data_2MKB # _entry.id 2MKB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2MKB pdb_00002mkb 10.2210/pdb2mkb/pdb RCSB RCSB103716 ? ? BMRB 19765 ? ? WWPDB D_1000103716 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 2lzp PDB 'structural study of NS2(2-32) GBVB' unspecified 2lzq PDB 'structural study of NS2(32-57) GBVB' unspecified 19765 BMRB . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2MKB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-02-04 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Montserret, R.' 1 'Martin, A.' 2 'Penin, F.' 3 # _citation.id primary _citation.title 'NS2 Proteins of GB Virus B and Hepatitis C Virus Share Common Protease Activities and Membrane Topologies.' _citation.journal_abbrev J.Virol. _citation.journal_volume 88 _citation.page_first 7426 _citation.page_last 7444 _citation.year 2014 _citation.journal_id_ASTM JOVIAM _citation.country US _citation.journal_id_ISSN 0022-538X _citation.journal_id_CSD 0825 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24741107 _citation.pdbx_database_id_DOI 10.1128/JVI.00656-14 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Boukadida, C.' 1 ? primary 'Marnata, C.' 2 ? primary 'Montserret, R.' 3 ? primary 'Cohen, L.' 4 ? primary 'Blumen, B.' 5 ? primary 'Gouttenoire, J.' 6 ? primary 'Moradpour, D.' 7 ? primary 'Penin, F.' 8 ? primary 'Martin, A.' 9 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Protease NS2-3' _entity.formula_weight 3116.610 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'UNP residues 845-869' _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code HAWYSHYVLKFFLLVFGENGVFFYK _entity_poly.pdbx_seq_one_letter_code_can HAWYSHYVLKFFLLVFGENGVFFYK _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 HIS n 1 2 ALA n 1 3 TRP n 1 4 TYR n 1 5 SER n 1 6 HIS n 1 7 TYR n 1 8 VAL n 1 9 LEU n 1 10 LYS n 1 11 PHE n 1 12 PHE n 1 13 LEU n 1 14 LEU n 1 15 VAL n 1 16 PHE n 1 17 GLY n 1 18 GLU n 1 19 ASN n 1 20 GLY n 1 21 VAL n 1 22 PHE n 1 23 PHE n 1 24 TYR n 1 25 LYS n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Hepatitis GB virus B' _pdbx_entity_src_syn.organism_common_name GBV-B _pdbx_entity_src_syn.ncbi_taxonomy_id 39113 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code POLG_GBVB _struct_ref.pdbx_db_accession Q69422 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code HAWYSHYVLKFFLLVFGENGVFFYK _struct_ref.pdbx_align_begin 845 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2MKB _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 25 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q69422 _struct_ref_seq.db_align_beg 845 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 869 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 25 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H TOCSY' 1 2 1 '2D 1H-1H NOESY' 1 3 1 '2D 1H-13C HSQC' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH 6.0 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '2 mM protein, 50% [U-99% 2H] TFE/50% H2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '50% [U-99% 2H] TFE/50% H2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 500 Bruker AVANCE 1 'Bruker Avance' 1000 Bruker AVANCE 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2MKB _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 28 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2MKB _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2MKB _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' collection TopSpin ? 1 'Bruker Biospin' processing TopSpin ? 2 Goddard 'chemical shift assignment' Sparky ? 3 Goddard 'data analysis' Sparky ? 4 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' 'X-PLOR NIH' 2.34 5 'Koradi, Billeter and Wuthrich' 'data analysis' MOLMOL ? 6 'Koradi, Billeter and Wuthrich' 'structure solution' MOLMOL ? 7 ? refinement 'X-PLOR NIH' ? 