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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIV-1 CROSS NEUTRALIZING MONOCLONAL ANTIBODY 2F5 IN COMPLEX WITH GP41 PEPTIDE ANALOG EQDKW-[DAP]-S (CYCLIC)
 
Authors :  S. Bryson, J. -P. Julien, R. C. Hynes, E. F. Pai
Date :  09 Aug 04  (Deposition) - 05 Oct 04  (Release) - 05 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Fab Complex, Hiv-1 Neutralization, Gp41 Peptide, Immune System (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 - ANTIBODY 2F5 (LIGHT CHAIN)
    Chains: A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTIBODY 2F5 (HEAVY CHAIN)
    Chains: B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GP41 PEPTIDE ANALOG
    Chains: C
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1U93)

(-) Sites  (0, 0)

(no "Site" information available for 1U93)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:140 -B:196

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:146 -Pro B:147
5Glu B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U93)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U93)

(-) Exons   (0, 0)

(no "Exon" information available for 1U93)

(-) 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:214
                                                                                                                                                                                                                                                       
               SCOP domains d1u93a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1u93a2 A:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1u93A01 A:1-107 Immunoglobulins                                                                            1u93A02 A:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u93 A    1 ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRPEDFATYYCQQLHFYPHTFGGGTRVDVRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYECEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains d1u93b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                                      d1u93b2 B:114-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1u93B01 B:1-113 Immunoglobulins                                                                                                     1u93B02 B:114-213 Immunoglobulins                                                           --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeee...ee....eeehhhhh...ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee......eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u93 B    1 RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQVVLVMTRVSPVDTATYFCAHRRGPTTLFGVPIARGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPGAAAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLQTYTCNVNHKPSNTKVDKRVEPKSC  216
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     |100E|||||||101       111       121    || 137       147       157       167       177       187 ||    199       209       
                                                             35A|                                             82A||               100A|||||100J||||                       126|                                                     189|                        
                                                              35B                                              82B|                100B|||||100K|||                        133                                                      192                        
                                                                                                                82C                 100C|||||100L||                                                                                                            
                                                                                                                                     100D|||||100M|                                                                                                            
                                                                                                                                      100E|||| 100N                                                                                                            
                                                                                                                                       100F|||                                                                                                                 
                                                                                                                                        100G||                                                                                                                 
                                                                                                                                         100H|                                                                                                                 
                                                                                                                                          100I                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:7
                                        
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                1u93 C    1 EQDKWAS    7
   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  (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 1U93)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1U93)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 1u93)
 
  Cis Peptide Bonds
    Glu B:148 - Pro B:149   [ RasMol ]  
    Phe B:146 - Pro B:147   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Tyr A:140 - Pro A:141   [ RasMol ]  
    Tyr A:94 - Pro A:95   [ RasMol ]  
 

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 Databases and Analysis Tools

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  1u93
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1U93)

(-) Related Entries Specified in the PDB File

1u8h THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ALDKWAS
1u8i THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ELDKWAN
1u8j THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ELDKWAG
1u8k THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE LELDKWASL
1u8l THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE DLDRWAS
1u8m THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ELDKYAS
1u8n THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ELDKFAS
1u8o THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ELDKHAS
1u8p THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ECDKWCS
1u8q THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ELEKWAS
1u91 THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ANALOG ENDKW- [DAP]-S(CYCLIC)
1u92 THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ANALOG E-[DAP] -DKWQS(CYCLIC)
1u95 THE SAME PROTEIN COMPLEXED WITH GP41 PEPTIDE ELDHWAS
2f5a
2f5b