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(-) Description

Title :  CRYSTAL STRUCTURE OF CLFA IN COMPLEX WITH THE FAB FRAGMENT OF TEFIBAZUMAB
 
Authors :  V. K. Ganesh
Date :  04 May 16  (Deposition) - 18 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Staphylococcal Infections, Clumping Factor A, Fibrinogen, Tefibazumab, Aurexis, Mscramm, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. K. Ganesh, X. Liang, J. A. Geoghegan, A. L. Cohen, N. Venugopalan, T. J. Foster, M. Hook
Lessons From The Crystal Structure Of The S. Aureus Surface Protein Clumping Factor A In Complex With Tefibazumab, An Inhibiting Monoclonal Antibody.
Ebiomedicine V. 13 328 2016
PubMed-ID: 27789272  |  Reference-DOI: 10.1016/J.EBIOM.2016.09.027

(-) Compounds

Molecule 1 - CLUMPING FACTOR A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 229-545
    Gene: CLFA
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
 
Molecule 2 - TEFIBAZUMAB FAB FRAGMENT HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 3 - TEFIBAZUMAB FAB FRAGMENT LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5JQ6)

(-) Sites  (0, 0)

(no "Site" information available for 5JQ6)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:327 -A:541
2H:22 -H:95
3H:148 -H:204
4L:23 -L:94
5L:139 -L:199

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe H:154 -Pro H:155
2Glu H:156 -Pro H:157
3Tyr L:145 -Pro L:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 5JQ6)

(-) Sequences/Alignments

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 A from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhheeeeeeee...eehhhhh..eeeeeeee.........eeeee....ee.................eeeee.....eeeee.hhhh.eeeeeeeeeeeeee........eeeeeeeee..eeeeeeeee.....eee..eeeeeeeeeee....eeeeeeee......eeeeeeeeee.......ee......eeeeee..hhhhh......hhhhhee.hhhheeeeee..eeeee......ee...eeeeeeeee.........eeeeeeee.....eeeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jq6 A 219 GSHHHHHHGSGTDITNQLTNVTVGIDSGTTVYPHQAGYVKLNYGFSVPNSAVKGDTFKITVPKELNLNGVTSTAKVPPIMQVLANGVIDSDGNVIYTFTDYVNTKCDVKATLTMPAYIDPENVKKTGNVTLATGIGSTTANKTVLVDYEKYGKFYNLSIKGTIDQIDKTNNTYRQTIYVNPSGDNVIAPVLTGNLKPNTDSNALIDQQNTSIKVYKVDNAADLSESYFVNPENFEDVTNSVNITFPNPNQYKVEFNTPDDQITTPYIVVVNGHIDPNSKGDLALRSTLYGYNSNIIWRSMSWDNEVAFNNGSGSGDGIDC 541
                                   228       238       248       258       268       278       288       298|      311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541
                                                                                                         298|                                                                                                                                                                                                                                               
                                                                                                          302                                                                                                                                                                                                                                               


Chain H from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee.....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeee..hhhhh.....ee...eeeee........eeeee...eeeeeeee.....eeee.hhh....eee...ee.....eeeeeee......eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jq6 H   1 QVQLKESGPGLVKPSQTLSITCTISGFSLSRYSVHWVRQPPGKGLEWLGMIWGGGNTDYNSALKSRLSISKDNSKNQVFLKMNSLTAADTAVYYCARKGEFYYGYDGFVYWGQGTLVTVSSASTKGPSVFPLAPALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSYICNVNHKPSNTKVDKRAE 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  150       160       170       180       190  |||| 206       216    
                                                                                                                                                               134|                                             193|||                  
                                                                                                                                                                145                                              195||                  
                                                                                                                                                                                                                  196|                  
                                                                                                                                                                                                                   202                  


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeee.......eeeee..hhhhhh...eeeeeeeeee.....eeeee........eeeee.........eeeeeeeeehhhhhhh...eeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jq6 L   1 DIVMTQSPDSLAVSLGERVTMNCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSVQAEDLAVYYCHQYLSSYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGPVTKSANR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    || 161       171       181       191       201   ||  214  
                                                                                                                                                                                    155|                                             205|       
                                                                                                                                                                                     157                                              209
   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 5JQ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JQ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JQ6)

(-) Gene Ontology  (5, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:156 - Pro H:157   [ RasMol ]  
    Phe H:154 - Pro H:155   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
 

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  5jq6
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  CLFA_STAAE | Q53653
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 Related Entries

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

UniProtKB/Swiss-Prot
        CLFA_STAAE | Q53653: 1n67

(-) Related Entries Specified in the PDB File

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