8 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.entry_id 2MKB _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2MKB _struct.title 'Structure of NS2(113-137) GBVB protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2MKB _struct_keywords.pdbx_keywords 'VIRAL PROTEIN' _struct_keywords.text 'NS2, GBVB, virus, protease, VIRAL PROTEIN' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id TYR _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 4 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id PHE _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 22 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id TYR _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 4 _struct_conf.end_auth_comp_id PHE _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 22 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 19 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2MKB _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 HIS 1 1 1 HIS HIS A . n A 1 2 ALA 2 2 2 ALA ALA A . n A 1 3 TRP 3 3 3 TRP TRP A . n A 1 4 TYR 4 4 4 TYR TYR A . n A 1 5 SER 5 5 5 SER SER A . n A 1 6 HIS 6 6 6 HIS HIS A . n A 1 7 TYR 7 7 7 TYR TYR A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 LEU 9 9 9 LEU LEU A . n A 1 10 LYS 10 10 10 LYS LYS A . n A 1 11 PHE 11 11 11 PHE PHE A . n A 1 12 PHE 12 12 12 PHE PHE A . n A 1 13 LEU 13 13 13 LEU LEU A . n A 1 14 LEU 14 14 14 LEU LEU A . n A 1 15 VAL 15 15 15 VAL VAL A . n A 1 16 PHE 16 16 16 PHE PHE A . n A 1 17 GLY 17 17 17 GLY GLY A . n A 1 18 GLU 18 18 18 GLU GLU A . n A 1 19 ASN 19 19 19 ASN ASN A . n A 1 20 GLY 20 20 20 GLY GLY A . n A 1 21 VAL 21 21 21 VAL VAL A . n A 1 22 PHE 22 22 22 PHE PHE A . n A 1 23 PHE 23 23 23 PHE PHE A . n A 1 24 TYR 24 24 24 TYR TYR A . n A 1 25 LYS 25 25 25 LYS LYS A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-05-07 2 'Structure model' 1 1 2014-06-18 3 'Structure model' 1 2 2023-06-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' database_2 2 3 'Structure model' pdbx_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' pdbx_nmr_spectrometer # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 3 'Structure model' '_pdbx_nmr_software.name' 5 3 'Structure model' '_pdbx_nmr_spectrometer.model' # _pdbx_nmr_exptl_sample.component entity-1 _pdbx_nmr_exptl_sample.concentration 2 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 1 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 PHE A 23 ? ? -159.21 45.09 2 2 TRP A 3 ? ? 66.14 156.42 3 2 TYR A 4 ? ? 38.20 32.50 4 3 ALA A 2 ? ? -143.28 35.94 5 4 PHE A 23 ? ? -107.38 -81.22 6 5 PHE A 23 ? ? -150.13 30.98 7 5 TYR A 24 ? ? 38.22 30.23 8 6 TYR A 4 ? ? -150.89 21.50 9 7 TYR A 4 ? ? -146.52 20.48 10 7 PHE A 23 ? ? -155.65 48.89 11 7 TYR A 24 ? ? -148.51 40.70 12 8 TRP A 3 ? ? -154.24 27.58 13 8 VAL A 15 ? ? -95.61 -60.60 14 8 TYR A 24 ? ? -104.05 46.71 15 9 TYR A 24 ? ? -153.15 57.61 16 10 TYR A 24 ? ? -152.45 67.22 17 11 ALA A 2 ? ? 53.01 -153.73 18 11 TYR A 24 ? ? -149.95 45.25 19 12 TYR A 4 ? ? -155.12 39.93 20 12 TYR A 24 ? ? -159.91 58.00 21 13 ALA A 2 ? ? -87.53 -155.30 22 13 TRP A 3 ? ? 68.51 -68.39 23 14 PHE A 23 ? ? -88.23 38.53 24 14 TYR A 24 ? ? -143.27 43.77 25 15 PHE A 23 ? ? -162.37 33.45 26 17 ALA A 2 ? ? 61.53 99.75 27 17 TRP A 3 ? ? -98.93 -60.44 28 17 PHE A 22 ? ? 67.56 -54.91 29 17 PHE A 23 ? ? -137.85 -63.63 30 18 TYR A 24 ? ? -145.86 30.65 31 19 ALA A 2 ? ? 67.11 150.90 32 19 PHE A 23 ? ? -98.48 35.42 33 19 TYR A 24 ? ? -159.10 36.62 34 20 TRP A 3 ? ? -116.00 59.43 35 20 VAL A 15 ? ? -104.79 -61.45 36 20 PHE A 23 ? ? -116.90 -75.46 37 21 ALA A 2 ? ? 67.38 120.30 38 21 TYR A 24 ? ? -157.80 34.48 39 22 PHE A 23 ? ? -110.11 -75.14 40 23 PHE A 23 ? ? -160.39 74.38 41 23 TYR A 24 ? ? -152.74 72.42 42 24 TYR A 4 ? ? -147.93 22.29 43 24 VAL A 15 ? ? -97.84 -62.92 44 24 PHE A 23 ? ? -152.34 70.95 45 24 TYR A 24 ? ? -167.69 46.10 46 25 TRP A 3 ? ? -80.87 -146.28 47 25 TYR A 24 ? ? -108.36 45.64 48 26 TRP A 3 ? ? 64.32 151.08 49 26 TYR A 4 ? ? 54.87 18.75 50 26 TYR A 24 ? ? -145.67 41.58 51 27 TRP A 3 ? ? 65.79 151.95 52 27 TYR A 4 ? ? 33.65 41.72 53 27 TYR A 24 ? ? -152.43 50.14 54 28 ALA A 2 ? ? -103.27 54.10 55 28 VAL A 15 ? ? -106.25 -64.41 56 28 PHE A 23 ? ? -146.45 35.70 57 28 TYR A 24 ? ? -159.55 -60.50 #