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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPATITIS B VIRUS T=4 CAPSID IN COMPLEX WITH THE ALLOSTERIC MODULATOR HAP18
 
Authors :  B. Venkatakrishnan, S. P. Katen, A. Zlotnick
Date :  14 Aug 15  (Deposition) - 17 Feb 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.89
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Capsid, Core Protein, Hepadnavirus, Icosahedral, Assembly Effector, Assembly Accelerator, Allosteric Modulator, Hap, Virus-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Venkatakrishnan, S. P. Katen, S. Francis, S. Chirapu, M. G. Finn, A. Zlotnick
Hepatitis B Virus Capsids Have Diverse Structural Responses To Small-Molecule Ligands Bound To The Heteroaryldihydropyrimidine Pocket.
J. Virol. V. 90 3994 2016
PubMed-ID: 26842475  |  Reference-DOI: 10.1128/JVI.03058-15

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11C
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-149
    Gene: C
    Organism Common: HBV-D
    Organism Scientific: HEPATITIS B VIRUS GENOTYPE D SUBTYPE ADW (ISOLATE UNITED KINGDOM/ADYW/1979)
    Organism Taxid: 10419
    Strain: ISOLATE UNITED KINGDOM/ADYW/1979
    Synonym: CORE ANTIGEN, CORE PROTEIN, HBCAG, P21.5
    Variant: CP150

 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
158H2Ligand/IonMETHYL (4R)-4-(2-CHLORO-4-FLUOROPHENYL)-6-{[4-(3-HYDROXYPENTA-1,4-DIYN-3-YL)PIPERIDIN-1-YL]METHYL}-2-(PYRIDIN-2-YL)-1,4-DIHYDROPYRIMIDINE-5-CARBOXYLATE
Biological Unit 1 (1, 120)
No.NameCountTypeFull Name
158H120Ligand/IonMETHYL (4R)-4-(2-CHLORO-4-FLUOROPHENYL)-6-{[4-(3-HYDROXYPENTA-1,4-DIYN-3-YL)PIPERIDIN-1-YL]METHYL}-2-(PYRIDIN-2-YL)-1,4-DIHYDROPYRIMIDINE-5-CARBOXYLATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:23 , PRO B:25 , ASP B:29 , LEU B:30 , THR B:33 , TRP B:102 , ILE B:105 , THR B:109 , PHE B:110 , LEU B:140 , VAL C:124 , TRP C:125 , THR C:128 , TYR C:132 , PRO C:134binding site for residue 58H B 201
2AC2SOFTWAREPHE C:23 , LEU C:30 , THR C:33 , TYR C:118 , LEU C:140 , SER C:141binding site for residue 58H C 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D7Y)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala C:80 -Ser C:81
2Ser C:81 -Arg C:82
3Met D:66 -Thr D:67
4Ala D:69 -Thr D:70
5Val D:86 -Ser D:87
6Arg D:133 -Pro D:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5D7Y)

(-) 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 .....hhhhh...............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7y A   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNMGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain B from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7y B   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNMGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTL 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   


Chain C from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7y C   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNMGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain D from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhh........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh........................hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7y D   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASPHHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNMGLKFRQLLWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILSTL 143
                                    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)
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  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 5D7Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D7Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D7Y)

(-) Gene Ontology  (13, 13)

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    Ala D:69 - Thr D:70   [ RasMol ]  
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  5d7y
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  CAPSD_HBVD1 | P03147
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_HBVD1 | P03147: 2g33 2g34 2qij 3kxs 4bmg 4g93 5e0i 5gmz 5wtw

(-) Related Entries Specified in the PDB File

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