Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY 3BNC117 IN COMPLEX WITH HIV-1 CLADE C C1086 GP120
 
Authors :  T. Zhou, S. Moquin, P. D. Kwong
Date :  23 Jul 13  (Deposition) - 21 Aug 13  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Neutralizing Antibody 3Bnc117, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Zhou, J. Zhu, X. Wu, S. Moquin, B. Zhang, P. Acharya, I. S. Georgiev, H. R. Altae-Tran, G. Y. Chuang, M. G. Joyce, Y. Do Kwon, N. S. Longo, M. K. Louder, T. Luongo, K. Mckee, C. A. Schramm, J. Skinner, Y. Yang, Z. Yang, Z. Zhang, A. Zheng, M. Bonsignori, B. F. Haynes, J. F. Scheid, M. C. Nussenzweig, M. Simek, D. R. Burton, W. C. Koff, J. C. Mullikin, M. Connors, L. Shapiro, G. J. Nabel, J. R. Mascola, P. D. Kwong
Multidonor Analysis Reveals Structural Elements, Genetic Determinants, And Maturation Pathway For Hiv-1 Neutralization By Vrc01-Class Antibodies.
Immunity V. 39 245 2013
PubMed-ID: 23911655  |  Reference-DOI: 10.1016/J.IMMUNI.2013.04.012

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP120
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: C1086
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY 3BNC117
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - LIGHT CHAIN OF ANTIBODY 3BNC117
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMIDS
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : GHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN L:37 , LYS L:45 , PRO L:59 , GLU L:81 , ASP L:82BINDING SITE FOR RESIDUE IMD L 302
02AC2SOFTWAREASN G:234 , THR G:236 , ILE G:272 , SER G:274BINDING SITE FOR MONO-SACCHARIDE NAG G 501 BOUND TO ASN G 234
03AC3SOFTWAREASN G:229 , ASN G:241BINDING SITE FOR MONO-SACCHARIDE NAG G 502 BOUND TO ASN G 241
04AC4SOFTWARELYS G:252 , ASN G:262 , ASN G:446 , SER G:447BINDING SITE FOR MONO-SACCHARIDE NAG G 503 BOUND TO ASN G 262
05AC5SOFTWAREGLU G:275 , ASN G:276 , GLY L:27 , TYR L:32 , TYR L:91BINDING SITE FOR MONO-SACCHARIDE NAG G 504 BOUND TO ASN G 276
06AC6SOFTWAREASN G:289 , GLU G:290 , LYS G:344 , HOH G:625 , ALA L:184BINDING SITE FOR MONO-SACCHARIDE NAG G 505 BOUND TO ASN G 289
07AC7SOFTWAREASN G:339 , ASN G:340 , GLN G:343 , SER L:127BINDING SITE FOR MONO-SACCHARIDE NAG G 506 BOUND TO ASN G 339
08AC8SOFTWAREASN G:386 , SER G:388 , ARG H:19BINDING SITE FOR MONO-SACCHARIDE NAG G 507 BOUND TO ASN G 386
09AC9SOFTWAREPRO G:363 , ASP G:389 , ASN G:392 , THR G:406 , ARG G:408 , THR H:12 , SER H:17BINDING SITE FOR MONO-SACCHARIDE NAG G 508 BOUND TO ASN G 392
10BC1SOFTWAREARG G:396 , ASN G:397BINDING SITE FOR MONO-SACCHARIDE NAG G 509 BOUND TO ASN G 397
11BC2SOFTWARESER G:291 , ASN G:446 , ASN G:448BINDING SITE FOR MONO-SACCHARIDE NAG G 510 BOUND TO ASN G 448
12BC3SOFTWARESER L:10 , THR L:20 , ARG L:65 , GLU L:70 , ASN L:72 , GLN L:199 , HOH L:403BINDING SITE FOR MONO-SACCHARIDE NAG L 301 BOUND TO ASN L 72

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1G:54 -G:74
2G:119 -G:205
3G:218 -G:247
4G:228 -G:239
5G:296 -G:331
6G:378 -G:445
7G:385 -G:418
8H:22 -H:92
9H:140 -H:196
10L:23 -L:88
11L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asp G:78 -Pro G:79
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Ser L:7 -Pro L:8
5Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LSV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LSV)

(-) Exons   (0, 0)

(no "Exon" information available for 4LSV)

(-) Sequences/Alignments

Asymmetric/Biological 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 G from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhh....ee..............eeee...hhhhhhhhhhhhhhhhhh....eee....eee............eeee....eeeeee.......eeee..eeee.........................eee..........eeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhh....eee......hhhhhheeeee..eeeee.......eeee..eeee.......eeeeee.ee.eee......eee..........eeeeeeeeeeee........eeee....hhhhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lsv G   44 VWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQNDTETFRPGGGDMRDNWRSELYKYKVVEIK  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296   ||  333       343       353||     364       374       384       394    || 407       417       427       437       447       457  ||   469       479       489   
                                                                                                          124|                                                                                                   300|                       354|                                        399|                                                      460|                             
                                                                                                           198                                                                                                    328                        356                                         403                                                       463                             


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eee.eeee..hhhhh.eeeeee......eeeeee......ee........eeeeee......eeeeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee.........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lsv H    1 QVQLLQSGAAVTKPGASVRVSCEASGYNIRDYFIHWWRQAPGQGLQWVGWINPKTGQPNNPRQFQGRVSLTRHASWDFDTYSFYMDLKALRSDDTAVYFCARQRSDYWDFDVWGSGTQVTVSSASTKGPSVFPLAPSSKSTSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69  ||||  75       82C        92      100B       110       120       130 ||    142       152       162       172       182       192       202       212 
                                                                              52A                 71A|||         82A||               100A|                             132|                                                                              
                                                                                                   71B||          82B|                100B                              135                                                                              
                                                                                                    71C|           82C                                                                                                                                   
                                                                                                     71D                                                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                            
               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..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhh....eeeeee.......ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4lsv L    1 DIQMTQSPSSLSASVGDTVTITCQANGYLNWYQQRRGKAPKLLIYDGSKLERGVPSRFSGRRWGQEYNLTINNLQPEDIATYFCQVYEFVVPGTRLDLKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20      ||34        44        54        64        74        84      ||98       108       118       128       138       148       158       168       178       188       198       208   
                                                     27|                                                         91|                                                                                                                   
                                                      32                                                          96
   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 4LSV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LSV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LSV)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp G:78 - Pro G:79   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4lsv
    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
  C6G099_9HIV1 | C6G099
    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
  C6G099_9HIV1 | C6G099
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        C6G099_9HIV1 | C6G099: 3tgr 3tgs 4i53 5f4l 5f4p 5f4r 5f4u

(-) Related Entries Specified in the PDB File

3ngb 3se8 3se9 4j6r 4jb9 4jpv 4jpw