2OK0 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   FAB ED10-DNA COMPLEX

Authors :   R. L. Stanfield, S. Sanguineti, I. A. Wilson, G. De Prat-Gay

Date :   15 Jan 07 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

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

Keywords :   Immunoglobulin Fold, Immune System-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sanguineti, J. M. Centeno Crowley, M. F. Lodeiro Merlo, M. L. Cerutti, I. A. Wilson, F. A. Goldbaum, R. L. Stanfield, G. De Prat-Gay
Specific Recognition Of A Dna Immunogen By Its Elicited Antibody
J. Mol. Biol. V. 370 183 2007
PubMed-ID: 17512945 | Reference-DOI: 10.1016/J.JMB.2007.04.046

*Molecule 1 - 5'-D(TPC)-3'*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - FAB ED10 LIGHT CHAIN
	Chains	:	L
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - FAB ED10 HEAVY CHAIN
	Chains	:	H
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3
Asymmetric/Biological Unit	:	D	H	L

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2OK0)

(no "Site" information available for 2OK0)

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:142	-	H:208
3	L:23	-	L:88
4	L:134	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Thr L:7	-	Pro L:8
2	Ile L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:148	-	Pro H:149
5	Glu H:150	-	Pro H:151
6	Trp H:200	-	Pro H:202

(no "SAP(SNP)/Variant" information available for 2OK0)

(no "PROSITE Motif" information available for 2OK0)

(no "Exon" information available for 2OK0)

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 D from PDB  Type:DNA  Length:2
                                   
                2ok0 D    1 TC    2

Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------d2ok0h1 H:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 2ok0H01 H:1-114 Immunoglobulins                                                                                      2ok0H02 H:115-228 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee..eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee........eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ok0 H    1 EVQLEESGPELVKPGASVKISCKASGYTFTDYYMNWLRQKPGQGLEWIGWVYPGSIKYNEKFKDKATLTADTSSSIVYMHLSSLTSDDNAVYFCTRWTYGSSFDYWGEGTLLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  228
                                    10        20        30        40        50  ||    61        71        81 |||    88        98  |    107       117       127  ||   139       149    |||164    || 175    || 187       199||     210       220  ||  
                                                                              52A|                         82A||               100A                           130|                  154|||    169|      180|          196|||                  223|  
                                                                                55                          82B|                                               133                   156||     171       183           199||                   226  
                                                                                                             82C                                                                      157|                              200|                        
                                                                                                                                                                                       162                               202

Chain L from PDB  Type:PROTEIN  Length:219
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
        A2NHM3_MOUSE      1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  219
               SCOP domains d2ok0l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d2ok0l2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2ok0L01 L:1-108 Immunoglobulins                                                                                  -2ok0L02 L:110-209 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains --V-set-2ok0L02 L:3-106                                                                                        ------------C1-set-2ok0L01 L:119-206                                                                -------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ok0 L    1 DILMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPTLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHIPLTFGAGTKLEVKRSDAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mus musculus (Yes) (2)

1a	2ok0L02	L:110-209
1b	2ok0H01	H:1-114
1c	2ok0H02	H:115-228
1d	2ok0L01	L:1-108

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Mus musculus (Mouse) (118)

C1-set-2ok0L01

L:119-206

Family: V-set (144)

Mus musculus (Mouse) (63)

V-set-2ok0L02

L:3-106

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2OK0)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:150 - Pro H:151	[ RasMol ]
		Ile L:94 - Pro L:95	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp H:200 - Pro H:202	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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2ojz	STRUCTURAL BASIS FOR THE RECOGNITION OF A DNA IMMUNOGEN BY ITS ELICITED ANTIBODY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (3, 3)

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