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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF ANTI-HIV-1 V3 FAB 2219 IN COMPLEX WITH UG29 PEPTIDE
 
Authors :  R. L. Stanfield, M. K. Gorny, S. Zolla-Pazner, I. A. Wilson
Date :  15 Sep 05  (Deposition) - 04 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Fab-Peptide Complex; Hiv-1; Gp120; V3 Loop, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Stanfield, M. K. Gorny, S. Zolla-Pazner, I. A. Wilson
Crystal Structures Of Human Immunodeficiency Virus Type 1 (Hiv-1) Neutralizing Antibody 2219 In Complex With Three Different V3 Peptides Reveal A New Binding Mode For Hiv-1 Cross-Reactivity.
J. Virol. V. 80 6093 2006
PubMed-ID: 16731948  |  Reference-DOI: 10.1128/JVI.00205-06

(-) Compounds

Molecule 1 - FAB 2219, LIGHT CHAIN
    Cell: PERIPHERAL BLOOD CELLS
    Chains: L
    Fragment: LIGHT CHAIN
    Organ: BLOOD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 2219, HEAVY CHAIN
    Cell: PERIPHERAL BLOOD CELLS
    Chains: H
    Fragment: HEAVY CHAIN
    Organ: BLOOD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - UG29 PEPTIDE OF EXTERIOR MEMBRANE GLYCOPROTEIN GP120
    Chains: P
    Engineered: YES
    Fragment: RESIDUES 96-118
    Other Details: THIS SEQUENCE OCCURS IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (ISOLATE MN)
    Synonym: GP120
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2B1H)

(-) Sites  (0, 0)

(no "Site" information available for 2B1H)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr L:140 -Pro L:141
2Phe H:148 -Pro H:149
3Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B1H)

(-) Exons   (0, 0)

(no "Exon" information available for 2B1H)

(-) 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:226
                                                                                                                                                                                                                                                                   
               SCOP domains d2b1hh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                              d2b1hh2 H:114-229 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 2b1hH01 H:1-113 Immunoglobulins                                                                                             2b1hH02 H:114-225 Immunoglobulins                                                                 ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee........eeeee....eeeeee...hhhhheeeeeeeee.........eeeee...eeeeee.......eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b1h H    1 EIQLEQSGAEVKKSGESLKISCQTSGYSFSDYWIGWVRQMPGKGLEWMGIFYPGDSDSRYSPSFEGQVTMSADRSTNTAHLQWSSLKPSDTALYYCARLGGDYEDSGADAFDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  229
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109       119       129||     141       151  |||| 166  ||   177  ||   188       198 |||   211       221||    
                                                                              52A                            82A||               100A||||||                           130|                  154|||    169|      180|               200||              222|    
                                                                                                              82B|                100B|||||                            133                   156||     171       182                203|               225    
                                                                                                               82C                 100C||||                                                   157|                                   205                      
                                                                                                                                    100D|||                                                    162                                                            
                                                                                                                                     100E||                                                                                                                   
                                                                                                                                      100F|                                                                                                                   
                                                                                                                                       100G                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2b1hL01 L:2-107 Immunoglobulins                                                                                 2b1hL02 L:108-211 Immunoglobulins                                                                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeeee......eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b1h L    1 QSVLTQPPSASGTPGQRISISCSGTSSNVENNYVYWYQHLPGTAPKLLIYRNDHRSSGIPDRFSASKSGTSASLAISGLRPEDEGDYYCAAWDDSRGGPDWVFGGGTKLTVLAQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPT  212
                                    11        21      ||29        39        49        59        69        79        89      |95D       105 |     114       124       134       144       154       164   ||  175       185       195    || 207     
                                    9|              27A|                                                                  95A|||        106A                                                           168|                           200|         
                                    11               27B                                                                   95B||                                                                        170                            203         
                                                                                                                            95C|                                                                                                                   
                                                                                                                             95D                                                                                                                   


Chain P from PDB  Type:PROTEIN  Length:16
                                                 
               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
                2b1h P  303 TKKSIKIRPRQAFYAT  320
                                  |314      
                                309|        
                                 312
   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 2B1H)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2B1H)

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  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ 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

2b0s THE SAME FAB COMPLEXED WITH MN PEPTIDE
2b1a THE SAME FAB COMPLEXES WITH UG1033 PEPTIDE