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 ANTIBODY VRC07-G54W IN COMPLEX WITH CLADE A/E 93TH057 HIV-1 GP120 CORE
 
Authors :  Y. D. Kwon, P. D. Kwong
Date :  25 Jan 14  (Deposition) - 03 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Vrc07 Antibody, Passive Transfer, Neutralization, In Vivo Protection, Autoreactivity, Lentiviral Infection, Enhanced Potency, Hiv-1 Gp120, Vrc07-G54W, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. S. Rudicell, Y. D. Kwon, S. Y. Ko, A. Pegu, M. K. Louder, I. S. Georgiev X. Wu, J. Zhu, J. C. Boyington, X. Chen, W. Shi, Z. Y. Yang, N. A. Doria-Rose, K. Mckee, S. O'Dell, S. D. Schmidt, G. Y. Chuang, A. Druz, C. Soto, Y. Yang, B. Zhang, T. Zhou, J. P. Todd, K. E. Lloyd, J. Eudailey, K. E. Roberts, B. R. Donald, R. T. Bailer, J. Ledgerwood, J. C. Mullikin, L. Shapiro, R. A. Koup, B. S. Graham, M. C. Nason, M. Connors, B. F. Haynes, S. S. Rao, M. Roederer, P. D. Kwong, J. R. Mascola, G. J. Nabel
Enhanced Potency Of A Broadly Neutralizing Hiv-1 Antibody I Vitro Improves Protection Against Lentiviral Infection In Vivo.
J. Virol. V. 88 12669 2014
PubMed-ID: 25142607  |  Reference-DOI: 10.1128/JVI.02213-14

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
    ChainsG
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System PlasmidPVRC8400
    Expression System Strain293F CELLS
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 43-122, 201-303, 325-486
    GeneENV, POL
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid11676
    Other DetailsHIV-1 GP120 WITH LEADER SEQUENCE
    Strain93TH057
 
Molecule 2
    ChainsH
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System PlasmidPVRC8400
    Expression System Strain293F CELLS
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    GeneHEAVY CHAIN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCODON-OPTIMIZED HUMAN ANTIBODY HEAVY CHAIN OF VRC01
 
Molecule 3
    ChainsL
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System PlasmidPVRC8400
    Expression System Strain293F CELLS
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    GeneLIGHT CHAIN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCODON-OPTIMIZED HUMAN ANTIBODY LIGHT CHAIN OF VRC01

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit GHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN G:234 , HIS G:352 , HOH G:685 , GLN H:192BINDING SITE FOR RESIDUE NAG G 501
02AC2SOFTWAREASP G:230 , LYS G:231 , ASN G:232 , ASN G:241BINDING SITE FOR RESIDUE NAG G 502
03AC3SOFTWAREASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , NAG G:510 , HOH G:601 , HOH G:638 , HOH G:649 , HOH G:683BINDING SITE FOR RESIDUE NAG G 503
04AC4SOFTWAREGLU G:275 , ASN G:276 , TYR L:28 , GLY L:29 , SER L:30 , TYR L:91 , HOH L:354BINDING SITE FOR RESIDUE NAG G 504
05AC5SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLN G:344 , LYS G:348 , HOH G:612BINDING SITE FOR RESIDUE NAG G 505
06AC6SOFTWAREASN G:295 , TYR G:330 , GLU G:332 , HOH G:605BINDING SITE FOR RESIDUE NAG G 506
07AC7SOFTWAREASN G:334 , LYS G:337 , THR G:413BINDING SITE FOR RESIDUE NAG G 507
08AC8SOFTWAREGLN G:117 , GLN G:203 , ASN G:386 , THR G:388BINDING SITE FOR RESIDUE NAG G 508
09AC9SOFTWAREGLN G:389 , ASN G:392 , CYS G:410BINDING SITE FOR RESIDUE NAG G 509
10BC1SOFTWARESER G:291 , ASN G:448 , NAG G:503BINDING SITE FOR RESIDUE NAG G 510

(-) SS Bonds  (14, 14)

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
8G:395 -G:410
9H:22 -H:92
10H:32 -H:98
11H:140 -H:196
12H:216 -L:216
13L:23 -L:88
14L:136 -L:196

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Ser L:7 -Pro L:8
4Tyr L:142 -Pro L:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OLZ)

(-) 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:342
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhheee.......eee....eeee.hhhhhhhhhhhhhhhhhhh.....eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee..hhhhhhhhhh.....eeeeeeee..eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4olz G   44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 329       339       349     ||360       370       380       390      |410       420       430       440       450       460       470       480       490  
                                                                                                          124|                                                                                                    301|                           355|                                     397|                                                                                    
                                                                                                           198                                                                                                     325                            357                                      408                                                                                    

Chain H from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeee....eeeeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4olz H    1 QVRLSQSGGQMKKPGDSMRISCRASGYEFINCPINWIRLAPGKRPEWMGWMKPRWGAVSYARQLQGRVTMTRDMYSETAFLELRSLTSDDTAVYFCTRGKYCTARDYYNWDFEHWGQGTPVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128       138       148       158       168       178       188       198       208        
                                                                              52A                            82A||               100A|||||||                                                                                                                    
                                                                                                              82B|                100B||||||                                                                                                                    
                                                                                                               82C                 100C|||||                                                                                                                    
                                                                                                                                    100D||||                                                                                                                    
                                                                                                                                     100E|||                                                                                                                    
                                                                                                                                      100F||                                                                                                                    
                                                                                                                                       100G|                                                                                                                    
                                                                                                                                        100H                                                                                                                    

Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.....eeeeeee......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee..ee...eeeee.........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4olz L    3 VLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  216
                                    12        22       |34        44        54        64        74        84      ||98       108       118       128       138       148       158       168       178       188       198       208        
                                                      30|                                                        91|                                                                                                                        
                                                       33                                                         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 4OLZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    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 ]
 
  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:142 - Pro L:143   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4olz
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q0ED31_9HIV1 | Q0ED31
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q0ED31_9HIV1 | Q0ED31
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q0ED31_9HIV1 | Q0ED313ngb 3se8 3se9 3tgt 3u7y 4dko 4dkp 4dkq 4dkr 4dku 4dkv 4dvs 4dvt 4dvv 4dvw 4dvx 4h8w 4i54 4jb9 4jdt 4jkp 4jpv 4jpw 4lsp 4lsq 4lsr 4lsu 4olu 4olv 4olw 4olx 4oly 4om0 4om1 4p9h 4rfn 4rfo 4rz8 4xnz 4xvt 4ydj 4ydk 4ydl 4yfl

(-) Related Entries Specified in the PDB File

4olu 4olv 4olw 4olx 4oly 4om0 4om1