197   203       
                                                      27B|||                                                                                           130                                                                                
                                                       27C||                                                                                                                                                                              
                                                        27D|                                                                                                                                                                              
                                                         27E

Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                             
               SCOP domains d1mh5b1 B:2-113 Immunoglobulin heavy chain variable domain, VH                                                        d1mh5b2 B:114-193 Immunoglobulin heavy chain gamma con SCOP domains
               CATH domains 1mh5B01 B:2-113 Immunoglobulins                                                                                       1mh5B02 B:114-191 Immunoglobulins                   -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeee.....eeeeeeee..hhh.eeeeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee......eee...eeeee.................eeee...............ee...ee....ee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mh5 B    2 VQLQQPGAELVKPGASVKLSCKASGYTFTSNWINWVKQRPGQGLEWIGNIYPDSYRTNYNEKFKRKATLTVDTSSSTAYMQLSSLTSDDSAVYYCVRKHYSYDGVVYWGQGTLVTVSAAKTTAPSVYPLAPVVTLGCLVKGYFPEPVTLTWVHTFPAVLQSDLYTLSSSVTV  193
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||  105       115       125 ||    145       157||     179||     191  
                                                                             52A                            82A||               100A|                        127|             154|||      180|          
                                                                                                             82B|                100B                         138              157||       183          
                                                                                                              82C                                                               158|                    
                                                                                                                                                                                 171

Chain H from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                               
               SCOP domains d1mh5h1 H:2-113 Immunoglobulin heavy chain variable domain, VH                                                        d1mh5h2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH SCOP domains
               CATH domains 1mh5H01 H:2-113 Immunoglobulins                                                                                       1mh5H02 H:114-212 Immunoglobulins                                     -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee......eee...eeeee.................eee............eeee.......eeee...eee..eee..eeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mh5 H    2 VQLQQPGAELVKPGASVKLSCKASGYTFTSNWINWVKQRPGQGLEWIGNIYPDSYRTNYNEKFKRKATLTVDTSSSTAYMQLSSLTSDDSAVYYCVRKHYSYDGVVYWGQGTLVTVSAAKTTAPSVYPLAPSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVITCNVAHPA  214
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||  105       115       125||     144       154|||    169|      180|      192||||   214
                                                                             52A                            82A||               100A|                       126|               154|||    169|      180|       193|||      
                                                                                                             82B|                100B                        136                157||     171       183        205||      
                                                                                                              82C                                                                158|                           206|      
                                                                                                                                                                                  162                            208

Chain L from PDB  Type:PROTEIN  Length:212
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:217
                                                                                                                                             1                                                                                                       
                                     -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97       
          IGKC_MOUSE      - -----------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  104
               SCOP domains d1mh5l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1mh5l2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1mh5L01 L:1-108 Immunoglobulins                                                                                  1mh5L02 L:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee......eeeee........eeeee.........eeeeeeeeeehhhhh...eeeeee.-----..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mh5 L    1 DIVMTQAAPSVSVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCLQHLEYPFTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEAT-----SPIVKSFNRN  212
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 |     205       
                                                     27A||||                                                                                                                                                                       197   203         
                                                      27B|||                                                                                                                                                                                         
                                                       27C||                                                                                                                                                                                         
                                                        27D|                                                                                                                                                                                         
                                                         27E

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	-	→ 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 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	1mh5L02	L:109-211
1b	1mh5A01	A:1-108
1c	1mh5L01	L:1-108
1d	1mh5H02	H:114-212
1e	1mh5B01	B:2-113
1f	1mh5H01	H:2-113
1g	1mh5B02	B:114-191
1h	1mh5A02	A:109-207

(no "Pfam Domain" information available for 1MH5)

Asymmetric Unit(hide GO term definitions)

Chain A,L (IGKC_MOUSE | P01837)

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.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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		Tyr L:94 - Pro L:95	[ RasMol ]

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1mie	CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS5-393
1mj7	CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS5-393D9 AND A TRANSITION-STATE ANALOG
1mj8	HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF THE ESTEROLYTIC ANTIBODY MS6-126 AND A TRANSITION-STATE ANALOG
1mjj	HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12 AND A TRANSITION- STATE ANALOG
1mju	1.22 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (7, 7)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (4, 8)

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