2JB5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   FAB FRAGMENT IN COMPLEX WITH SMALL MOLECULE HAPTEN, CRYSTAL FORM-1

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

Date :   03 Dec 06 (Deposition) - 08 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : H,L

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
	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
	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
Asymmetric/Biological Unit	:	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	T5C	1	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 (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR H:32 , ALA H:33 , ASN H:35 , ASN H:50 , TYR H:99 , MET H:101 , LYS H:104 , LEU H:106 , HOH H:2016 , HOH H:2017 , HOH H:2027 , ASN L:33 , TYR L:34 , VAL L:35 , TYR L:51 , GLY L:52 , TRP L:93 , LEU L:97 , HOH L:2003	BINDING SITE FOR RESIDUE T5C H1223

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:96
2	H:147	-	H:203
3	L:22	-	L:90
4	L:139	-	L:198

Asymmetric/Biological Unit

No.	Residues
1	Phe H:153	-	Pro H:154
2	Glu H:155	-	Pro H:156
3	Tyr L:145	-	Pro L:146

(no "SAP(SNP)/Variant" information available for 2JB5)

Asymmetric/Biological Unit (1, 1)

	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	1	L:196-202

Asymmetric/Biological Unit (1, 1)

	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	1	L:112-214	103

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d2jb5h1 H:3-120 Immunoglobulin heavy chain variable domain, VH                                                        d2jb5h2 H:121-222 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 2jb5H01 H:3-120 Immunoglobulins                                                                                       2jb5H02 H:121-222 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eee.....eeeeeee.........eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeee....eeeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee..hhhhh.eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jb5 H   3 QLVQSGAEVKKPGSSVKVSCKASGGTFSNYAINWVRQAPGQGLEWMGNIEPYFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARYFMSYKHLSDYWGQGTLVTVSSASTKGPSVFPLAPSSKSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 222
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    || 145       155       165       175       185       195       205       215       
                                                                                                                                                                137|                                                                                 
                                                                                                                                                                 141

Chain L 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 d2jb5l1 L:3-112 automated matches                                                                             d2jb5l2 L:113-214 automated matches                                                                    SCOP domains
               CATH domains 2jb5L01 L:3-112 Immunoglobulins                                                                               2jb5L02 L:113-214 Immunoglobulins                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....eeeeee....hhhhh..eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee......eee...eeeee...........ee..hhhhhhh..eeeee.eeee.....eeeeee..ee.................eee..eeee..........eeeeeee..eeeeeee... 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
                 2jb5 L   3 ALTQPASVSGSPGQSITISCTGTSSDVGSNNYVSWYQQHPGKAPKLMIYGGSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCRSWDSNLSYSVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

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/Biological 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	2jb5H02	H:121-222
1b	2jb5L01	L:3-112
1c	2jb5H01	H:3-120
1d	2jb5L02	L:113-214

(no "Pfam Domain" information available for 2JB5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (IGLC2_HUMAN | P0DOY2)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:155 - Pro H:156	[ RasMol ]
		Phe H:153 - Pro H:154	[ RasMol ]
		Tyr L:145 - Pro L:146	[ RasMol ]

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2c0v	IGG RHEUMATOID FACTOR IN HOMO SAPIENS
2jb6	FAB FRAGMENT IN COMPLEX WITH SMALL MOLECULE HAPTEN, CRYSTAL FORM-2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (4, 4)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (24, 43)

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