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(-) Description

Title :  HEPATITIS B VIRUS CORE PROTEIN Y132A MUTANT IN COMPLEX WITH SULFAMOYLBENZAMIDE (SBA_R01)
 
Authors :  Z. Zhou, Z. H. Xu
Date :  24 Aug 16  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hepatitis B Virus, Hbv, Core Protein, Capsid, Y132A Dimer, Y132A Hexamer, Sulfamoylbenzamide, Sba_r01, 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  (5, 26)

Asymmetric/Biological Unit (5, 26)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3GOL3Ligand/IonGLYCEROL
4IPA10Ligand/IonISOPROPYL ALCOHOL
5K896Ligand/Ion4-FLUORANYL-3-(4-OXIDANYLPIPERIDIN-1-YL)SULFONYL-~{N}-[3,4,5-TRIS(FLUORANYL)PHENYL]BENZAMIDE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:25 , LEU A:30 , THR A:33 , TRP A:102 , ILE A:105 , SER A:106 , PHE A:110 , TYR A:118 , LEU A:140 , HOH A:339 , TRP D:125 , ARG D:127 , THR D:128 , ALA D:132 , PRO D:134 , HOH D:339binding site for residue K89 A 201
02AC2SOFTWARELYS A:96 , LEU A:100 , GLN B:57 , LEU B:60 , CYS B:61 , ASP B:64 , HOH B:325binding site for residue IPA A 202
03AC3SOFTWARESER A:17 , LEU A:19 , LEU A:95 , GLN A:99binding site for residue IPA A 203
04AC4SOFTWAREPRO B:25 , LEU B:30 , THR B:33 , TRP B:102 , ILE B:105 , SER B:106 , TYR B:118 , ILE B:139 , LEU B:140 , HOH B:317 , HOH B:343 , TRP C:125 , ARG C:127 , THR C:128 , PRO C:134 , HOH C:319binding site for residue K89 B 201
05AC5SOFTWAREARG B:39 , ASP B:40 , HOH B:362binding site for residue DMS B 202
06AC6SOFTWAREPRO B:130 , ALA B:131 , ARG B:133 , PRO B:134 , PRO B:135 , PRO E:135 , ASN E:136 , ALA E:137binding site for residue IPA B 203
07AC7SOFTWAREASP B:29 , HOH B:315 , HOH B:329 , HOH B:348 , PRO C:20 , ARG C:127 , HOH C:318binding site for residue GOL B 204
08AC8SOFTWAREPRO C:25 , LEU C:30 , THR C:33 , TRP C:102 , ILE C:105 , SER C:106 , TYR C:118 , ILE C:139 , LEU C:140 , TRP F:125 , ARG F:127 , THR F:128 , PRO F:134 , HOH F:335binding site for residue K89 C 201
09AC9SOFTWAREPRO B:135 , ASN B:136 , ALA B:137 , PRO C:130 , ALA C:131 , ALA C:132 , ARG C:133binding site for residue DMS C 202
10AD1SOFTWAREARG C:39 , ASP C:40binding site for residue CL C 203
11AD2SOFTWAREALA C:137 , PRO F:130 , ALA F:131 , ARG F:133binding site for residue IPA C 204
12AD3SOFTWAREGLN C:57 , LEU C:60 , ASP C:64 , LYS D:96 , LEU D:100binding site for residue IPA C 205
13AD4SOFTWAREASP C:29 , HOH C:307 , PRO F:20binding site for residue IPA C 206
14AD5SOFTWAREPRO D:25 , LEU D:30 , THR D:33 , TRP D:102 , ILE D:105 , SER D:106 , TYR D:118 , ILE D:139 , LEU D:140 , TRP E:125 , ARG E:127 , THR E:128 , PRO E:134 , HOH E:335binding site for residue K89 D 201
15AD6SOFTWAREALA D:137 , ARG E:133binding site for residue CL D 202
16AD7SOFTWAREARG D:39 , ASP D:40binding site for residue CL D 203
17AD8SOFTWARELYS C:96 , LEU C:100 , GLN D:57 , LEU D:60 , ASP D:64binding site for residue IPA D 204
18AD9SOFTWAREGLU D:117binding site for residue GOL D 205
19AE1SOFTWAREASP D:29 , HOH D:306 , PRO E:20 , ARG E:127binding site for residue GOL D 206
20AE2SOFTWAREVAL B:124 , TRP B:125 , ARG B:127 , THR B:128 , PRO B:134 , HOH B:328 , PRO E:25 , LEU E:30 , THR E:33 , TRP E:102 , ILE E:105 , SER E:106 , PHE E:110 , TYR E:118 , ILE E:139 , LEU E:140 , HOH E:327binding site for residue K89 E 201
21AE3SOFTWAREASP E:40binding site for residue CL E 202
22AE4SOFTWAREGLN E:57 , CYS E:61 , ASP E:64 , LYS F:96 , LEU F:100binding site for residue IPA E 203
23AE5SOFTWAREPRO B:20 , HOH B:426 , ASP E:29 , HOH E:312binding site for residue IPA E 204
24AE6SOFTWARETRP A:125 , ARG A:127 , THR A:128 , PRO A:134 , HOH A:323 , LEU F:30 , THR F:33 , TRP F:102 , ILE F:105 , SER F:106 , PHE F:110 , TYR F:118 , LEU F:140binding site for residue K89 F 201
25AE7SOFTWAREASP F:40 , HOH F:357binding site for residue CL F 202
26AE8SOFTWAREPRO A:130 , ALA A:131 , ARG A:133 , PRO F:135 , ASN F:136 , ALA F:137binding site for residue IPA 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 5T2P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T2P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T2P)

(-) Exons   (0, 0)

(no "Exon" information available for 5T2P)

(-) 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:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2p A   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSVENLYFQ 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140||      
                                                                                                                                                                      141|      
                                                                                                                                                                       149      


Chain B from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2p B   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVVENLYFQ 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     


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.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2p 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:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2p D   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVVENLYFQ 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     


Chain E from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t2p E   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLVENLYFQ 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  ||   155
                                                                                                                                                                        143|      
                                                                                                                                                                         149      


Chain F from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t2p F   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTENLYFQ 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 ||     
                                                                                                                                                                       142|     
                                                                                                                                                                        150
   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 5T2P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T2P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T2P)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  5t2p
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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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(-) Related Entries Specified in the PDB File

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