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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HBV CAPSID Y132A MUTANT (VCID 8772) IN COMPLEX WITH NVR10-001E2 AT 1.95A RESOLUTION
 
Authors :  C. M. Lukacs, J. Abendroth, K. Klumpp
Date :  28 Sep 15  (Deposition) - 09 Dec 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  Nvr10-001E2, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Klumpp, A. M. Lam, C. Lukacs, R. Vogel, S. Ren, C. Espiritu, R. Baydo, K. Atkins, J. Abendroth, G. Liao, A. Efimov, G. Hartman, O. A. Flores
High-Resolution Crystal Structure Of A Hepatitis B Virus Replication Inhibitor Bound To The Viral Core Protein.
Proc. Natl. Acad. Sci. Usa V. 112 15196 2015
PubMed-ID: 26598693  |  Reference-DOI: 10.1073/PNAS.1513803112

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 469008
    Fragment: HBV CAPSID Y132A
    Mutation: YES
    Organism Common: HBV-D
    Organism Scientific: HEPATITIS B VIRUS GENOTYPE D SUBTYPE ADW
    Organism Taxid: 10419
    Strain: ISOLATE UNITED KINGDOM/ADYW/1979
    Synonym: CORE ANTIGEN,CORE PROTEIN,HBCAG,P21.5

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABCDEF
Biological Unit 2 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
15J66Ligand/IonMETHYL 4-(2-BROMO-4-FLUOROPHENYL)-6-(MORPHOLIN-4-YLMETHYL)-2-(1,3-THIAZOL-2-YL)PYRIMIDINE-5-CARBOXYLATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
15J66Ligand/IonMETHYL 4-(2-BROMO-4-FLUOROPHENYL)-6-(MORPHOLIN-4-YLMETHYL)-2-(1,3-THIAZOL-2-YL)PYRIMIDINE-5-CARBOXYLATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15J62Ligand/IonMETHYL 4-(2-BROMO-4-FLUOROPHENYL)-6-(MORPHOLIN-4-YLMETHYL)-2-(1,3-THIAZOL-2-YL)PYRIMIDINE-5-CARBOXYLATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:23 , PRO A:25 , ASP A:29 , LEU A:30 , THR A:33 , LEU A:37 , TRP A:102 , SER A:106 , THR A:109 , PHE A:110 , TYR A:118 , LEU A:140 , HOH A:622 , HOH A:655 , VAL D:124 , ARG D:127 , THR D:128 , ALA D:132 , PRO D:134binding site for residue 5J6 A 500
2AC2SOFTWAREPHE 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 , LEU B:140 , HOH B:641 , VAL C:124 , ARG C:127 , THR C:128 , ALA C:132 , PRO C:134binding site for residue 5J6 B 500
3AC3SOFTWAREPHE 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 , THR C:109 , PHE C:110 , TYR C:118 , LEU C:140 , HOH C:625 , HOH C:649 , VAL F:124 , ARG F:127 , THR F:128 , ALA F:132 , PRO F:134binding site for residue 5J6 C 500
4AC4SOFTWAREPHE D:23 , PRO D:25 , ASP D:29 , THR D:33 , LEU D:37 , TRP D:102 , ILE D:105 , SER D:106 , THR D:109 , PHE D:110 , TYR D:118 , LEU D:140 , HOH D:628 , HOH D:646 , VAL E:124 , TRP E:125 , ARG E:127 , THR E:128 , ALA E:132 , PRO E:134binding site for residue 5J6 D 500
5AC5SOFTWAREVAL B:124 , ARG B:127 , THR B:128 , ALA B:132 , 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 , LEU E:140 , HOH E:614 , HOH E:637binding site for residue 5J6 E 500
6AC6SOFTWAREVAL A:124 , ARG A:127 , THR A:128 , ALA A:132 , 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 , LEU F:140 , HOH F:611binding site for residue 5J6 F 500

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val C:72 -Gly C:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E0I)

(-) Exons   (0, 0)

(no "Exon" information available for 5E0I)

(-) 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:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e0i A   0 SMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVENLYF 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       152    
                                                                                                                                                                              148|    
                                                                                                                                                                               152    


Chain B from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e0i B   0 SMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVENLYF 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       152    
                                                                                                                                                                              148|    
                                                                                                                                                                               152    


Chain C from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e0i C   0 SMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVGTDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVENLYF 156
                                     9        19        29        39        49        59        69    ||  87        97       107       117       127       137       147||    
                                                                                                     74|                                                              148|    
                                                                                                      83                                                               152    


Chain D from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e0i D   1 MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVSRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVENLYF 156
                                    10        20        30        40        50        60        70 ||     88        98       108       118       128       138       148|    
                                                                                                  72|                                                                148|    
                                                                                                   81                                                                 152    


Chain E from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5e0i E   0 SMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWRDLVVSYVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVENLYF 156
                                     9        19        29        39        49        59        69 ||     89        99       109       119       129       139       152    
                                                                                                  71|                                                               148|    
                                                                                                   82                                                                152    


Chain F from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e0i F   0 SMDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHCSPHHTALRQAILCWGDLMTLATWVNTNVGLKFRQLLWFHISCLTFGRETVLEYLVSFGVWIRTPPAARPPNAPILSTLPETTVENLYF 156
                                     9        19        29        39        49        59        69 ||     96       106       116       126       136       146 ||    
                                                                                                  71|                                                        148|    
                                                                                                   89                                                         152
   Legend:   → Mismatch (orange background)
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    → 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 5E0I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E0I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E0I)

(-) Gene Ontology  (13, 13)

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  CAPSD_HBVD1 | P03147
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        CAPSD_HBVD1 | P03147: 2g33 2g34 2qij 3kxs 4bmg 4g93 5d7y 5gmz 5wtw

(-) Related Entries Specified in the PDB File

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