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(-) Description

Title :  HEPATITIS B VIRUS CORE PROTEIN Y132A MUTANT IN COMPLEX WITH 4-METHYL HETEROARYLDIHYDROPYRIMIDINE
 
Authors :  Z. H. Xu, Z. Zhou
Date :  18 Jul 16  (Deposition) - 10 Aug 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hbv, Capid Assembly, Hap, Core Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Qiu, X. Lin, M. Zhou, Y. Liu, W. Zhu, W. Chen, W. Zhang, L. Guo, H. Liu, G. Wu, M. Huang, M. Jiang, Z. Xu, Z. Zhou, N. Qin, S. Ren, H. Qiu, S. Zhong, Y. Zhang, Y. Zhang, X. Wu, L. Shi, F. Shen, Y. Mao, X. Zhou, W. Yang, J. Z. Wu, G. Yang, A. V. Mayweg, H. C. Shen, G. Tang
Design And Synthesis Of Orally Bioavailable 4-Methyl Heteroaryldihydropyrimidine Based Hepatitis B Virus (Hbv) Capsid Inhibitors
J. Med. Chem. V. 59 7651 2016
PubMed-ID: 27458651  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00879

(-) 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
    Gene: C
    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, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
16XU7Ligand/Ion(2S)-4,4-DIFLUORO-1-[[(4S)-4-(4-FLUOROPHENYL)-5-METHOXYCARBONYL-4-METHYL-2-(1,3-THIAZOL-2-YL)-1H-PYRIMIDIN-6-YL]METHYL]PYRROLIDINE-2-CARBOXYLIC ACID
2CL1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4IPA11Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:96 , LEU A:100 , GLN B:57 , LEU B:60 , ASP B:64binding site for residue IPA A 201
02AC2SOFTWAREGLN A:57 , LEU A:60 , CYS A:61 , ASP A:64 , LYS B:96 , LEU B:100binding site for residue IPA A 202
03AC3SOFTWAREALA A:131 , ARG A:133 , TRP F:125 , PRO F:135 , ASN F:136 , ALA F:137binding site for residue IPA A 203
04AC4SOFTWAREARG A:39 , ASP A:40 , HOH A:316binding site for residue IPA A 204
05AC5SOFTWAREPHE A:23 , PRO A:25 , ASP A:29 , LEU A:30 , THR A:33 , LEU A:37 , TRP A:102 , SER A:106 , PHE A:110 , TYR A:118 , ILE A:139 , LEU A:140 , SER A:141 , HOH A:338 , HOH A:348 , HOH A:363 , VAL D:124 , TRP D:125 , ARG D:127 , THR D:128 , ALA D:132 , ARG D:133 , PRO D:134binding site for residue 6XU A 205
06AC6SOFTWARETRP A:71 , THR A:74 , ASN A:75 , HOH A:321 , LEU B:76 , ALA B:80 , SER B:81 , LEU B:84 , VAL B:85 , CYS C:107 , LEU C:108 , GLY C:111binding site for residue 6XU A 206
07AC7SOFTWAREPRO B:135 , ASN B:136 , ALA B:137 , HOH B:334 , ALA C:131 , ARG C:133binding site for residue GOL B 201
08AC8SOFTWAREPHE B:23 , PRO B:25 , ASP B:29 , LEU B:30 , THR B:33 , LEU B:37 , TRP B:102 , SER B:106 , THR B:109 , PHE B:110 , TYR B:118 , ILE B:139 , LEU B:140 , SER B:141 , HOH B:332 , HOH B:371 , VAL C:124 , TRP C:125 , ARG C:127 , THR C:128 , ALA C:132 , ARG C:133 , PRO C:134binding site for residue 6XU B 202
09AC9SOFTWAREGLN C:57 , LEU C:60 , ASP C:64 , LYS D:96 , LEU D:100binding site for residue IPA C 201
10AD1SOFTWAREPHE C:23 , PRO C:25 , ASP C:29 , LEU C:30 , THR C:33 , LEU C:37 , TRP C:102 , SER C:106 , THR C:109 , PHE C:110 , TYR C:118 , ILE C:139 , LEU C:140 , SER C:141 , HOH C:352 , HOH C:353 , HOH C:357 , VAL F:124 , TRP F:125 , ARG F:127 , THR F:128 , ALA F:132 , ARG F:133 , PRO F:134binding site for residue 6XU C 202
11AD2SOFTWARELYS C:96 , LEU C:100 , GLN D:57 , LEU D:60 , CYS D:61 , ASP D:64binding site for residue IPA D 201
12AD3SOFTWAREASP D:29 , ARG E:127binding site for residue IPA D 202
13AD4SOFTWAREHOH D:316 , HOH D:365binding site for residue CL D 203
14AD5SOFTWAREPHE D:23 , PRO D:25 , ASP D:29 , LEU D:30 , THR D:33 , LEU D:37 , TRP D:102 , SER D:106 , PHE D:110 , TYR D:118 , ILE D:139 , LEU D:140 , SER D:141 , HOH D:313 , HOH D:367 , HOH D:383 , VAL E:124 , TRP E:125 , ARG E:127 , THR E:128 , ALA E:132 , ARG E:133 , PRO E:134binding site for residue 6XU D 204
15AD6SOFTWARELEU E:37 , TYR E:38 , ARG E:39 , ASP E:40binding site for residue IPA E 201
16AD7SOFTWAREGLN E:57 , LEU E:60 , ASP E:64 , LYS F:96 , LEU F:100binding site for residue IPA E 202
17AD8SOFTWARETRP D:125 , PRO D:135 , ASN D:136 , ALA D:137 , ALA E:131 , ARG E:133binding site for residue IPA E 203
18AD9SOFTWAREALA B:131 , ARG B:133 , TRP E:125 , PRO E:135 , ASN E:136 , ALA E:137binding site for residue IPA E 204
19AE1SOFTWAREVAL 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 , SER E:106 , THR E:109 , PHE E:110 , TYR E:118 , ILE E:139 , LEU E:140 , SER E:141 , HOH E:326 , HOH E:333 , HOH E:348binding site for residue 6XU E 205
20AE2SOFTWAREPRO C:135 , ASN C:136 , ALA C:137 , PRO F:130 , ALA F:131 , ARG F:133 , HOH F:334binding site for residue GOL F 201
21AE3SOFTWAREVAL 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 , SER F:106 , THR F:109 , PHE F:110 , TYR F:118 , ILE F:139 , LEU F:140 , SER F:141 , HOH F:319 , HOH F:343binding site for residue 6XU F 202

(-) 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 5GMZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GMZ)

(-) 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:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gmz A   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTL 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   


Chain B 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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gmz B   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTENLYFQ 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 ||     
                                                                                                                                                                       142|     
                                                                                                                                                                        150     


Chain C from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               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
                 5gmz C   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTL 143
                                    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.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gmz 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:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gmz E   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTL 143
                                    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.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gmz 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 5GMZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5d7y 5e0i 5wtw
        L7R9I1_HBV | L7R9I1: 5wtw
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        L7R9I1_HBV | L7R9I1: 5t2p 5wre

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5GMZ)