Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TIER 2 NEUTRALIZING ANTIBODY DH427 FROM A RHESUS MACAQUE IN COMPLEX WITH HIV-1 GP120 CORE
 
Authors :  D. Fera, S. C. Harrison
Date :  06 Dec 15  (Deposition) - 13 Jan 16  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  6.63
Chains :  Asym. Unit :  A,B,E,F,G,H
Biol. Unit 1:  A,B,G  (1x)
Biol. Unit 2:  E,F,H  (1x)
Keywords :  Fab Fragment, Hiv-1, Antibody, Viral Protein-Immue System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Bradley, D. Fera, J. Bhiman, L. Eslamizar, X. Lu, K. Anasti, R. Zhang L. L. Sutherland, R. M. Scearce, C. M. Bowman, C. Stolarchuk, K. E. Lloyd, R. Parks, A. Eaton, A. Foulger, X. Nie, S. S. Karim, S. Barnett, G. Kelsoe, T. B. Kepler, S. M. Alam, D. C. Montefiori, M. A. Moody, H. X. Liao, L. Morris, S. Santra, S. C. Harrison, B. F. Hayne
Structural Constraints Of Vaccine-Induced Tier-2 Autologous Hiv Neutralizing Antibodies Targeting The Receptor-Binding Site.
Cell Rep V. 14 43 2016
PubMed-ID: 26725118  |  Reference-DOI: 10.1016/J.CELREP.2015.12.017

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE C
    Chains: G, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293T
    Expression System Plasmid: PVRC-8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - DH427 ANTIBODY LIGHT CHAIN
    Chains: A, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293T
    Expression System Plasmid: PVRC-8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544
 
Molecule 3 - DH427 ANTIBODY HEAVY CHAIN
    Chains: B, H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293T
    Expression System Plasmid: PVRC-8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABEFGH
Biological Unit 1 (1x): AB  G 
Biological Unit 2 (1x):   EF H

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5F6J)

(-) Sites  (0, 0)

(no "Site" information available for 5F6J)

(-) SS Bonds  (22, 22)

Asymmetric Unit
No.Residues
1A:22 -A:90
2A:138 -A:197
3B:22 -B:96
4B:144 -B:200
5E:54 -E:74
6E:119 -E:205
7E:218 -E:247
8E:228 -E:239
9E:296 -E:331
10E:378 -E:445
11E:385 -E:418
12F:22 -F:90
13F:138 -F:197
14G:54 -G:74
15G:119 -G:205
16G:218 -G:247
17G:228 -G:239
18G:296 -G:331
19G:378 -G:445
20G:385 -G:418
21H:22 -H:96
22H:144 -H:200

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:144 -Pro A:145
2Phe B:150 -Pro B:151
3Glu B:152 -Pro B:153
4Tyr F:144 -Pro F:145
5Phe H:150 -Pro H:151
6Glu H:152 -Pro H:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F6J)

(-) Exons   (0, 0)

(no "Exon" information available for 5F6J)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee............eeeee......eeee.............eeeeee..eeeeee.........eeeeeeee...eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f6j A   2 SALTQPPSVSKSLGQSVTISCTGTSSDIGAYTGVSWYQQHSGTAPRLLIYDVSKRPSGVSDRFSGSKSGNTASLTISGLQTDDEADYYCCSYRTGATYIFGTGTRVTVLGQPKGAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee............eeeee........eeeee....eeeeeeeeee.....eeee.........ee...ee.....eeeeeeeee..hhhhh..eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f6j B   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFSNSGMIWVRQAPGKGLEWVSYISLSGANTYYADSVKGRFTISRDNSQNTLSLQMNSLRVEDTAMYYCAKEGWSYFDFWGQGVLVTVSGASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|      147       157       167       177       187       197       207       217
                                                                                                                                                           130|                                                                               
                                                                                                                                                            138                                                                               


