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(-) Description

Title :  FAB STRUCTURE OF A NEUTRALIZING ANTIBODY L1 FROM AN EARLY SUBTYPE A HIV-1 INFECTED PATIENT
 
Authors :  R. M. Pan, X. P. Kong
Date :  12 May 12  (Deposition) - 27 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Ig, Antibody, Gp120, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Murphy, L. Yue, R. Pan, S. Boliar, A. Sethi, J. Tian, K. Pfafferot, E. Karita, S. A. Allen, E. Cormier, P. A. Goepfert, P. Borrow, J. E. Robinson, S. Gnanakaran, E. Hunter, X. P. Kong, C. A. Derdeyn
Viral Escape From Neutralizing Antibodies In Early Subtype Hiv-1 Infection Drives An Increase In Autologous Neutralization Breadth.
Plos Pathog. V. 9 03173 2013
PubMed-ID: 23468623  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003173

(-) Compounds

Molecule 1 - LIGHT CHAIN OF FAB OF A NEUTRALIZING ANTIBODY L1
    Chains: L
    Fragment: LIGHT CHAIN OF L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HEAVY CHAIN OF FAB OF A NEUTRALIZING ANTIBODY L1
    Chains: H
    Fragment: HEAVY CHAIN OF L1
    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  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY H:9 , GLY H:10 , ARG H:100D , LEU H:108 , HOH H:430 , HOH H:502 , TYR L:91 , SER L:95 , HOH L:379BINDING SITE FOR RESIDUE GOL H 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:193

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr L:140 -Pro L:141
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F57)

(-) Exons   (0, 0)

(no "Exon" information available for 4F57)

(-) 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:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.......ee.......eeeeee....eeeeee...hhhhheeeeeeee............eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4f57 H    1 EVQLVESGGGVVQPGGSLRLSCVASGFSFSDFGMNWVRQAPGKGLEWVAFVPFDRRINYYAESVRGRFTISRDDSKNTVFLQMDSLRPEDTAIYYCAKHRSQWNFWPREGGLDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128       138       148       158       168       178       188       198       208     
                                                                              52A                            82A||               100A|||||||                                                                                                                 
                                                                                                              82B|                100B||||||                                                                                                                 
                                                                                                               82C                 100C|||||                                                                                                                 
                                                                                                                                    100D||||                                                                                                                 
                                                                                                                                     100E|||                                                                                                                 
                                                                                                                                      100F||                                                                                                                 
                                                                                                                                       100G|                                                                                                                 
                                                                                                                                        100H                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d4f57l1 L:1-108 automated matches                                                                               d4f57l2 L:109-209 automated matches                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4f57 L    1 QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYRQHPGEAPKAIIFDVTNRPSGISNRFSGSKFGNTASLTISGLQAEDEADYYCAAYTVASTLLFGGGTKVTVLRQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                    11        21      ||28        38        48        58        68        78        88       |97      106A       116       126       136       146       156       166       176       186       196       206   
                                    9|              27A||                                                                  95A        106A                                                                                                       
                                    11               27B|                                                                                                                                                                                        
                                                      27C
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 4F57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F57)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4F57)

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  Cis Peptide Bonds
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  4f57
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 Related Entries

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(-) Related Entries Specified in the PDB File

4f58