data_4UYD # _entry.id 4UYD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4UYD PDBE EBI-61641 WWPDB D_1290061641 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 4UYE unspecified 'BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-DIMETHYL-2- OXO-6-(PIPERIDIN-1-YL)-2,3-DIHYDRO-1H-1,3- BENZODIAZOL-5-YL-2-METHOXYBENZAMIDE' PDB 4UYF unspecified 'THE DISCOVERY OF I-BET726 (GSK1324726A), A POTENT TETRAHYDROQUINOLINE APOA1 UP-REGULATOR AND SELECTIVE BET BROMODOMAIN INHIBITOR' PDB 4UYG unspecified 'THE DISCOVERY OF I-BET726 (GSK1324726A), A POTENT TETRAHYDROQUINOLINE APOA1 UP-REGULATOR AND SELECTIVE BET BROMODOMAIN INHIBITOR' PDB 4UYH unspecified ;N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-((2R,4S )-2-METHYL-4-(PHENYLAMINO)-6-(4-(PIPERIDIN-1-YLMETHYL )PHENYL)-3,4-DIHYDROQUINOLIN-1(2H)-YL)ETHANONE ; # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4UYD _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2014-08-30 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Chung, C.' 1 'Bamborough, P.' 2 'Demont, E.' 3 # _citation.id primary _citation.title '1,3-Dimethyl Benzimidazolones are Potent, Selective Inhibitors of the Brpf1 Bromodomain.' _citation.journal_abbrev 'Acs Med.Chem.Lett.' _citation.journal_volume 5 _citation.page_first 1190 _citation.page_last ? _citation.year 2014 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1948-5875 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25408830 _citation.pdbx_database_id_DOI 10.1021/ML5002932 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Demont, E.H.' 1 primary 'Bamborough, P.' 2 primary 'Chung, C.W.' 3 primary 'Craggs, P.D.' 4 primary 'Fallon, D.' 5 primary 'Gordon, L.J.' 6 primary 'Grandi, P.' 7 primary 'Hobbs, C.I.' 8 primary 'Hussain, J.' 9 primary 'Jones, E.J.' 10 primary 'Le Gall, A.' 11 primary 'Michon, A.M.' 12 primary 'Mitchell, D.J.' 13 primary 'Prinjha, R.K.' 14 primary 'Roberts, A.D.' 15 primary 'Sheppard, R.J.' 16 primary 'Watson, R.J.' 17 # _cell.entry_id 4UYD _cell.length_a 37.420 _cell.length_b 44.200 _cell.length_c 78.260 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4UYD _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'BROMODOMAIN-CONTAINING PROTEIN 4' 17961.586 1 ? ? 'N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-183' ? 2 non-polymer syn 'DIMETHYL SULFOXIDE' 78.133 1 ? ? ? ? 3 non-polymer syn 1,2-ETHANEDIOL 62.068 1 ? ? ? ? 4 non-polymer syn 1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide 205.213 1 ? ? ? ? 5 water nat water 18.015 275 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'PROTEIN HUNK1' # _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 ;GSSHHHHHHSSGMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTI KKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRGRGR ; _entity_poly.pdbx_seq_one_letter_code_can ;GSSHHHHHHSSGMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTI KKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRGRGR ; _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 GLY n 1 2 SER n 1 3 SER n 1 