2JB6 - 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 :   FAB FRAGMENT IN COMPLEX WITH SMALL MOLECULE HAPTEN, CRYSTAL FORM-2

Authors :   R. C. Hillig, S. Baesler, G. Malawski, V. Badock, I. Bahr, M. Schirner,

Date :   03 Dec 06 (Deposition) - 08 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Cdr, Tsc, Fab, Hucal, Fluorescent Dye, Immunoglobulin Domain, Antibody Fragment, Diagnostic Imaging, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. C. Hillig, S. Urlinger, J. Fanghanel, B. Brocks, C. Haenel, Y. Stark D. Sulzle, D. I. Svergun, S. Baesler, G. Malawski, D. Moosmayer, A. Menrad, M. Schirner, K. Licha
Fab Mor03268 Triggers Absorption Shift Of A Diagnostic Dye Via Packaging In A Solvent-Shielded Fab Dimer Interface
J. Mol. Biol. V. 377 206 2008
PubMed-ID: 18241888 | Reference-DOI: 10.1016/J.JMB.2007.12.071
(for further references see the PDB file header)

Molecule 1 - FAB FRAGMENT MOR03268 HEAVY CHAIN
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	IN VITRO SELECTED FROM A LIBRARY AND OPTIMIZED IN SEVERAL MATURATION STEPS

Molecule 2 - FAB FRAGMENT MOR03268 LIGHT CHAIN
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	IN VITRO SELECTED FROM A LIBRARY AND OPTIMIZED IN SEVERAL MATURATION STEPS

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (2x)	:			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	T5C	2	Ligand/Ion	2-{(1E,3Z,5E,7E)-7-[3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]-4-METHYLHEPTA-1,3,5-TRIEN-1-YL}-3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-3H-INDOLIUM

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	T5C	2	Ligand/Ion	2-{(1E,3Z,5E,7E)-7-[3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]-4-METHYLHEPTA-1,3,5-TRIEN-1-YL}-3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-3H-INDOLIUM

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	T5C	2	Ligand/Ion	2-{(1E,3Z,5E,7E)-7-[3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]-4-METHYLHEPTA-1,3,5-TRIEN-1-YL}-3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-3H-INDOLIUM

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:34 , VAL A:35 , SER A:36 , TYR A:51 , GLY A:52 , TRP A:93 , HOH A:2001 , TYR B:32 , ALA B:33 , ASN B:35 , ASN B:50 , TYR B:99 , MET B:101 , LYS B:104 , HOH B:2001	BINDING SITE FOR RESIDUE T5C B1222
2	AC2	SOFTWARE	TYR H:32 , ALA H:33 , ASN H:35 , ASN H:50 , TYR H:99 , LYS H:104 , TYR L:34 , VAL L:35 , SER L:36 , TYR L:51 , GLY L:52 , TRP L:93	BINDING SITE FOR RESIDUE T5C H1222

Asymmetric Unit

No.	Residues
1	A:22	-	A:90
2	A:139	-	A:198
3	B:22	-	B:96
4	B:147	-	B:203
5	H:22	-	H:96
6	H:147	-	H:203
7	L:22	-	L:90
8	L:139	-	L:198

Asymmetric Unit

No.	Residues
1	Tyr A:145	-	Pro A:146
2	Phe B:153	-	Pro B:154
3	Glu B:155	-	Pro B:156
4	Glu B:219	-	Pro B:220
5	Phe H:153	-	Pro H:154
6	Glu H:155	-	Pro H:156
7	Glu H:219	-	Pro H:220
8	Tyr L:145	-	Pro L:146

(no "SAP(SNP)/Variant" information available for 2JB6)

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.	IGLC2_HUMAN	85-91	2	A:196-202 L:196-202

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGLC2_HUMAN	85-91	2	A:196-202 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGLC2_HUMAN	85-91	2	- L:196-202

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000390323	1	ENSE00001721671	chr22:23243156-23243617	462	IGLC2_HUMAN	1-106	106	2	A:112-214 L:112-214	103 103

