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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIV-2 NEUTRALIZING FAB FRAGMENT 7C8
 
Authors :  H Uchtenhagen, R Friemann, G Raszewski, A-L Spetz, L Nilsson, A A
Date :  16 Jul 10  (Deposition) - 18 May 11  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  H,L  (1x)
Keywords :  Antigen Binding, Antibody, Fab, Immunological, Hiv-2, V3, Gp125, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Uchtenhagen, R. Friemann, G. Raszewski, A. L. Spetz, L. Nilsson, A. Achour
Crystal Structure Of The Hiv-2 Neutralizing Fab Fragment 7C With High Specificity To The V3 Region Of Gp125.
Plos One V. 6 E1876 2011
PubMed-ID: 21541316  |  Reference-DOI: 10.1371/JOURNAL.PONE.0018767

(-) Compounds

Molecule 1 - MOUSE ANTI V3 ANTIBODY 7C8 FAB, HEAVY CHAIN
    Chains: A, H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Fragment: FAB
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - MOUSE ANTI V3 ANTIBODY 7C8 FAB, LIGHT CHAIN
    Chains: B, L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Fragment: FAB
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:30A , GLY B:91BINDING SITE FOR RESIDUE GOL B 3968

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:195
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6H:140 -H:195
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Phe A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Trp A:188 -Pro A:189
4Thr B:7 -Pro B:8
5Val B:94 -Pro B:95
6Tyr B:140 -Pro B:141
7Phe H:146 -Pro H:147
8Glu H:148 -Pro H:149
9Trp H:188 -Pro H:189
10Thr L:7 -Pro L:8
11Val L:94 -Pro L:95
12Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 3NZ8)

(-) 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:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee.......ee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nz8 A    1 AVQLEESGPELVKPGALVKISCKASGYTFTTYDINWVKQRPGQGLEWIGWIYPGDGSNKYNEKFKDKATLTVDKSSSTAYMHLSSLTSENSAVYFCARGYGKNVYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123   ||  137       147       157       167       177       187       197       207       
                                                                              52A                            82A||               100A||                        127|                                                                                  
                                                                                                              82B|                100B|                         132                                                                                  
                                                                                                               82C                 100C                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d3nz8b1 B:1-107 automated matches                                                                               d3nz8b2 B:108-212 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nz8 B    1 DVVMTQTPLSLPVSLGDQASISCRSSQTIVHSNGYTYLDWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20        30|||||   35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                        30A||||                                                                                                                                                                                      
                                                         30B|||                                                                                                                                                                                      
                                                          30C||                                                                                                                                                                                      
                                                           30D|                                                                                                                                                                                      
                                                            30E                                                                                                                                                                                      


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee...............eeeee........eeeee........eeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeee...........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nz8 H    1 AVQLEESGPELVKPGALVKISCKASGYTFTTYDINWVKQRPGQGLEWIGWIYPGDGSNKYNEKFKDKATLTVDKSSSTAYMHLSSLTSENSAVYFCARGYGKNVYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123   ||  137       147       157       167       177       187       197       207       
                                                                              52A                            82A||               100A||                        127|                                                                                  
                                                                                                              82B|                100B|                         132                                                                                  
                                                                                                               82C                 100C                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d3nz8l1 L:1-107 automated matches                                                                               d3nz8l2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nz8 L    1 DVVMTQTPLSLPVSLGDQASISCRSSQTIVHSNGYTYLDWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20        30|||||   35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                        30A||||                                                                                                                                                                                       
                                                         30B|||                                                                                                                                                                                       
                                                          30C||                                                                                                                                                                                       
                                                           30D|                                                                                                                                                                                       
                                                            30E
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NZ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NZ8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3NZ8)

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