4 HIS n 1 5 HIS n 1 6 HIS n 1 7 HIS n 1 8 HIS n 1 9 HIS n 1 10 SER n 1 11 SER n 1 12 GLY n 1 13 MET n 1 14 ASN n 1 15 PRO n 1 16 PRO n 1 17 PRO n 1 18 PRO n 1 19 GLU n 1 20 THR n 1 21 SER n 1 22 ASN n 1 23 PRO n 1 24 ASN n 1 25 LYS n 1 26 PRO n 1 27 LYS n 1 28 ARG n 1 29 GLN n 1 30 THR n 1 31 ASN n 1 32 GLN n 1 33 LEU n 1 34 GLN n 1 35 TYR n 1 36 LEU n 1 37 LEU n 1 38 ARG n 1 39 VAL n 1 40 VAL n 1 41 LEU n 1 42 LYS n 1 43 THR n 1 44 LEU n 1 45 TRP n 1 46 LYS n 1 47 HIS n 1 48 GLN n 1 49 PHE n 1 50 ALA n 1 51 TRP n 1 52 PRO n 1 53 PHE n 1 54 GLN n 1 55 GLN n 1 56 PRO n 1 57 VAL n 1 58 ASP n 1 59 ALA n 1 60 VAL n 1 61 LYS n 1 62 LEU n 1 63 ASN n 1 64 LEU n 1 65 PRO n 1 66 ASP n 1 67 TYR n 1 68 TYR n 1 69 LYS n 1 70 ILE n 1 71 ILE n 1 72 LYS n 1 73 THR n 1 74 PRO n 1 75 MET n 1 76 ASP n 1 77 MET n 1 78 GLY n 1 79 THR n 1 80 ILE n 1 81 LYS n 1 82 LYS n 1 83 ARG n 1 84 LEU n 1 85 GLU n 1 86 ASN n 1 87 ASN n 1 88 TYR n 1 89 TYR n 1 90 TRP n 1 91 ASN n 1 92 ALA n 1 93 GLN n 1 94 GLU n 1 95 CYS n 1 96 ILE n 1 97 GLN n 1 98 ASP n 1 99 PHE n 1 100 ASN n 1 101 THR n 1 102 MET n 1 103 PHE n 1 104 THR n 1 105 ASN n 1 106 CYS n 1 107 TYR n 1 108 ILE n 1 109 TYR n 1 110 ASN n 1 111 LYS n 1 112 PRO n 1 113 GLY n 1 114 ASP n 1 115 ASP n 1 116 ILE n 1 117 VAL n 1 118 LEU n 1 119 MET n 1 120 ALA n 1 121 GLU n 1 122 ALA n 1 123 LEU n 1 124 GLU n 1 125 LYS n 1 126 LEU n 1 127 PHE n 1 128 LEU n 1 129 GLN n 1 130 LYS n 1 131 ILE n 1 132 ASN n 1 133 GLU n 1 134 LEU n 1 135 PRO n 1 136 THR n 1 137 GLU n 1 138 GLU n 1 139 THR n 1 140 GLU n 1 141 ILE n 1 142 MET n 1 143 ILE n 1 144 VAL n 1 145 GLN n 1 146 ALA n 1 147 LYS n 1 148 GLY n 1 149 ARG n 1 150 GLY n 1 151 ARG n 1 152 GLY n 1 153 ARG n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name HUMAN _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'HOMO SAPIENS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code BRD4_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession O60885 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4UYD _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 14 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 153 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O60885 _struct_ref_seq.db_align_beg 44 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 183 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 44 _struct_ref_seq.pdbx_auth_seq_align_end 183 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4UYD GLY A 1 ? UNP O60885 ? ? 'expression tag' 31 1 1 4UYD SER A 2 ? UNP O60885 ? ? 'expression tag' 32 2 1 4UYD SER A 3 ? UNP O60885 ? ? 'expression tag' 33 3 1 4UYD HIS A 4 ? UNP O60885 ? ? 'expression tag' 34 4 1 4UYD HIS A 5 ? UNP O60885 ? ? 'expression tag' 35 5 1 4UYD HIS A 6 ? UNP O60885 ? ? 'expression tag' 36 6 1 4UYD HIS A 7 ? UNP O60885 ? ? 'expression tag' 37 7 1 4UYD HIS A 8 ? UNP O60885 ? ? 'expression tag' 38 8 1 4UYD HIS A 9 ? UNP O60885 ? ? 'expression tag' 39 9 1 4UYD SER A 10 ? UNP O60885 ? ? 'expression tag' 40 10 1 4UYD SER A 11 ? UNP O60885 ? ? 