5GKR - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SLE PATIENT-DERIVED ANTI-DNA ANTIBODY IN COMPLEX WITH OLIGONUCLEOTIDE

Authors :   T. Arimori, S. Sakakibara, H. Kikutani, J. Takagi

Date :   05 Jul 16 (Deposition) - 05 Jul 17 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D,T
Biol. Unit 1: A,B,T  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Antibody, Lupus, Dna, Fab, Immune System-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sakakibara, T. Arimori, K. Yamashita, H. Jinzai, D. Motooka, S. Nakamura, S. Li, K. Takeda, T. Yasui, M. Narazaki, T. Tanaka, D. M. Standley, J. Takagi, H. Kikutani
Clonal Evolution And Antigen-Recognition Of Anti-Nuclear Antibodies In Acute Systemic Lupus Erythematosus
To Be Published
PubMed: search

Molecule 1 - IGG2, FAB (HEAVY CHAIN)
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - LAMBDA, FAB (LIGHT CHAIN)
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

*Molecule 3 - DNA (5'-D(PTPTPTPT)-3')*
	Chains	:	T
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	T
Biological Unit 1 (1x)	:	A	B			T
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 5GKR)

(no "Site" information available for 5GKR)

Asymmetric Unit

No.	Residues
1	A:22	-	A:92
2	A:140	-	A:196
3	B:23	-	B:88
4	B:135	-	B:194
5	C:22	-	C:92
6	C:140	-	C:196
7	D:23	-	D:88
8	D:135	-	D:194

Asymmetric Unit

No.	Residues
1	Phe A:146	-	Pro A:147
2	Glu A:148	-	Pro A:149
3	Tyr B:141	-	Pro B:142
4	Phe C:146	-	Pro C:147
5	Glu C:148	-	Pro C:149
6	Tyr D:141	-	Pro D:142

(no "SAP(SNP)/Variant" information available for 5GKR)

(no "PROSITE Motif" information available for 5GKR)

(no "Exon" information available for 5GKR)

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:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee......eeeeeee....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkr A   2 VQLQESGPGLVKSSETLSLTCTVSGGSISSYFWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISLHTSKNQFSLKLSSVTAADTAVYYCARHRNWLFDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVDHKPSNTKVDKTVE 212
                                    11        21        31        41        51        61        71        81 |||    88        98       108       118       135       145       155       165       175       185       195       205       
                                                                                                           82A||                                         126|                                                                              
                                                                                                            82B|                                          134                                                                              
                                                                                                             82C

Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkr B   1 QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKVMIYDVSKRPSGVPDRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSYTYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 210
                                    11        21       30A||      38        48        58        68        78        88       |97       107       117       127       137       147       157       167       177       187       197       207   
                                    9|                 30A||                                                               95A                                                                                                                   
                                    11                  30B|                                                                                                                                                                                     
                                                         30C

Chain C from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee....eeeeeee......eeeeeee....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee.......eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkr C   2 VQLQESGPGLVKSSETLSLTCTVSGGSYFWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISLHTSKNQFSLKLSSVTAADTAVYYCARHRNWLFDYWGQGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSGTQTYTCNVDHKPSNTKVDKTVER 213
                                    11        21      ||34        44        54        64        74       82B|       91       101       111       121    || 139       149       159       169       179       191       201       211  
                                                     28|                                                82A||                                         126|                                                 187|                       
                                                      32                                                 82B|                                          135                                                  190                       
                                                                                                          82C

Chain D from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.....eee...eeeee....eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkr D   3 ALTQPRSVSGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKVMIYDVSKRPSGVPDRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSYTYVFGTGTKVTVLGNPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP 209
                                  ||13        23       30C        40        50        60        70        80        90     |  99       113       123       133       143       153       163       173       183       193       203      
                                  9|                 30A||                                                               95A          108|                                                                                                
                                  11                  30B|                                                                             113                                                                                                
                                                       30C

Chain T from PDB  Type:DNA  Length:4
                                    
                 5gkr T   1 TTTT   4

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 '\|'

(no "SCOP Domain" information available for 5GKR)

(no "CATH Domain" information available for 5GKR)

(no "Pfam Domain" information available for 5GKR)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 5GKR)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5gkr)

	Sites
(no "Sites" information available for 5gkr)

	Cis Peptide Bonds
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu C:148 - Pro C:149	[ RasMol ]
		Phe A:146 - Pro A:147	[ RasMol ]
		Phe C:146 - Pro C:147	[ RasMol ]
		Tyr B:141 - Pro B:142	[ RasMol ]
		Tyr D:141 - Pro D:142	[ RasMol ]

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

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	5gkr
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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