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(-) Description

Title :  HEPATITIS B VIRUS CORE PROTEIN Y132A MUTANT IN COMPLEX WITH HETEROARYLDIHYDROPYRIMIDINE (HAP_R01)
 
Authors :  Z. Zhou, Z. H. Xu
Date :  01 Dec 16  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hepatitis B Virus, Hbv, Core Protein, Capsid, Y132A Dimer, Y132A Hexamer, Heteroaryldihydropyrimidine, Hap, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhou, T. Hu, X. Zhou, S. Wildum, F. Garcia-Alcalde, Z. H. Xu, D. Wu, Y. Mao, X. Tian, Y. Zhou, F. Shen, Z. Zhang, G. Tang, I. Najera, G. Yang, H. C. Shen, J. A. T. Young, N. Qin
Heteroaryldihydropyrimidine (Hap) And Sulfamoylbenzamide (Sba) Inhibit Hepatitis B Virus Replication By Different Molecular Mechanisms
Sci Rep V. 7 42374 2017
PubMed: search  |  Reference-DOI: 10.1038/SREP42374

(-) Compounds

Molecule 1 - CORE PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-149
    Mutation: YES
    Organism Common: HBV
    Organism Scientific: HEPATITIS B VIRUS
    Organism Taxid: 10407

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
17TL6Ligand/Ion(2S)-1-[[(4R)-4-(2-CHLORANYL-4-FLUORANYL-PHENYL)-5-METHOXYCARBONYL-2-(1,3-THIAZOL-2-YL)-1,4-DIHYDROPYRIMIDIN-6-YL]METHYL]-4,4-BIS(FLUORANYL)PYRROLIDINE-2-CARBOXYLIC ACID
2CL3Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4IPA7Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:23 , PRO A:25 , ASP A:29 , LEU A:30 , THR A:33 , LEU A:37 , TRP A:102 , ILE A:105 , SER A:106 , THR A:109 , PHE A:110 , TYR A:118 , ILE A:139 , LEU A:140 , SER A:141 , HOH A:316 , HOH A:317 , VAL D:124 , TRP D:125 , ARG D:127 , THR D:128 , ALA D:132 , ARG D:133 , PRO D:134binding site for residue 7TL A 201
02AC2SOFTWARELYS A:96 , LEU A:100 , GLN B:57 , CYS B:61 , ASP B:64binding site for residue IPA A 202
03AC3SOFTWAREGLN A:57 , LEU A:60 , CYS A:61 , ASP A:64 , LYS B:96 , LEU B:100binding site for residue IPA A 203
04AC4SOFTWAREALA A:131 , ARG A:133 , PRO F:135 , ASN F:136 , ALA F:137binding site for residue IPA A 204
05AC5SOFTWAREPHE B:23 , PRO B:25 , ASP B:29 , LEU B:30 , THR B:33 , LEU B:37 , TRP B:102 , ILE B:105 , SER B:106 , PHE B:110 , TYR B:118 , ILE B:139 , LEU B:140 , SER B:141 , HOH B:319 , HOH B:343 , VAL C:124 , TRP C:125 , ARG C:127 , THR C:128 , ALA C:132 , ARG C:133 , PRO C:134binding site for residue 7TL B 201
06AC6SOFTWAREASP A:2 , ARG B:39 , GLU B:43binding site for residue CL B 203
07AC7SOFTWAREPRO B:135 , ASN B:136 , ALA B:137 , PRO C:130 , ALA C:131 , ARG C:133 , PRO C:135binding site for residue GOL B 204
08AC8SOFTWAREALA B:35 , ALA B:36 , LEU B:37 , ARG B:39 , ASP B:40 , HOH B:354binding site for residue GOL B 205
09AC9SOFTWAREPHE C:23 , PRO C:25 , ASP C:29 , LEU C:30 , THR C:33 , LEU C:37 , TRP C:102 , ILE C:105 , SER C:106 , PHE C:110 , TYR C:118 , ILE C:139 , LEU C:140 , SER C:141 , HOH C:322 , VAL F:124 , TRP F:125 , ARG F:127 , THR F:128 , ALA F:132 , ARG F:133 , PRO F:134binding site for residue 7TL C 201
10AD1SOFTWAREGLN C:57 , ASP C:64 , LYS D:96 , PHE D:97 , LEU D:100binding site for residue IPA C 202
11AD2SOFTWAREASP C:2 , ASP C:4 , LYS C:7 , HOH C:334binding site for residue GOL C 203
12AD3SOFTWAREPHE D:23 , PRO D:25 , ASP D:29 , LEU D:30 , THR D:33 , LEU D:37 , TRP D:102 , ILE D:105 , SER D:106 , THR D:109 , PHE D:110 , TYR D:118 , ILE D:139 , LEU D:140 , SER D:141 , HOH D:339 , VAL E:124 , TRP E:125 , ARG E:127 , THR E:128 , ALA E:132 , ARG E:133 , PRO E:134binding site for residue 7TL D 201
13AD4SOFTWARELYS C:96 , LEU C:100 , GLN D:57 , LEU D:60 , CYS D:61 , ASP D:64binding site for residue IPA D 202
14AD5SOFTWAREHOH D:345 , HOH D:390binding site for residue CL D 203
