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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN HEPATITIS B VIRUS T = 4 CAPSID, ADYW STRAIN, IN COMPLEX WITH THE PHENYLPROPENAMIDE ASSEMBLY ACCELERATOR AT-130
 
Authors :  S. P. Katen, A. Zlotnick
Date :  23 Jul 12  (Deposition) - 24 Jul 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Virus, Capsid, Hepadnavirus, Icosahedral, Assembly Effector, Assembly Accelerator, Kinetic Effector, Phenylpropenamide, Virus-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. Katen, Z. Tan, S. R. Chirapu, M. G. Finn, A. Zlotnick
Assembly-Directed Antivirals Differentially Bind Quasiequivalent Pockets To Modify Hepatitis B Virus Capsid Tertiary And Quaternary Structure.
Structure V. 21 1406 2013
PubMed-ID: 23871485  |  Reference-DOI: 10.1016/J.STR.2013.06.013

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11B
    Expression System Strain: BL21 DE3 GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: C
    Organism Common: HBV-D
    Organism Scientific: HEPATITIS B VIRUS SUBTYPE ADYW
    Organism Taxid: 10419
    Strain: ADYW
    Synonym: CORE ANTIGEN, CORE PROTEIN, HBCAG, P21.5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (60x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
10YP2Ligand/IonN-[(1E)-1-BROMO-1-(2-METHOXYPHENYL)-3-OXO-3-(PIPERIDIN-1-YL)PROP-1-EN-2-YL]-4-NITROBENZAMIDE
Biological Unit 1 (1, 120)
No.NameCountTypeFull Name
10YP120Ligand/IonN-[(1E)-1-BROMO-1-(2-METHOXYPHENYL)-3-OXO-3-(PIPERIDIN-1-YL)PROP-1-EN-2-YL]-4-NITROBENZAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:25 , TRP B:102 , SER B:106 , VAL B:115 , ARG C:127 , THR C:128BINDING SITE FOR RESIDUE 0YP B 201
2AC2SOFTWAREPRO C:25 , TRP C:102 , SER C:106 , TYR C:118BINDING SITE FOR RESIDUE 0YP C 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G93)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G93)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G93)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G93)

(-) Exons   (0, 0)

(no "Exon" information available for 4G93)

(-) 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:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh........hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh......................................hhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g93 A   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain B from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhh.........hhhhhhhhhhh............hhhhhhhhhhhhhhhh.....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g93 B   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPIL 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140


Chain C from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhh.......hhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g93 C   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPI 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         


Chain D from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh.......hhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhhh.hhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g93 D   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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 4G93)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G93)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G93)

(-) Gene Ontology  (13, 13)

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
    0YP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4g93)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4g93
    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
  CAPSD_HBVD1 | P03147
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  CAPSD_HBVD1 | P03147
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_HBVD1 | P03147: 2g33 2g34 2qij 3kxs 4bmg 5d7y 5e0i 5gmz 5wtw

(-) Related Entries Specified in the PDB File

2g33 HUMAN HEPATITIS B VIRUS T=4 CAPSID, STRAIN ADYW
2g34 HUMAN HEPATITIS B VIRUS T=4 CAPSID STRAIN ADYW COMPLEXED WITH ASSEMBLY EFFECTOR HAP1