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(-) Description

Title :  CRYSTAL STRUCTURE OF SLE PATIENT-DERIVED ANTI-DNA ANTIBODY
 
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 :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibody, Lupus, Fab, Immune System (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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:117 , SER A:120 , ASP A:144 , LYS B:130 , PO4 C:501binding site for residue PO4 A 501
2AC2SOFTWAREPO4 A:501 , LYS C:117 , SER C:120 , ASP C:144binding site for residue PO4 C 501

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (6, 6)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GKS)

(-) Sequences/Alignments

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:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee....eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee...hhhhhh..eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gks A   2 VQLQESGPGLVKSSETLSLTCTVSGGSISSYFWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISLHTSKNQFSLKLSSVTAADTAVYYCARHRNWLFDYWGQGTLVTVSSASTKGPSVFPLAPSAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVDHKPSNTKVDKTVE 212
                                    11        21        31        41        51        61        71        81 |||    88        98       108       118       136       146       156       166       176       186       196       206      
                                                                                                           82A||                                          127|                                                                            
                                                                                                            82B|                                           136                                                                            
                                                                                                             82C                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               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.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gks B   2 SALTQPRSVSGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKVMIYDVSKRPSGVPDRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSYTYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP 209
                                   |12        22       30B|       39        49        59        69        79        89      | 98       108       118       128       138       148       158       168       178       188       198       208 
                                   9|                 30A||                                                               95A                                                                                                                  
                                   11                  30B|                                                                                                                                                                                    
                                                        30C                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee...eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gks C   2 VQLQESGPGLVKSSETLSLTCTVSGGSISSYFWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISLHTSKNQFSLKLSSVTAADTAVYYCARHRNWLFDYWGQGTLVTVSSASTKGPSVFPLAPAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSTYTCNVDHKPSNTKVDKTVER 213
                                    11        21        31        41        51        61        71        81 |||    88        98       108       118       137       147       157       167       177       193       203       213
                                                                                                           82A||                                         126|                                               186|                    
                                                                                                            82B|                                          136                                                193                    
                                                                                                             82C                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee....eeeeeee...........eeeeee......eeee.............eeeeee..eeeeeee..hhhhheeeeeeee.....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee...eeeeeeeeehhhhhhhh..eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gks D   2 SALTQPRSVSGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKVMIYDVSKRPSGVPDRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSYTYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP 209
                                   |12        22       30B|       39        49        59        69        79        89      | 98       108       118       128       138       148       158       168|      180       190       200         
                                   9|                 30A||                                                               95A                                                                      168|                                      
                                   11                  30B|                                                                                                                                         171                                      
                                                        30C
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5GKS)

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5gkr