1MJJ - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12 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. Sun, Y. Nishi, D. W. Rice

Date :   28 Aug 02 (Deposition) - 23 Sep 03 (Release) - 24 Feb 09 (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 MS6-12
	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 MS6-12
	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 (3, 7)

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	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

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	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	3	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	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:211 , ASN A:212 , HOH A:2224 , HOH A:2279 , SER L:203	BINDING SITE FOR RESIDUE SO4 A 2001
2	AC2	SOFTWARE	PRO B:7 , GLY B:8 , HOH B:2035	BINDING SITE FOR RESIDUE SO4 B 2002
3	AC3	SOFTWARE	ARG B:40 , LYS B:62 , HOH B:2061 , HOH B:2200	BINDING SITE FOR RESIDUE SO4 B 2003
4	AC4	SOFTWARE	TYR A:32 , HIS A:91 , LEU A:92 , PHE A:96 , HOH A:2160 , HOH A:2203 , HOH A:2245 , TRP B:33 , ASN B:35 , ASN B:50 , LYS B:95 , HAL H:1002 , HOH L:347	BINDING SITE FOR RESIDUE HAL A 1001
5	AC5	SOFTWARE	HAL A:1001 , TRP H:33 , ASN H:35 , ASN H:50 , LYS H:95 , HOH H:1142 , TYR L:32 , HIS L:91 , LEU L:92 , TYR L:94 , PHE L:96 , HOH L:374 , HOH L:552	BINDING SITE FOR RESIDUE HAL H 1002

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:142	-	B:208
5	H:22	-	H:92
6	H:142	-	H:208
7	L:23	-	L:88
8	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	Trp B:199	-	Pro B:200
6	Tyr L:94	-	Pro L:95
7	Tyr L:140	-	Pro L:141
8	Phe H:148	-	Pro H:149
9	Glu H:150	-	Pro H:151
10	Trp H:199	-	Pro H:200

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

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

(no "Exon" information available for 1MJJ)

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:218
                                                                                                                                                                                                                                                          
               SCOP domains d1mjja1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1mjja2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1mjjA01 A:1-108 Immunoglobulins                                                                                  1mjjA02 A:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mjj A   1 DIVMTQAAPSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCLQHLEYPFTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d1mjjb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                      d1mjjb2 B:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains -1mjjB01 B:2-113 Immunoglobulins                                                                                    1mjjB02 B:114-227 Immunoglobulins                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mjj B   1 xVQLQQPGAELVKPGASVKLSCKASGYTFTNYWINWVKQRPGQGLEWIGNIYPGSSYTHYNEKFKNKATLTVDTSSSTAYMQLSSLTSDDSAVYYCANKLGWFPYWGQGTLVTVSAAKTTAPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                            |       10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127||     144       154|||    169|      180|      192   || |204 ||    215       227 
                            1-PCA                                             52A                            82A||               99|                        128|               154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|               101                         136                157||     171       183           198 ||  208             226  
                                                                                                               82C                                                               158|                               200|                       
                                                                                                                                                                                  162                                202

Chain H from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d1mjjh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                      d1mjjh2 H:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains -1mjjH01 H:2-113 Immunoglobulins                                                                                    1mjjH02 H:114-226 Immunoglobulins                                                            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mjj H   1 xVQLQQPGAELVKPGASVKLSCKASGYTFTNYWINWVKQRPGQGLEWIGNIYPGSSYTHYNEKFKNKATLTVDTSSSTAYMQLSSLTSDDSAVYYCANKLGWFPYWGQGTLVTVSAAKTTAPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP 227
                            |       10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127||     144       154|||    169|      180|      192   || |204 ||    215       227
                            |                                                 52A                            82A||               99|                        128|               154|||    169|      180|          196| || 206|            223| 
                            1-PCA                                                                             82B|               101                         136                157||     171       183           198 ||  208             226 
                                                                                                               82C                                                               158|                               200|                      
                                                                                                                                                                                  162                                202

Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d1mjjl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1mjjl2 L:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1mjjL01 L:1-108 Immunoglobulins                                                                                  1mjjL02 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..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mjj L   1 DIVMTQAAPSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCLQHLEYPFTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                                                                                                                                        
                                                      27B|||                                                                                                                                                                                        
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E

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 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	1mjjA02	A:109-211
1b	1mjjA01	A:1-108
1c	1mjjL01	L:1-108
1d	1mjjB02	B:114-227
1e	1mjjH02	H:114-226
1f	1mjjB01	B:2-113
1g	1mjjH01	H:2-113
1h	1mjjL02	L:109-211

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

Asymmetric Unit(hide GO term definitions)

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

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		HAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PCA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:150 - Pro B:151	[ RasMol ]
		Glu H:150 - Pro H:151	[ RasMol ]
		Phe B:148 - Pro B:149	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Trp B:199 - Pro B:200	[ RasMol ]
		Trp H:199 - Pro H:200	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr A:94 - Pro A:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr L:94 - Pro L:95	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1mjj
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

(no "Entries Sharing at Least One Protein Chain" available for 1MJJ)

1mh5	THE STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF THEESTEROLYTIC ANTIBODY MS6-164 AND A TRANSITION-STATE ANALOG
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
1mju	1.22 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (5, 5)

SS Bonds (8, 8)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 8)

CATH Domains (1, 8)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File