Chain E from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee.......hhhhhhhhhhh........eeee....ee.....hhhhhhhhhhhhhhhhhhh...eee....eee............eeee....eeeeee.........ee..eeee.............eee.........eee..hhhhh...eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh.....ee......hhhhhheee......eee.......ee......eeeeeeee..eee......eee........eeeeeeeeeeeeee.......eeee....hhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f6j E  44 VWKEAKTTLFCASDAKAYEREVHNVWATHACVPTDPNPQEMALGNVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTGGSTVTQACPKVSFDPIPIHYCAPAGYAILKCNNETFEGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAKEEIVIRSENLTDNAKTIIVHLKESVEIVCTRPGDTRQAHCNISEEKWNKTLQKVSKILQEHFPNKAIKFEPHSGGDLEITTHSFNCRGEFFYCNTTKLFNGTYNSSNTTITLPCRIKQIVNMWQGVGRAMYAPPIKGNITCKSIITGLLLTRDKDSNTETFRPGGGDMRDNWRSELYKYKVVEIK 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296   ||  330       340       350    || 361       371       381       391     ||413       423       433       443       453    || 466       476       486      
                                                                                                          124|                                                                                                   300|                           355|                                     397|                                             458|                              
                                                                                                           198                                                                                                    325                            357                                      410                                              462                              


Chain F from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee............eeeee......eeee.............eeeeee..eeeeee.........eeeeeeee...eeee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f6j F   2 SALTQPPSVSKSLGQSVTISCTGTSSDIGAYTGVSWYQQHSGTAPRLLIYDVSKRPSGVSDRFSGSKSGNTASLTISGLQTDDEADYYCCSYRTGATYIFGTGTRVTVLGQPKGAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  


Chain G from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee.......hhhhhhhhhhh........eeee....ee.....hhhhhhhhhhhhhhhhhhh...eee....eee............eeee....eeeeee.........ee..eeee.............eee.........eee..hhhhh...eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh.....ee......hhhhhheee......eee.......ee......eeeeeeee..eee......eee........eeeeeeeeeeeeee.......eeee....hhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f6j G  44 VWKEAKTTLFCASDAKAYEREVHNVWATHACVPTDPNPQEMALGNVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTGGSTVTQACPKVSFDPIPIHYCAPAGYAILKCNNETFEGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAKEEIVIRSENLTDNAKTIIVHLKESVEIVCTRPGDTRQAHCNISEEKWNKTLQKVSKILQEHFPNKAIKFEPHSGGDLEITTHSFNCRGEFFYCNTTKLFNGTYNSSNTTITLPCRIKQIVNMWQGVGRAMYAPPIKGNITCKSIITGLLLTRDKDSNTETFRPGGGDMRDNWRSELYKYKVVEIK 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296   ||  330       340       350    || 361       371       381       391     ||413       423       433       443       453    || 466       476       486      
                                                                                                          124|                                                                                                   300|                           355|                                     397|                                             458|                              
                                                                                                           198                                                                                                    325                            357                                      410                                              462                              


Chain H from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee............eeeee........eeeee....eeeeeeeeee..................ee...ee.....eeeeeeeee..hhhhh..eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f6j H   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFSNSGMIWVRQAPGKGLEWVSYISLSGANTYYADSVKGRFTISRDNSQNTLSLQMNSLRVEDTAMYYCAKEGWSYFDFWGQGVLVTVSGASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|      147       157       167       177       187       197       207       217
                                                                                                                                                           130|                                                                               
                                                                                                                                                            138
   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 5F6J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F6J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F6J)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5f6j)
 
  Sites
(no "Sites" information available for 5f6j)
 
  Cis Peptide Bonds
    Glu B:152 - Pro B:153   [ RasMol ]  
    Glu H:152 - Pro H:153   [ RasMol ]  
    Phe B:150 - Pro B:151   [ RasMol ]  
    Phe H:150 - Pro H:151   [ RasMol ]  
    Tyr A:144 - Pro A:145   [ RasMol ]  
    Tyr F:144 - Pro F:145   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5f6j
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  R4GRV3_9HIV1 | R4GRV3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  R4GRV3_9HIV1 | R4GRV3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        R4GRV3_9HIV1 | R4GRV3: 4jan 4lst

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5F6J)