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:212
 aligned with IGLC2_HUMAN | P0DOY2 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:212
                                                                                                                                         1                                                                                                      
                                     -         -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71        81        91       101  
          IGLC2_HUMAN     - -------------------------------------------------------------------------------------------------------------GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 103
               SCOP domains d2jb6a1 A:3-112 automated matches                                                                             d2jb6a2 A:113-214 automated matches                                                                    SCOP domains
               CATH domains 2jb6A01 A:3-112 Immunoglobulins                                                                               2jb6A02 A:113-214 Immunoglobulins                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee......eee...eeeee........eeeee..hhhhhhh...eeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeee.hhhhhhhh..eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------ PROSITE
               Transcript 1 -------------------------------------------------------------------------------------------------------------Exon 1.1  PDB: A:112-214 UniProt: 1-106 [INCOMPLETE]                                                    Transcript 1
                 2jb6 A   3 ALTQPASVSGSPGQSITISCTGTSSDVGSNNYVSWYQQHPGKAPKLMIYGGSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCRSWDSNLSYSVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d2jb6b1 B:3-120 Immunoglobulin heavy chain variable domain, VH                                                   d2jb6b2 B:121-221 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 2jb6B01 B:3-120 Immunoglobulins                                                                                  2jb6B02 B:121-221 Immunoglobulins                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eee.....eeeeee.....eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeee....eeeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eeeeeeee.....eeeeeeeee.........eeeeeeehhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jb6 B   3 QLVQSGAEVKKPGSSVKVSCKASNYAINWVRQAPGQGLEWMGNIEPYFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARYFMSYKHLSDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 221
                                    12        22 ||     37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217    
                                                24|                                                                                                                                                                                               
                                                 30

Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d2jb6h1 H:3-120 Immunoglobulin heavy chain variable domain, VH                                                  d2jb6h2 H:121-221 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 2jb6H01 H:3-120 Immunoglobulins                                                                                 2jb6H02 H:121-221 Immunoglobulins                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eee.......eeeeee.....eeeeeee......eee.......eeeeee....eeeeee........eeeeeeeeee....eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jb6 H   3 QLVQSGAEVKKPGSSVKVSCKANYAINWVRQAPGQGLEWMGNIEPYFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARYFMSYKHLSDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 221
                                    12        22 ||     38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
                                                24|                                                                                                                                                                                              
                                                 31

Chain L from PDB  Type:PROTEIN  Length:211
 aligned with IGLC2_HUMAN | P0DOY2 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:211
                                                                                                                                        1                                                                                                      
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102 
          IGLC2_HUMAN     - ------------------------------------------------------------------------------------------------------------GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 103
               SCOP domains d2jb6l1 L:4-112 automated matches                                                                            d2jb6l2 L:113-214 automated matches                                                                    SCOP domains
               CATH domains 2jb6L01 L:4-112 Immunoglobulins                                                                              2jb6L02 L:113-214 Immunoglobulins                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeeeee....hhhhh...............................eeeeee..eeeeee...hhhhheeeeeeee............eeeee........eeeee..hhhhhhh...eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.hhhhhhh...eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------ PROSITE
               Transcript 1 ------------------------------------------------------------------------------------------------------------Exon 1.1  PDB: L:112-214 UniProt: 1-106 [INCOMPLETE]                                                    Transcript 1
                 2jb6 L   4 LTQPASVSGSPGQSITISCTGTSSDVGSNNYVSWYQQHPGKAPKLMIYGGSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCRSWDSNLSYSVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 214
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213

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)

Human (Homo sapiens) (912)

1a	2jb6B02	B:121-221
1b	2jb6H02	H:121-221
1c	2jb6L01	L:4-112
1d	2jb6A01	A:3-112
1e	2jb6H01	H:3-120
1f	2jb6B01	B:3-120
1g	2jb6A02	A:113-214
1h	2jb6L02	L:113-214

(no "Pfam Domain" information available for 2JB6)

Asymmetric Unit(hide GO term definitions)

Chain A,L (IGLC2_HUMAN | P0DOY2)

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
		T5C	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:155 - Pro B:156	[ RasMol ]
		Glu B:219 - Pro B:220	[ RasMol ]
		Glu H:155 - Pro H:156	[ RasMol ]
		Glu H:219 - Pro H:220	[ RasMol ]
		Phe B:153 - Pro B:154	[ RasMol ]
		Phe H:153 - Pro H:154	[ RasMol ]
		Tyr A:145 - Pro A:146	[ RasMol ]
		Tyr L:145 - Pro L:146	[ 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
	2jb6
		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
	IGHG1_HUMAN \| P01857
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	IGLC2_HUMAN \| P0DOY2
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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
	IGHG1_HUMAN \| P01857
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	IGLC2_HUMAN \| P0DOY2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2c0v	IGG RHEUMATOID FACTOR IN HOMO SAPIENS
2jb5	FAB FRAGMENT IN COMPLEX WITH SMALL MOLECULE HAPTEN, CRYSTAL FORM-1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 8)

CATH Domains (1, 8)

Pfam Domains (0, 0)

Gene Ontology (24, 43)

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