'expression tag' 41 11 1 4UYD GLY A 12 ? UNP O60885 ? ? 'expression tag' 42 12 1 4UYD MET A 13 ? UNP O60885 ? ? 'expression tag' 43 13 # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 DMS non-polymer . 'DIMETHYL SULFOXIDE' ? 'C2 H6 O S' 78.133 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 V1T non-polymer . 1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide ? 'C10 H11 N3 O2' 205.213 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 4UYD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.80 _exptl_crystal.density_percent_sol 31.73 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '20% PEG3350, 0.2M NAAC' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2014-06-26 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97917 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID23-1' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID23-1 _diffrn_source.pdbx_wavelength 0.97917 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4UYD _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 39.13 _reflns.d_resolution_high 1.37 _reflns.number_obs 186100 _reflns.number_all ? _reflns.percent_possible_obs 98.7 _reflns.pdbx_Rmerge_I_obs 0.07 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 15.70 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.1 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.37 _reflns_shell.d_res_low 1.44 _reflns_shell.percent_possible_all 92.1 _reflns_shell.Rmerge_I_obs 0.28 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.30 _reflns_shell.pdbx_redundancy 4.4 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4UYD _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 26265 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 39.13 _refine.ls_d_res_high 1.37 _refine.ls_percent_reflns_obs 98.72 _refine.ls_R_factor_obs 0.17483 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.17413 _refine.ls_R_factor_R_free 0.18788 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 1385 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.959 _refine.correlation_coeff_Fo_to_Fc_free 0.950 _refine.B_iso_mean 11.581 _refine.aniso_B[1][1] 0.62 _refine.aniso_B[2][2] -0.44 _refine.aniso_B[3][3] -0.17 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.063 _refine.pdbx_overall_ESU_R_Free 0.060 _refine.overall_SU_ML 0.035 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.632 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1053 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 23 _refine_hist.number_atoms_solvent 275 _refine_hist.number_atoms_total 1351 _refine_hist.d_res_high 1.37 _refine_hist.d_res_low 39.13 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.006 0.020 ? 1134 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 775 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.144 1.964 ? 1547 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.854 3.000 ? 1911 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.348 5.000 ? 132 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 39.855 25.926 ? 