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(-) Description

Title :  3B4 IN COMPLEX WITH CXCL13 - 3B4-CXCL13
 
Authors :  C. Tu, J. Bard, L. Mosyak
Date :  30 Jun 15  (Deposition) - 04 Nov 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Anti-Cxcl13, Cxcl13, Scfv, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Tu, V. Terraube, A. Tam, W. Stochaj, B. Fennell, L. Lin, M. Stahl, E. Lavallie, W. Somers, W. Finlay, L. Mosyak, J. Bard, O. Cunningham
Optimization Of A Scfv-Based Biotherapeutic By Cdr Side-Chain Clash Repair
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3B4 HEAVY CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: MAMMALIA
    Expression System Taxid: 40674
    Gene: IGHV1-69-2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 3B4 LIGHT CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: MAMMALIA
    Expression System Taxid: 40674
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - C-X-C MOTIF CHEMOKINE 13
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA
    Expression System Taxid: 561
    Gene: CXCL13, BCA1, BLC, SCYB13
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANGIE,B CELL-ATTRACTING CHEMOKINE 1,BCA-1,B LYMPHOCYTE CHEMOATTRACTANT,CXC CHEMOKINE BLC,SMALL-INDUCIBLE CYTOKINE B13

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:95 , ASP A:100H , TYR B:91 , ARG E:21 , ARG E:22binding site for residue EDO A 201
2AC2SOFTWARESER A:7 , GLY A:8 , ALA A:9 , GLN A:105 , GLY A:106 , THR A:107 , THR A:108binding site for residue PEG A 202
3AC3SOFTWAREASP A:100H , TYR B:30 , ASP B:31 , ASP B:50 , SER F:6binding site for residue EDO B 201
4AC4SOFTWAREGLU C:95 , ASP C:100H , TYR D:91 , ARG F:22binding site for residue EDO C 201
5AC5SOFTWAREGLN E:13 , SER E:15 , VAL E:51 , CYS E:52 , HOH E:203binding site for residue EDO E 101

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2B:23 -B:88
3C:22 -C:92
4D:23 -D:88
5E:9 -E:36
6E:11 -E:52
7F:9 -F:36
8F:11 -F:52

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg F:32 -Gly F:33
2Asn F:34 -Gly F:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CBA)

(-) 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:127
                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.eeee..eeee.....ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cba A    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCAREPDYYDSSGYYPIDAFDIWGQGTTVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       
                                                                              52A                            82A||               100A|||||100J             
                                                                                                              82B|                100B|||||||              
                                                                                                               82C                 100C||||||              
                                                                                                                                    100D|||||              
                                                                                                                                     100E||||              
                                                                                                                                      100F|||              
                                                                                                                                       100G||              
                                                                                                                                        100H|              
                                                                                                                                         100I              


Chain B from PDB  Type:PROTEIN  Length:112
                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee.....eee...eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                5cba B    1 QSALTQPASVSASPGQSITISCTGTSSDVGAYDWVSWYQQHPGKAPKLLIFDVNNRPSGVSHRFSGSKSGNTASLTISGLQAEDEADYYCSSYTRRDTYVFGTGTKVTVLGE  108
                                    11        21      ||28        38        48        58        68        78        88       |97      106A  
                                    9|              27A||                                                                  95A        106A  
                                    11               27B|                                                                                   
                                                      27C                                                                                   


Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.eee....eee.....ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cba C    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCAREPDYYDSSGYYPIDAFDIWGQGTTVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       
                                                                              52A                            82A||               100A|||||100J             
                                                                                                              82B|                100B|||||||              
                                                                                                               82C                 100C||||||              
                                                                                                                                    100D|||||              
                                                                                                                                     100E||||              
                                                                                                                                      100F|||              
                                                                                                                                       100G||              
                                                                                                                                        100H|              
                                                                                                                                         100I              


Chain D from PDB  Type:PROTEIN  Length:111
                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee.....eee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                5cba D    1 QSALTQPASVSASPGQSITISCTGTSSDVGAYDWVSWYQQHPGKAPKLLIFDVNNRPSGVSHRFSGSKSGNTASLTISGLQAEDEADYYCSSYTRRDTYVFGTGTKVTVLG  107
                                    11        21      ||28        38        48        58        68        78        88       |97      106A 
                                    9|              27A||                                                                  95A        106A 
                                    11               27B|                                                                                  
                                                      27C                                                                                  


Chain E from PDB  Type:PROTEIN  Length:61
                                                                                              
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeeee.........eeeeee....eeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                5cba E    8 RCRCVQESSVFIPRRFIDRIQILPRGNGCPRKEIIVWKKNKSIVCVDPQAEWIQRMMEVLR   68
                                    17        27        37        47        57        67 


Chain F from PDB  Type:PROTEIN  Length:64
                                                                                                 
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhh.eeeeeee.........eeeeee....eeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                5cba F    6 SLRCRCVQESSVFIPRRFIDRIQILPRGNGCPRKEIIVWKKNKSIVCVDPQAEWIQRMMEVLRK   69
                                    15        25        35        45        55        65
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 62)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        CXL13_HUMAN | O43927: 4zai 5cbe
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(-) Related Entries Specified in the PDB File

5c2b 5C2B IS THE SCFV