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(-) Description

Title :  CRYSTAL STRUCTURE OF A32 FAB, AN ADCC MEDIATING ANTI-HIV-1 ANTIBODY
 
Authors :  X. Wu, M. Pazgier
Date :  01 Sep 11  (Deposition) - 26 Sep 12  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Adcc, Non-Neutralizing, Anti-Hiv-1 Env Antibody A32, Cd4I Antibody, Fab, Viral Glycoprotein Gp120, Hiv-1 Env, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Guan, M. Pazgier, M. M. Sajadi, R. Kamin-Lewis, S. Al-Darmarki, R. Flinko, E. Lovo, X. Wu, J. E. Robinson, M. S. Seaman, T. R. Fouts, R. C. Gallo, A. L. Devico, G. K. Lewis
Diverse Specificity And Effector Function Among Human Antibodies To Hiv-1 Envelope Glycoprotein Epitopes Exposed By Cd4 Binding.
Proc. Natl. Acad. Sci. Usa V. 110 E69 2013
PubMed-ID: 23237851  |  Reference-DOI: 10.1073/PNAS.1217609110

(-) Compounds

Molecule 1 - FAB HEAVY CHAIN OF HUMAN ANTI-HIV-1 ENV ANTIBODY A32
    Chains: H, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK 293
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB LIGHT CHAIN OF HUMAN ANTI-HIV-1 ENV ANTIBODY A32
    Chains: L, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Strain: HEK 293
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL3Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:60 , SER B:76 , ARG L:54BINDING SITE FOR RESIDUE ACT L 1
2AC2SOFTWAREGLY A:8 , PRO A:9 , GLY A:10 , THR A:107 , MET A:108BINDING SITE FOR RESIDUE CL A 222
3AC3SOFTWARESER L:152BINDING SITE FOR RESIDUE CL L 213

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:193
5H:22 -H:92
6H:140 -H:196
7L:23 -L:88
8L:134 -L:193

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Tyr L:140 -Pro L:141
4Phe A:146 -Pro A:147
5Glu A:148 -Pro A:149
6Val B:4 -Leu B:5
7Gly B:28 -Gly B:29
8Tyr B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TNM)

(-) 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:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....eeeeeee..eeeeeeeee.....eeeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeeee.........ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3tnm A    1 QVQLQESGPGLVKPSQTLSLSCTVSGAHYWSWIRQYPGKGLEWIGYIHYSGNTYYNPSLKSRITISQHTSENQFSLKLNSVTVADTAVYYCARGTRLRTLRNAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20    || 35A|       44        54        64        74       82B|       91      100A||||   106       116       126       136       146       156       166       176       186       196       206        
                                                   25| 35A|                                             82A||               100A||||                                                                                                                  
                                                    32  35B                                              82B|                100B|||                                                                                                                  
                                                                                                          82C                 100C||                                                                                                                  
                                                                                                                               100D|                                                                                                                  
                                                                                                                                100E                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains d3tnmb1 B:4-107 automated matches                                                                            d3tnmb2 B:108-208 automated matches                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee.....eeeeee...........eeeeee......eeee.............eeeee...eeeeee...hhhhheeeeeeeee...eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3tnm B    4 VLTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQHHPGKAPKLIISEVNNRPSGVPDRFSGSKSGNTASLTVSGLQAEDEAEYYCSSYTDIHNFVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    13        23    ||| 30        40        50        60        70        80        90     |  99       108       118       128       138       148       158       168       178       188       198       208
                                                  27A||                                                                  95A        106A                                                                                                      
                                                   27B|                                                                                                                                                                                       
                                                    27C                                                                                                                                                                                       


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee.....eeeeeeee...eeee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeee.......eeeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhhh....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3tnm H    1 QVQLQESGPGLVKPSQTLSLSCTVSGGSSSSGAHYWSWIRQYPGKGLEWIGYIHYSGNTYYNPSLKSRITISQHTSENQFSLKLNSVTVADTAVYYCARGTRLRTLRNAFDIWGQGTMVTVSSASTKGPSVFPLAPSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     |100E       110       120      |133       143       153       163       173       183       193       203       213 
                                                             35A|                                             82A||               100A||||                        127|                                                                                   
                                                              35B                                              82B|                100B|||                         131                                                                                   
                                                                                                                82C                 100C||                                                                                                               
                                                                                                                                     100D|                                                                                                               
                                                                                                                                      100E                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains d3tnml1 L:4-107 automated matches                                                                            d3tnml2 L:108-208 automated matches                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee.....eeeeee............eeeee......eeee.............eeeee...eeeeee...hhhhheeeeeeeee...eeee...eeeee....ee..eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3tnm L    4 VLTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQHHPGKAPKLIISEVNNRPSGVPDRFSGSKSGNTASLTVSGLQAEDEAEYYCSSYTDIHNFVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    13        23    ||| 30        40        50        60        70        80        90     |  99       108       118       128       138       148       158       168       178       188       198       208
                                                  27A||                                                                  95A        106A                                                                                                      
                                                   27B|                                                                                                                                                                                       
                                                    27C
   Legend:   → Mismatch (orange background)
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    → 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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
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(-) Related Entries Specified in the PDB File

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3tnn