54 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 10.968 15.000 ? 203 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 8.982 15.000 ? 3 'X-RAY DIFFRACTION' ? r_chiral_restr 0.067 0.200 ? 164 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.021 ? 1225 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 208 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.370 _refine_ls_shell.d_res_low 1.406 _refine_ls_shell.number_reflns_R_work 1575 _refine_ls_shell.R_factor_R_work 0.216 _refine_ls_shell.percent_reflns_obs 87.45 _refine_ls_shell.R_factor_R_free 0.205 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 76 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 4UYD _struct.title 'N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1,3-dimethyl-2-oxo-2,3- dihydro-1H-1,3-benzodiazole-5-carboxamide' _struct.pdbx_descriptor 'BROMODOMAIN-CONTAINING PROTEIN 4' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4UYD _struct_keywords.pdbx_keywords TRANSCRIPTION _struct_keywords.text 'TRANSCRIPTION, INHIBITOR, HISTONE, EPIGENETIC READER, ANTAGONIST' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 THR A 30 ? VAL A 39 ? THR A 60 VAL A 69 1 ? 10 HELX_P HELX_P2 2 VAL A 39 ? LYS A 46 ? VAL A 69 LYS A 76 1 ? 8 HELX_P HELX_P3 3 ALA A 50 ? GLN A 54 ? ALA A 80 GLN A 84 5 ? 5 HELX_P HELX_P4 4 ASP A 66 ? ILE A 71 ? ASP A 96 ILE A 101 1 ? 6 HELX_P HELX_P5 5 ASP A 76 ? ASN A 86 ? ASP A 106 ASN A 116 1 ? 11 HELX_P HELX_P6 6 ASN A 91 ? ASN A 110 ? ASN A 121 ASN A 140 1 ? 20 HELX_P HELX_P7 7 ASP A 114 ? ASN A 132 ? ASP A 144 ASN A 162 1 ? 19 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE DMS A 1169' AC2 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE EDO A 1170' AC3 Software ? ? ? ? 10 'BINDING SITE FOR RESIDUE V1T A 1171' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 TRP A 51 ? TRP A 81 . ? 1_555 ? 2 AC1 4 LYS A 69 ? LYS A 99 . ? 4_575 ? 3 AC1 4 HOH E . ? HOH A 2235 . ? 1_555 ? 4 AC1 4 HOH E . ? HOH A 2236 . ? 1_555 ? 5 AC2 7 ILE A 70 ? ILE A 100 . ? 1_555 ? 6 AC2 7 ILE A 71 ? ILE A 101 . ? 1_555 ? 7 AC2 7 LYS A 72 ? LYS A 102 . ? 1_555 ? 8 AC2 7 THR A 73 ? THR A 103 . ? 1_555 ? 9 AC2 7 ASN A 105 ? ASN A 135 . ? 1_555 ? 10 AC2 7 HOH E . ? HOH A 2184 . ? 1_555 ? 11 AC2 7 HOH E . ? HOH A 2275 . ? 1_555 ? 12 AC3 10 TRP A 51 ? TRP A 81 . ? 1_555 ? 13 AC3 10 PRO A 52 ? PRO A 82 . ? 1_555 ? 14 AC3 10 GLN A 55 ? GLN A 85 . ? 1_555 ? 15 AC3 10 VAL A 57 ? VAL A 87 . ? 1_555 ? 16 AC3 10 LEU A 62 ? LEU A 92 . ? 1_555 ? 17 AC3 10 ASN A 110 ? ASN A 140 . ? 1_555 ? 18 AC3 10 HOH E . ? HOH A 2131 . ? 1_555 ? 19 AC3 10 HOH E . ? HOH A 2144 . ? 1_555 ? 20 AC3 10 HOH E . ? HOH A 2171 . ? 4_575 ? 21 AC3 10 HOH E . ? HOH A 2175 . ? 