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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROADLY NEUTRALIZING ANTI-HIV FAB F105
 
Authors :  R. A. Wilkinson, C. Piscitelli, M. Teintze, C. M. Lawrence
Date :  29 Jul 04  (Deposition) - 09 Aug 05  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Fab, F105, Gp120, Hiv, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Wilkinson, C. Piscitelli, M. Teintze, L. A. Cavacini, M. R. Posner, C. M. Lawrence
Structure Of The Fab Fragment Of F105, A Broadly Reactive Anti-Human Immunodeficiency Virus (Hiv) Antibody That Recognizes The Cd4 Binding Site Of Hiv Type 1 Gp120.
J. Virol. V. 79 13060 2005
PubMed-ID: 16189008  |  Reference-DOI: 10.1128/JVI.79.20.13060-13069.2005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - F105 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Fragment: ANTIGEN-BINDING FRAGMENT, FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: EXPRESSION: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
 
Molecule 2 - F105 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Fragment: ANTIGEN-BINDING FRAGMENT, FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: EXPRESSION: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER

 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 1U6A)

(-) Sites  (0, 0)

(no "Site" information available for 1U6A)

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Gly H:95 -Pro H:96
4Asp H:101 -Pro H:102
5Phe H:146 -Pro H:147
6Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U6A)

(-) Exons   (0, 0)

(no "Exon" information available for 1U6A)

(-) 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:222
 aligned with Q6N089_HUMAN | Q6N089 from UniProtKB/TrEMBL  Length:472

    Alignment length:223
                                                                                                                                    126                                                                                                                    
                                                                                                                                  125 |                                                                                                                    
                                    30        40        50        60        70        80        90       100       110       120    | |129       139       149       159       169       179       189       199       209       219       229       239   
        Q6N089_HUMAN     21 VQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGSIAYADSVKGRFTISRDNGKNSLYLQMNSLRAEDTALYYCAKEIGAHNFY-YYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  242
               SCOP domains d1u6ah1 H:2-113 Immunoglobulin heavy chain variable  domain, VH                                                            d1u6ah2 H:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1u6aH01 H:2-113 Immunoglobulins                                                                                            1u6aH02 H:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeeee.-...eeehhhhhh.eeeeee....eeeeee...hhhhheeeeeee...................eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u6a H    2 VQLQESGPGLVKPSETLSLTCTVSGGSISSHYWSWIRQSPGKGLQWIGYIYY-SGSTNYSPSLKSRVTISVETAKNQFSLKLTSMTAADTAVYYCARGPVPAVFYGDYRLDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    11        21        31        41        51 | |    60        70        80  |||   87        97   |||100G       110       120       130       140       150       160       170       180       190       200       210   
                                                                              53 |                          82A||               100A||||||                                                                                                                 
                                                                                54                           82B|                100B|||||                                                                                                                 
                                                                                                              82C                 100C||||                                                                                                                 
                                                                                                                                   100D|||                                                                                                                 
                                                                                                                                    100E||                                                                                                                 
                                                                                                                                     100F|                                                                                                                 
                                                                                                                                      100G                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:214
 aligned with Q6PIL8_HUMAN | Q6PIL8 from UniProtKB/TrEMBL  Length:236

    Alignment length:215
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
        Q6PIL8_HUMAN     21 ENVLTQSPGTLSLSPGERATLSCRASQSLSSSYLAWYQQKPGQAPRLLIYGVSSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGTSRPITFGQGTRLDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  235
               SCOP domains d1u6al1 L:1-107 automated matches                                                                            d1u6al2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains 1u6aL01 L:1-108 Immunoglobulins                                                                               1u6aL02 L:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeeeeeeehhhhheeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeeeee..-eeee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u6a L    1 EIVLTQSPGTLSLSAGERATLSCRASQSVSSRYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRVEPEDFAVYYCQQYDNS-VCTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       |29        39        49        59        69        79        89    | | 98       108       118       128       138       148       158       168       178       188       198       208     
                                                     27A                                                                 94 |                                                                                                                      
                                                                                                                           95
   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 1U6A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1U6A)

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Asymmetric/Biological Unit
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  Sites
(no "Sites" information available for 1u6a)
 
  Cis Peptide Bonds
    Asp H:101 - Pro H:102   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly H:95 - Pro H:96   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  1u6a
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  Q6N089_HUMAN | Q6N089
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  Q6PIL8_HUMAN | Q6PIL8
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6N089_HUMAN | Q6N089: 2oqj 3mnv 3qct 3qcu 3qcv 4nm4 4nm8 4nuj 5ewi 5ug0
        Q6PIL8_HUMAN | Q6PIL8: 5ug0
UniProtKB/TrEMBL
        Q6N089_HUMAN | Q6N089: 3cfj 3cfk 4hpy
        Q6PIL8_HUMAN | Q6PIL8: 3dvg 3dvn 3eyq 3hi1 4oqt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1U6A)