15AD6SOFTWAREVAL B:124 , TRP B:125 , ARG B:127 , THR B:128 , ALA B:132 , ARG B:133 , PRO B:134 , PHE E:23 , PRO E:25 , ASP E:29 , LEU E:30 , THR E:33 , LEU E:37 , TRP E:102 , ILE E:105 , SER E:106 , THR E:109 , PHE E:110 , TYR E:118 , ILE E:139 , LEU E:140 , SER E:141 , HOH E:318 , HOH E:329binding site for residue 7TL E 201
16AD7SOFTWARELEU E:37 , TYR E:38 , ARG E:39 , ASP E:40binding site for residue IPA E 202
17AD8SOFTWAREGLN E:57 , LEU E:60 , ASP E:64 , LYS F:96 , LEU F:100binding site for residue IPA E 203
18AD9SOFTWAREPRO D:135 , ASN D:136 , ALA D:137 , ALA E:131 , ARG E:133binding site for residue GOL E 204
19AE1SOFTWAREVAL A:124 , TRP A:125 , ARG A:127 , THR A:128 , ALA A:132 , ARG A:133 , PRO A:134 , PHE F:23 , PRO F:25 , ASP F:29 , LEU F:30 , THR F:33 , LEU F:37 , TRP F:102 , ILE F:105 , SER F:106 , THR F:109 , PHE F:110 , TYR F:118 , ILE F:139 , LEU F:140 , SER F:141 , HOH F:307 , HOH F:326binding site for residue 7TL F 201
20AE2SOFTWAREPRO C:135 , ASN C:136 , ALA C:137 , ALA F:131 , ARG F:133 , HOH F:318binding site for residue GOL F 202
21AE3SOFTWARETHR A:12 , ALA F:35 , ALA F:36 , ARG F:39binding site for residue GOL F 203

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:61 -B:61
2C:61 -D:61
3E:61 -F:61

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5WRE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5WRE)

(-) 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 A from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wre A   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain B from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wre B   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILST 142
                                    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.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wre C   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain D from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wre D   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPENLYFQ 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   ||  155
                                                                                                                                                                         144|     
                                                                                                                                                                          150     


Chain E from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wre E   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILST 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  


Chain F from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wre F   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLVENLYFQ 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  ||   155
                                                                                                                                                                        143|      
                                                                                                                                                                         149
   Legend:   → Mismatch (orange background)
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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 5WRE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

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        L7R9I1_HBV | L7R9I1: 5gmz 5wtw
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        L7R9I1_HBV | L7R9I1: 5t2p

(-) Related Entries Specified in the PDB File

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