1_555 ? # _database_PDB_matrix.entry_id 4UYD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 4UYD _atom_sites.fract_transf_matrix[1][1] 0.026724 _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] 0.022624 _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] 0.012778 _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 N O S # 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 GLY 1 31 ? ? ? A . n A 1 2 SER 2 32 ? ? ? A . n A 1 3 SER 3 33 ? ? ? A . n A 1 4 HIS 4 34 ? ? ? A . n A 1 5 HIS 5 35 ? ? ? A . n A 1 6 HIS 6 36 ? ? ? A . n A 1 7 HIS 7 37 ? ? ? A . n A 1 8 HIS 8 38 ? ? ? A . n A 1 9 HIS 9 39 ? ? ? A . n A 1 10 SER 10 40 ? ? ? A . n A 1 11 SER 11 41 ? ? ? A . n A 1 12 GLY 12 42 ? ? ? A . n A 1 13 MET 13 43 43 MET MET A . n A 1 14 ASN 14 44 44 ASN ASN A . n A 1 15 PRO 15 45 45 PRO PRO A . n A 1 16 PRO 16 46 46 PRO PRO A . n A 1 17 PRO 17 47 47 PRO PRO A . n A 1 18 PRO 18 48 48 PRO PRO A . n A 1 19 GLU 19 49 49 GLU GLU A . n A 1 20 THR 20 50 50 THR THR A . n A 1 21 SER 21 51 51 SER SER A . n A 1 22 ASN 22 52 52 ASN ASN A . n A 1 23 PRO 23 53 53 PRO PRO A . n A 1 24 ASN 24 54 54 ASN ASN A . n A 1 25 LYS 25 55 55 LYS LYS A . n A 1 26 PRO 26 56 56 PRO PRO A . n A 1 27 LYS 27 57 57 LYS LYS A . n A 1 28 ARG 28 58 58 ARG ARG A . n A 1 29 GLN 29 59 59 GLN GLN A . n A 1 30 THR 30 60 60 THR THR A . n A 1 31 ASN 31 61 61 ASN ASN A . n A 1 32 GLN 32 62 62 GLN GLN A . n A 1 33 LEU 33 63 63 LEU LEU A . n A 1 34 GLN 34 64 64 GLN GLN A . n A 1 35 TYR 35 65 65 TYR TYR A . n A 1 36 LEU 36 66 66 LEU LEU A . n A 1 37 LEU 37 67 67 LEU LEU A . n A 1 38 ARG 38 68 68 ARG ARG A . n A 1 39 VAL 39 69 69 VAL VAL A . n A 1 40 VAL 40 70 70 VAL VAL A . n A 1 41 LEU 41 71 71 LEU LEU A . n A 1 42 LYS 42 72 72 LYS LYS A . n A 1 43 THR 43 73 73 THR THR A . n A 1 44 LEU 44 74 74 LEU LEU A . n A 1 45 TRP 45 75 75 TRP TRP A . n A 1 46 LYS 46 76 76 LYS LYS A . n A 1 47 HIS 47 77 77 HIS HIS A . n A 1 48 GLN 48 78 78 GLN GLN A . n A 1 49 PHE 49 79 79 PHE PHE A . n A 1 50 ALA 50 80 80 ALA ALA A . n A 1 51 TRP 51 81 81 TRP TRP A . n A 1 52 PRO 52 82 82 PRO PRO A . n A 1 53 PHE 53 83 83 PHE PHE A . n A 1 54 GLN 54 84 84 GLN GLN A . n A 1 55 GLN 55 85 85 GLN GLN A . n A 1 56 PRO 56 86 86 PRO PRO A . n A 1 57 VAL 57 87 87 VAL VAL A . n A 1 58 ASP 58 88 88 ASP ASP A . n A 1 59 ALA 59 89 89 ALA ALA A . n A 1 60 VAL 60 90 90 VAL VAL A . n A 1 61 LYS 61 91 91 LYS LYS A . n A 1 62 LEU 62 92 92 LEU LEU A . n A 1 63 ASN 63 93 93 ASN ASN A . n A 1 64 LEU 64 94 94 LEU LEU A . n A 1 65 PRO 65 95 95 PRO PRO A . n A 1 66 ASP 66 96 96 ASP ASP A . n A 1 67 TYR 67 97 97 TYR TYR A . n A 1 68 TYR 68 98 98 TYR TYR A . n A 1 69 LYS 69 99 99 LYS LYS A . n A 1 70 ILE 70 100 100 ILE ILE A . n A 1 71 ILE 71 101 101 ILE ILE A . n A 1 72 LYS 72 102 102 LYS LYS A . n A 1 73 THR 73 103 103 THR THR A . n A 1 74 PRO 74 104 104 PRO PRO A . n A 1 75 MET 75 105 105 MET MET A . n A 1 76 ASP 76 106 106 ASP ASP A . n A 1 77 MET 77 107 107 MET MET A . n A 1 78 GLY 78 108 108 GLY GLY A . n A 1 79 THR 79 109 109 THR THR A . n A 1 80 ILE 80 110 110 ILE ILE A . n A 1 81 LYS 81 111 111 LYS LYS A . n A 1 82 LYS 82 112 112 LYS LYS A . n A 1 83 ARG 83 113 113 ARG ARG A . n A 1 84 LEU 84 114 114 LEU LEU A . n A 1 85 GLU 85 115 115 GLU GLU A . n A 1 86 ASN 86 116 116 ASN ASN A . n A 1 87 ASN 87 117 117 ASN ASN A . n A 1 88 TYR 88 118 118 TYR TYR A . n A 1 89 TYR 89 119 119 TYR TYR A . n A 1 90 TRP 90 120 120 TRP TRP