3MJ8 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HL4E10 FAB, A HAMSTER AB STIMULATORY FOR GAMMADELTA T CELLS

Authors :   P. Verdino, I. A. Wilson

Date :   12 Apr 10 (Deposition) - 13 Apr 11 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.94

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

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

Reference :   P. Verdino, D. A. Witherden, K. Podshivalova, S. E. Rieder, W. L. Havran, I. A. Wilson
Cdna Sequence And Fab Crystal Structure Of Hl4E10, A Hamste Igg Lambda Light Chain Antibody Stimulatory For Gammadelta Cells.
Plos One V. 6 19828 2011
PubMed-ID: 21629689 | Reference-DOI: 10.1371/JOURNAL.PONE.0019828

Molecule 1 - STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
	Chains	:	L, A
	Organism Common	:	ARMENIAN HAMSTER
	Organism Scientific	:	CRICETULUS MIGRATORIUS
	Organism Taxid	:	10032
	Other Details	:	HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
	Strain	:	HYBRIDOMA

Molecule 2 - STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN
	Chains	:	H, B
	Organism Common	:	ARMENIAN HAMSTER
	Organism Scientific	:	CRICETULUS MIGRATORIUS
	Organism Taxid	:	10032
	Other Details	:	HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
	Strain	:	HYBRIDOMA

		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)

(no "Ligand,Modified Residues,Ions" information available for 3MJ8)

(no "Site" information available for 3MJ8)

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 L:140	-	Pro L:141
2	Phe H:148	-	Pro H:149
3	Glu H:150	-	Pro H:151
4	Trp H:198	-	Pro H:200
5	Tyr A:140	-	Pro A:141
6	Phe B:148	-	Pro B:149
7	Glu B:150	-	Pro B:151
8	Trp B:198	-	Pro B:200

(no "SAP(SNP)/Variant" information available for 3MJ8)

(no "PROSITE Motif" information available for 3MJ8)

(no "Exon" information available for 3MJ8)

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:209
                                                                                                                                                                                                                                                  
               SCOP domains d3mj8a1 A:1-107 automated matches                                                                            d3mj8a2 A:108-211 automated matches                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eeeeee.........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee...ee...eee...eee..eeeeeeeeeeehhhhhhh..eeeeeee..eee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mj8 A    1 SYTLTQPPLVSVALGQKATITCSGDKLSDVYVHWYQQKAGQAPVLVIYEDNRRPSGIPDHFSGSNSGNMATLTISKAQAGDEADYYCQSWDGTNSAWVFGSGTKVTVLGQPNAAPSVTLFPPSSEELKTNQATLVCMINGFYPADVAVTWEADGTPITQGVKTTQPSKSDSKYMATSYLTMTADAWKSRNTFICKVTHGGNTVEKSLSP  211
                                    11        21        31        41        51        61        71        81        91    ||  99       108       118       128       138       148       158       170       180       190       200|        
                                    9|                                                                                  95A|        106A                                                         166||                           200|        
                                    11                                                                                   95B                                                                      168|                            203        
                                                                                                                                                                                                   170

Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh..........eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mj8 B    1 QVQLKESGPGLLQPSQTLSLTCTVSGISLSDYGVHWVRQAPGKGLEWMGIIGHAGGTDYNSNLKSRVSISRDTSKSQVFLKLNSLQQEDTAMYFCARHFYTYFDVWGQGIQVTVSSATTTAPSVYPLAPACNTVTLGCLVKGYFPEPVTVSWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPG  228
                                    10        20        30        40        50        60        70        80  |||   87        97       107       117       127||     144       154|||    169|      180|      192     ||205       215       227 
                                                                                                            82A||                                           128|               154|||    169|      180|            198||||               223|  
                                                                                                             82B|                                            136                156||     171       183             200|||                226  
                                                                                                              82C                                                                157|                                202||                     
                                                                                                                                                                                  162                                 203|                     
                                                                                                                                                                                                                       205

Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee............eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhhhhh.eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mj8 H    1 QVQLKESGPGLLQPSQTLSLTCTVSGISLSDYGVHWVRQAPGKGLEWMGIIGHAGGTDYNSNLKSRVSISRDTSKSQVFLKLNSLQQEDTAMYFCARHFYTYFDVWGQGIQVTVSSATTTAPSVYPLAPACNTVTLGCLVKGYFPEPVTVSWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPG  228
                                    10        20        30        40        50        60        70        80  |||   87        97       107       117       127||     144       154|||    169|      180|      192     ||205       215       227 
                                                                                                            82A||                                           128|               154|||    169|      180|            198||||               223|  
                                                                                                             82B|                                            136                156||     171       183             200|||                226  
                                                                                                              82C                                                                157|                                202||                     
                                                                                                                                                                                  162                                 203|                     
                                                                                                                                                                                                                       205

Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains d3mj8l1 L:1-107 automated matches                                                                            d3mj8l2 L:108-211 automated matches                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eeeeee........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eee...eee..eeeeeeeeeeehhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mj8 L    1 SYTLTQPPLVSVALGQKATITCSGDKLSDVYVHWYQQKAGQAPVLVIYEDNRRPSGIPDHFSGSNSGNMATLTISKAQAGDEADYYCQSWDGTNSAWVFGSGTKVTVLGQPNAAPSVTLFPPSSEELKTNQATLVCMINGFYPADVAVTWEADGTPITQGVKTTQPSKSDSKYMATSYLTMTADAWKSRNTFICKVTHGGNTVEKSLSP  211
                                    11        21        31        41        51        61        71        81        91    ||  99       108       118       128       138       148       158       170       180       190       200|        
                                    9|                                                                                  95A|        106A                                                         166||                           200|        
                                    11                                                                                   95B                                                                      168|                            203        
                                                                                                                                                                                                   170

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Cricetulus migratorius [TaxId: 10032] (5)

1a	d3mj8a1	A:1-107
1b	d3mj8a2	A:108-211
1c	d3mj8l1	L:1-107
1d	d3mj8l2	L:108-211

(no "CATH Domain" information available for 3MJ8)

(no "Pfam Domain" information available for 3MJ8)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3MJ8)

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
(no "Ligands, Modified Residues, Ions" information available for 3mj8)

	Sites
(no "Sites" information available for 3mj8)

	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:198 - Pro B:200	[ RasMol ]
		Trp H:198 - Pro H:200	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ 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 \| Biol. Unit 1 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
	3mj8
		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 3MJ8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

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