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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROADLY HIV-1 NEUTRALIZING FAB X5 AT 1.90 ANGSTROM RESOLUTION
 
Authors :  R. Darbha, S. Phogat, A. F. Labrijn, Y. Shu, Y. Gu, M. Andrykovitch, M. Y. Zhang, R. Pantophlet, L. Martin, C. Vita, D. R. Burton, D. S. Dimitrov, X. Ji
Date :  14 Nov 03  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Fab, Antibody, X5, Hiv-1, Broadly Neutralizing, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Darbha, S. Phogat, A. F. Labrijn, Y. Shu, Y. Gu, M. Andrykovitch, M. Y. Zhang, R. Pantophlet, L. Martin, C. Vita, D. R. Burton, D. S. Dimitrov, X. Ji
Crystal Structure Of The Broadly Cross-Reactive Hiv-1-Neutralizing Fab X5 And Fine Mapping Of Its Epitope
Biochemistry V. 43 1410 2004
PubMed-ID: 14769016  |  Reference-DOI: 10.1021/BI035323X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB X5, LIGHT CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB X5, HEAVY CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1RHH)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:133 -A:193
3A:213 -B:216
4B:23 -B:92
5B:140 -B:196
6C:23 -C:88
7C:133 -C:193
8C:213 -D:216
9D:23 -D:92
10D:140 -D:196

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Ser A:94 -Pro A:95
3Phe B:146 -Pro B:147
4Glu B:148 -Pro B:149
5Ser C:7 -Pro C:8
6Ser C:94 -Pro C:95
7Tyr C:139 -Pro C:140
8Phe D:146 -Pro D:147
9Glu D:148 -Pro D:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RHH)

(-) Sequences/Alignments

Asymmetric 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:215
                                                                                                                                                                                                                                                        
               SCOP domains d1rhha1 A:1-106A Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1rhha2 A:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1rhhA01 A:1-107 Immunoglobulins                                                                              1rhhA02 A:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee...hhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rhh A    1 ELVLTQSPGTLSLSAGERATLSCRASQSVSSGSLAWYQQKPGQAPRLLIYGASTRATGIPDRFSGSGSGTDFTLTIGRLEPEDLAVYYCQQYGTSPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSRDSTYSLGSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  213
                                    10        20       |29        39        49        59        69        79        89        99       108       118       128       138       148       158       168       178       188       198       208     
                                                     27A                                                                            106A                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                          
               SCOP domains d1rhhb1 B:3-113 Immunoglobulin heavy chain variable domain, VH                                                                    d1rhhb2 B:114-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1rhhB01 B:3-113 Immunoglobulins                                                                                                   1rhhB02 B:114-213 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee........eeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee....................ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rhh B    3 QLLEQSGAEVKKPGSSVQVSCKASGGTFSMYGFNWVRQAPGHGLEWMGGIIPIFGTSNYAQKFRGRVTFTADQATSTAYMELTNLRSDDTAVYYCARDFGPDWEDGDSYDGSGRGFFDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    12        22        32   |    41        51 |      60        70        80  |||   87        97   |||100G|||||||103       113       123       133       143       153       163       173       183       193       203       213   
                                                           35A               52A                            82A||               100A|||||100J||||                                                                                                                    
                                                                                                             82B|                100B|||||100K|||                                                                                                                    
                                                                                                              82C                 100C|||||100L||                                                                                                                    
                                                                                                                                   100D|||||100M|                                                                                                                    
                                                                                                                                    100E|||| 100N                                                                                                                    
                                                                                                                                     100F|||                                                                                                                         
                                                                                                                                      100G||                                                                                                                         
                                                                                                                                       100H|                                                                                                                         
                                                                                                                                        100I                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains d1rhhc1 C:1-106A Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1rhhc2 C:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1rhhC01 C:1-107 Immunoglobulins                                                                              1rhhC02 C:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee...hhhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rhh C    1 ELVLTQSPGTLSLSAGERATLSCRASQSVSSGSLAWYQQKPGQAPRLLIYGASTRATGIPDRFSGSGSGTDFTLTIGRLEPEDLAVYYCQQYGTSPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSRDSTYSLGSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  213
                                    10        20       |29        39        49        59        69        79        89        99       108       118       128       138       148       158       168       178       188       198       208     
                                                     27A                                                                            106A                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                         
               SCOP domains d1rhhd1 D:4-113 Immunoglobulin heavy chain variable domain, VH                                                                   d1rhhd2 D:114-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1rhhD01 D:4-113 Immunoglobulins                                                                                                  1rhhD02 D:114-213 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eee.....eeeeee.hhhh....eeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee....................ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rhh D    4 LLEQSGAEVKKPGSSVQVSCKASGGTFSMYGFNWVRQAPGHGLEWMGGIIPIFGTSNYAQKFRGRVTFTADQATSTAYMELTNLRSDDTAVYYCARDFGPDWEDGDSYDGSGRGFFDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    13        23        33  |     42        52|       61        71        81 |||    88        98  ||||100H|||||| 104       114       124       134       144       154       164       174       184       194       204       214  
                                                          35A               52A                            82A||               100A|||||100J||||                                                                                                                    
                                                                                                            82B|                100B|||||100K|||                                                                                                                    
                                                                                                             82C                 100C|||||100L||                                                                                                                    
                                                                                                                                  100D|||||100M|                                                                                                                    
                                                                                                                                   100E|||| 100N                                                                                                                    
                                                                                                                                    100F|||                                                                                                                         
                                                                                                                                     100G||                                                                                                                         
                                                                                                                                      100H|                                                                                                                         
                                                                                                                                       100I
   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, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1rhhA02A:108-210
1b1rhhA01A:1-107
1c1rhhC01C:1-107
1d1rhhB02B:114-213
1e1rhhD02D:114-213
1f1rhhD01D:4-113
1g1rhhB01B:3-113
1h1rhhC02C:108-210

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RHH)

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Glu B:148 - Pro B:149   [ RasMol ]  
    Glu D:148 - Pro D:149   [ RasMol ]  
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  1rhh
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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

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