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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GP120 V2 ANTIBODY RE505-22 FAB FROM IGH- AND IGK-HUMANIZED MOUSE
 
Authors :  N. I. Nicely
Date :  13 Jun 16  (Deposition) - 25 Jan 17  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Hiv-1 Gp120 Antibody Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wiehe, N. I. Nicely, B. Lockwood, M. Kuraoka, K. Anasti, S. Arora, C. M. Bowman, C. Stolarchuk, R. Parks, K. E. Lloyd, S. M. Xia, R. Duffy, X. Shen, C. A. Kyratsous, L. E. Macdonald, A. J. Murphy, R. M. Scearce, M. A. Moody, S. M. Alam, L. Verkoczy, G. D. Tomaras, G. Kelsoe, B. F. Haynes
Immunodominance Of Antibody Recognition Of The Hiv Envelope V2 Region In Ig-Humanized Mice.
J. Immunol. V. 198 1047 2017
PubMed-ID: 28011932  |  Reference-DOI: 10.4049/JIMMUNOL.1601640

(-) Compounds

Molecule 1 - ANTIBODY RE505-22 FAB HEAVY CHAIN
    Chains: H, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: EXPI392
    Expression System Strain: HEK293
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 2 - ANTIBODY RE505-22 FAB LIGHT CHAIN
    Chains: L, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: EXPI293
    Expression System Strain: HEK293
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5KG9)

(-) Sites  (0, 0)

(no "Site" information available for 5KG9)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:22 -B:88
4B:135 -B:194
5H:22 -H:92
6H:140 -H:196
7L:22 -L:88
8L:135 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Tyr L:141 -Pro L:142
4Phe A:146 -Pro A:147
5Glu A:148 -Pro A:149
6Tyr B:141 -Pro B:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KG9)

(-) Exons   (0, 0)

(no "Exon" information available for 5KG9)

(-) 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:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee.....eeeeee......eeeee........ee.......eeee...eeeee...hhhhheeeeeee......ee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kg9 A   2 VQLVESGGGLVQPGRALRLSCAASGFDYAMHWVRQAPGKGLEWVSGISWNSGSRGYADSVKGRFTISRDSQYLQMNSLRVEDTAFYYCARMNGTFDYWGQGTLVTVSLASTKGPSVFPLAPSSKSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 213
                                    11        21     || 34        44        53        63        77     |||84        94    || 105       115       125    || 137       147       157       167       177       187       197       207      
                                                    27|                   52A                  72|   82A||               99|                          130|                                                                                
                                                     31                                         77    82B|               101                           133                                                                                
                                                                                                       82C                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeeee....eeeeeee.hhhh...eeeeee......eeeeee.....eee.......eeeeee..eeeeee...hhhhh.eeeeeeee......eeee...eeeeee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kg9 B   1 QLVLTQSSSASFSLGASAKLTCTLSSQHSTYTIEWYQQQPLKPPKFVMELRKDGSHNTGDGIPDRFSGSSSGADRYLSISNIQPEDEAIYICGVGDTIKEQFVYVFGGGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 210
                                    10        20        30        40        50  ||||  56        66        76        86       95A|||    102       112       122       132       142       152       162       172       182       192       202        
                                                                              52A|||                                         95A|||                                                                                                                   
                                                                               52B||                                          95B||                                                                                                                   
                                                                                52C|                                           95C|                                                                                                                   
                                                                                 52D                                            95D                                                                                                                   


Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeeee........eeeeeee.....eeeeeee......eee.......eeeee.....eeeeee...hhhhheeeeeeee...eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kg9 H   2 VQLVESGGGLVQPGRALRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGSRGYADSVKGRFTISRDNAKKSQYLQMNSLRVEDTAFYYCARMNGTFDYWGQGTLVTVSLASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 213
                                    11        21        31        41        51 |      60        70        80  |||   87        97 ||    108       118       128|      142       152       162       172       182       192       202       212 
                                                                             52A                            82A||               99|                        128|                                                                                
                                                                                                             82B|               101                         133                                                                                
                                                                                                              82C                                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..eeeee....eeeeee.........eeeeee......eeeeee.....eee.......eeeeee..eeeeee...hhhhh.eeeeeeeeee..eeeeee...eeeeee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kg9 L   1 QLVLTQSSSASFSLGASAKLTCTLSSQHSTYTIEWYQQQPLKPPKFVMELRKDGSHNTGDGIPDRFSGSSSGADRYLSISNIQPEDEAIYICGVGDTIKEQFVYVFGGGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 210
                                    10        20        30        40        50  ||||  56        66        76        86       95A|||    102       112       122       132       142       152       162       172       182       192       202        
                                                                              52A|||                                         95A|||                                                                                                                   
                                                                               52B||                                          95B||                                                                                                                   
                                                                                52C|                                           95C|                                                                                                                   
                                                                                 52D                                            95D
   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  (0, 0)

(no "SCOP Domain" information available for 5KG9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KG9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KG9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5KG9)

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  Sites
(no "Sites" information available for 5kg9)
 
  Cis Peptide Bonds
    Glu A:148 - Pro A:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe A:146 - Pro A:147   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Tyr B:141 - Pro B:142   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
 
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