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(-) Description

Title :  CRYSTAL STRUCTURE OF DH511.2 FAB IN COMPLEX WITH HIV-1 GP41 MPER 662-683 PEPTIDE
 
Authors :  G. Ofek, L. Wu, C. S. Lougheed, L. D. Williams, N. I. Nicely, B. F. Haynes
Date :  02 Dec 16  (Deposition) - 15 Feb 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B,C,H,L,P
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Hiv-1, Neutralizing, Antibody, Gp41, Mper, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. D. Williams, G. Ofek, S. Schatzle, J. R. Mcdaniel, X. Lu, N. I. Nicely L. Wu, C. S. Lougheed, T. Bradley, M. K. Louder, K. Mckee, R. T. Bailer, S. O'Dell, I. S. Georgiev, M. S. Seaman, R. J. Parks, D. J. Marshall, K. Anasti, G. Yang, X. Nie, N. L. Tumba, K. Wiehe, K. Wagh, B. Korber, T. B. Kepler, S. M. Alam, L. Morris, G. Kamanga, M. S. Cohen, M. Bonsignori, S. -M. Xia, D. C. Montefiori, G. Kelsoe, F. Gao, J. R. Mascola, M. A. Moody, K. O. Saunders, H. -X. Liao, G. D. Tomaras, G. Georgiou, B. F. Haynes
Potent And Broad Hiv Neutralizing Antibodies In Memory B Cells And Plasma
Sci Immunol 2017
PubMed: search  |  Reference-DOI: 10.1126/SCIIMMUNOL.AAL2200

(-) Compounds

Molecule 1 - DH511.2 FAB HEAVY CHAIN
    Chains: H, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Gene: IGG HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DH511.2 FAB LIGHT CHAIN
    Chains: L, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Gene: IGG LIGHT CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GP41 MPER PEPTIDE
    Chains: P, C
    Engineered: YES
    Fragment: GP41 656-683
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: GP41 MPER 662-683 PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCHLP
Biological Unit 1 (1x):    HLP
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP H:30 , ASP H:73 , ASN H:76binding site for residue CA H 301
2AC2SOFTWARESER A:115 , HOH A:426 , THR B:109 , VAL B:110binding site for residue CL A 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6H:140 -H:196
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3K)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3K)

(-) 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 ..eeeeee.eee.....eeeeeeee..hhhhheeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeee..hhhhh..eeeeeeee...eeeee........eeeee...eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee..eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3k A    1 QVQLVQSGGGLVKPGGSLTLSCSASGFFFDNSWMGWVRQAPGKGLEWVGRIRRLKDGATGEYGAAVKDRFTISRDDSRNMLYLHMRTLKTEDSGTYYCTMDEGTPVTRFLEWGYFYYYMAVWGRGTTVIVSSASTKGPSVFPLAGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||101       111       121   ||  138       148       158       168       178       195       205        
                                                                              52A||                            82A||               100A|||||100J|||                      125|                                                  186|                   
                                                                               52B|                             82B|                100B|||||100K||                       133                                                   194                   
                                                                                52C                              82C                 100C|||||100L|                                                                                                   
                                                                                                                                      100D|||||100M                                                                                                   
                                                                                                                                       100E||||                                                                                                       
                                                                                                                                        100F|||                                                                                                       
                                                                                                                                         100G||                                                                                                       
                                                                                                                                          100H|                                                                                                       
                                                                                                                                           100I                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.............eeeee.......eeeee.........eeeeeeee.....eeeeee.......eeeee.........eeeeeee.....eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3k B    1 DIVMTQSPSSVSASVGDRVTITCRASQNIRDYLNWYQHKPGGSPRLLIYAASTLQTGVPSRFSGSGSGNLFTLTITNLQPEDFATYYCQENYNTIPSLSFGQGTKVDIRRTVAAPSVFIFPPSDEQTASVVCLLNNFYPREAKVQWKVDNLQSGNSQESVTEQDSKDSTYSLSSTLTKHKVYACEVTHQGLSSPVTKSF  209
                                    10        20        30        40        50        60        70        80        90     || 98       108       118     ||132       142       152|      163       173      |190       200         
                                                                                                                         95A|                          124|                    152|                       180|                     
                                                                                                                          95B                           129                     154                        188                     


Chain C from PDB  Type:PROTEIN  Length:19
                                                    
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                5u3k C  667 ASLWNWFDITNWLWYIRKK  685
                                   676         


Chain H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.eee.....eeeeeeee..hhhhheeeeeee......eeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeee..hhhhh..eeeeeeee...eeeee........eeeee.....eeeeeeee.....eeee........eee...ee.....eeeeeee.hhhhh....eeeeeeehhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5u3k H    1 QVQLVQSGGGLVKPGGSLTLSCSASGFFFDNSWMGWVRQAPGKGLEWVGRIRRLKDGATGEYGAAVKDRFTISRDDSRNMLYLHMRTLKTEDSGTYYCTMDEGTPVTRFLEWGYFYYYMAVWGRGTTVIVSSASTKGPSVFPLAPSAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTPSSSLGTQTYICNVNHKPSNTKVDKRVE  212
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||101       111       121     ||139       149       159       169       179   ||  190       200       210  
                                                                              52A||                            82A||               100A|||||100J|||                        127|                                            183|                           
                                                                               52B|                             82B|                100B|||||100K||                         136                                             185                           
                                                                                52C                              82C                 100C|||||100L|                                                                                                       
                                                                                                                                      100D|||||100M                                                                                                       
                                                                                                                                       100E||||                                                                                                           
                                                                                                                                        100F|||                                                                                                           
                                                                                                                                         100G||                                                                                                           
                                                                                                                                          100H|                                                                                                           
                                                                                                                                           100I                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee.............eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3k L    1 DIVMTQSPSSVSASVGDRVTITCRASQNIRDYLNWYQHKPGGSPRLLIYAASTLQTGVPSRFSGSGSGNLFTLTITNLQPEDFATYYCQENYNTIPSLSFGQGTKVDIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B                                                                                                                     


Chain P from PDB  Type:PROTEIN  Length:20
                                                     
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                5u3k P  666 WASLWNWFDITNWLWYIRKK  685
                                   675       685
   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 5U3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3K)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)

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        ENV_HV1B9 | Q73372: 4r4h 5u3l 5u3m 5u3n 5u3o

(-) Related Entries Specified in the PDB File

5u3j CRYSTAL STRUCTURE OF DH511.1 FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3l CRYSTAL STRUCTURE OF DH511.2 FAB IN COMPLEX WITH HIV-1 GP41 MPER 670-683 PEPTIDE
5u3m CRYSTAL STRUCTURE OF DH511.11P FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3n CRYSTAL STRUCTURE OF DH511.12P FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3o CRYSTAL STRUCTURE OF DH511.2_K3 FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3p CRYSTAL STRUCTURE OF DH511.4 FAB