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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB' FROM THE HIV-1 NEUTRALIZING ANTIBODY 2F5
 
Authors :  S. Bryson, J. P. Julien, R. C. Hynes, E. F. Pai
Date :  08 Apr 99  (Deposition) - 15 Jul 03  (Release) - 29 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fab, Hiv-1 Neutralization, Gp41, Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bryson, J. P. Julien, R. C. Hynes, E. F. Pai
Crystallographic Definition Of The Epitope Promiscuity Of The Broadly Neutralizing Anti-Human Immunodeficiency Virus Type 1 Antibody 2F5: Vaccine Design Implications.
J. Virol. V. 83 11862 2009
PubMed-ID: 19740978  |  Reference-DOI: 10.1128/JVI.01604-09
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ANTIBODY 2F5 (LIGHT CHAIN))
    Chains: L
    Fragment: FAB'
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PROTEIN (ANTIBODY 2F5 (HEAVY CHAIN))
    Chains: H
    Fragment: FAB'
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2F5A)

(-) Sites  (0, 0)

(no "Site" information available for 2F5A)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:97
2H:159 -H:215
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:165 -Pro H:166
5Glu H:167 -Pro H:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F5A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F5A)

(-) Exons   (0, 0)

(no "Exon" information available for 2F5A)

(-) 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 H from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains d2f5ah1 H:1-132 Immunoglobulin heavy chain variable domain, VH                                                                      d2f5ah2 H:133-232 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                  SCOP domains
               CATH domains 2f5aH01 H:1-132 Immunoglobulins                                                                                                     2f5aH02 H:133-231 Immunoglobulins                                                              - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee.........eeeeeee.....eeeeeeee....eee.hhh...eeeeeehhh.eeeeee....hhh.eeeeeeee....hhh......hhh.........eee..........eeeee.......eeeeeeeeee.....eeeehhh.....eee..........eeeeeeeee.hhh.....eeeeeeehhh.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2f5a H   1 RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQVVLVMTRVSPVDTATYFCAHRRGPTTLAAAAAAAGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEP 232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     ||154       164       174       184       194       204       214       224        
                                                                                                                                                                           146|                                                                                 
                                                                                                                                                                            151                                                                                 


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d2f5al1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d2f5al2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 2f5aL01 L:1-107 Immunoglobulins                                                                            2f5aL02 L:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee....hhh..eeeeee............eeee.......eeeee...hhhhhh.eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f5a L   1 ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRPEDFATYYCQQLHFYPHTFGGGTRVDVRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYECEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F5A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2F5A)

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  Sites
(no "Sites" information available for 2f5a)
 
  Cis Peptide Bonds
    Glu H:167 - Pro H:168   [ RasMol ]  
    Phe H:165 - Pro H:166   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr L:94 - Pro L:95   [ RasMol ]  
 

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 Related Entries

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