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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIV-1 CROSS NEUTRALIZING MONOCLONAL ANTIBODY 2F5 IN COMPLEX WITH GP41 PEPTIDE ELLELDKWASLWN
 
Authors :  J. P. Julien, S. Bryson, E. F. Pai
Date :  22 Mar 07  (Deposition) - 15 May 07  (Release) - 15 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Nmab 2F5, Hiv-1, Gp41 Epitope, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Julien, S. Bryson, J. L. Nieva, E. F. Pai
Structural Details Of Hiv-1 Recognition By The Broadly Neutralizing Monoclonal Antibody 2F5: Epitope Conformation, Antigen-Recognition Loop Mobility, And Anion-Binding Site.
J. Mol. Biol. V. 384 377 2008
PubMed-ID: 18824005  |  Reference-DOI: 10.1016/J.JMB.2008.09.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NMAB 2F5, LIGHT CHAIN
    Chains: A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - NMAB 2F5, HEAVY CHAIN
    Chains: B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GP41 PEPTIDE
    Chains: C
    Engineered: YES
    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 2P8L)

(-) Sites  (0, 0)

(no "Site" information available for 2P8L)

(-) 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 2P8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P8L)

(-) Exons   (0, 0)

(no "Exon" information available for 2P8L)

(-) 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p8lA01 A:1-107 Immunoglobulins                                                                            2p8lA02 A:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee.......eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2p8l 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:222
                                                                                                                                                                                                                                                               
               SCOP domains d2p8lb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                                      d2p8lb2 B:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma            SCOP domains
               CATH domains 2p8lB01 B:1-113 Immunoglobulins                                                                                                     2p8lB02 B:114-213 Immunoglobulins                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeeeee...ee....eeehhhhh...ee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2p8l B    1 RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQVVLVMTRVSPVDTATYFCAHRRGPTTLFGVPIARGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLQTYTCNVNHKPSNTKVDKRVEP  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     |100E|||||||101       111       121    || 139       149       159       169       179       189|      201       211  
                                                             35A|                                             82A||               100A|||||100J||||                       126|                                                   189|                     
                                                              35B                                              82B|                100B|||||100K|||                        135                                                    192                     
                                                                                                                82C                 100C|||||100L||                                                                                                       
                                                                                                                                     100D|||||100M|                                                                                                       
                                                                                                                                      100E|||| 100N                                                                                                       
                                                                                                                                       100F|||                                                                                                            
                                                                                                                                        100G||                                                                                                            
                                                                                                                                         100H|                                                                                                            
                                                                                                                                          100I                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...ee...... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                2p8l C    0 ELLELDKWASL   10
                                     9
   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  (2, 2)

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 2P8L)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2P8L)

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  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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 Related Entries

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

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(-) Related Entries Specified in the PDB File

2p8m 2p8p