A . n A 1 91 ASN 91 121 121 ASN ASN A . n A 1 92 ALA 92 122 122 ALA ALA A . n A 1 93 GLN 93 123 123 GLN GLN A . n A 1 94 GLU 94 124 124 GLU GLU A . n A 1 95 CYS 95 125 125 CYS CYS A . n A 1 96 ILE 96 126 126 ILE ILE A . n A 1 97 GLN 97 127 127 GLN GLN A . n A 1 98 ASP 98 128 128 ASP ASP A . n A 1 99 PHE 99 129 129 PHE PHE A . n A 1 100 ASN 100 130 130 ASN ASN A . n A 1 101 THR 101 131 131 THR THR A . n A 1 102 MET 102 132 132 MET MET A . n A 1 103 PHE 103 133 133 PHE PHE A . n A 1 104 THR 104 134 134 THR THR A . n A 1 105 ASN 105 135 135 ASN ASN A . n A 1 106 CYS 106 136 136 CYS CYS A . n A 1 107 TYR 107 137 137 TYR TYR A . n A 1 108 ILE 108 138 138 ILE ILE A . n A 1 109 TYR 109 139 139 TYR TYR A . n A 1 110 ASN 110 140 140 ASN ASN A . n A 1 111 LYS 111 141 141 LYS LYS A . n A 1 112 PRO 112 142 142 PRO PRO A . n A 1 113 GLY 113 143 143 GLY GLY A . n A 1 114 ASP 114 144 144 ASP ASP A . n A 1 115 ASP 115 145 145 ASP ASP A . n A 1 116 ILE 116 146 146 ILE ILE A . n A 1 117 VAL 117 147 147 VAL VAL A . n A 1 118 LEU 118 148 148 LEU LEU A . n A 1 119 MET 119 149 149 MET MET A . n A 1 120 ALA 120 150 150 ALA ALA A . n A 1 121 GLU 121 151 151 GLU GLU A . n A 1 122 ALA 122 152 152 ALA ALA A . n A 1 123 LEU 123 153 153 LEU LEU A . n A 1 124 GLU 124 154 154 GLU GLU A . n A 1 125 LYS 125 155 155 LYS LYS A . n A 1 126 LEU 126 156 156 LEU LEU A . n A 1 127 PHE 127 157 157 PHE PHE A . n A 1 128 LEU 128 158 158 LEU LEU A . n A 1 129 GLN 129 159 159 GLN GLN A . n A 1 130 LYS 130 160 160 LYS LYS A . n A 1 131 ILE 131 161 161 ILE ILE A . n A 1 132 ASN 132 162 162 ASN ASN A . n A 1 133 GLU 133 163 163 GLU GLU A . n A 1 134 LEU 134 164 164 LEU LEU A . n A 1 135 PRO 135 165 165 PRO PRO A . n A 1 136 THR 136 166 166 THR THR A . n A 1 137 GLU 137 167 167 GLU GLU A . n A 1 138 GLU 138 168 168 GLU GLU A . n A 1 139 THR 139 169 169 THR THR A . n A 1 140 GLU 140 170 ? ? ? A . n A 1 141 ILE 141 171 ? ? ? A . n A 1 142 MET 142 172 ? ? ? A . n A 1 143 ILE 143 173 ? ? ? A . n A 1 144 VAL 144 174 ? ? ? A . n A 1 145 GLN 145 175 ? ? ? A . n A 1 146 ALA 146 176 ? ? ? A . n A 1 147 LYS 147 177 ? ? ? A . n A 1 148 GLY 148 178 ? ? ? A . n A 1 149 ARG 149 179 ? ? ? A . n A 1 150 GLY 150 180 ? ? ? A . n A 1 151 ARG 151 181 ? ? ? A . n A 1 152 GLY 152 182 ? ? ? A . n A 1 153 ARG 153 183 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 DMS 1 1169 1169 DMS DMS A . C 3 EDO 1 1170 1170 EDO EDO A . D 4 V1T 1 1171 1171 V1T V1T A . E 5 HOH 1 2001 2001 HOH HOH A . E 5 HOH 2 2002 2002 HOH HOH A . E 5 HOH 3 2003 2003 HOH HOH A . E 5 HOH 4 2004 2004 HOH HOH A . E 5 HOH 5 2005 2005 HOH HOH A . E 5 HOH 6 2006 2006 HOH HOH A . E 5 HOH 7 2007 2007 HOH HOH A . E 5 HOH 8 2008 2008 HOH HOH A . E 5 HOH 9 2009 2009 HOH HOH A . E 5 HOH 10 2010 2010 HOH HOH A . E 5 HOH 11 2011 2011 HOH HOH A . E 5 HOH 12 2012 2012 HOH HOH A . E 5 HOH 13 2013 2013 HOH HOH A . E 5 HOH 14 2014 2014 HOH HOH A . E 5 HOH 15 2015 2015 HOH HOH A . E 5 HOH 16 2016 2016 HOH HOH A . E 5 HOH 17 2017 2017 HOH HOH A . E 5 HOH 18 2018 2018 HOH HOH A . E 5 HOH 19 2019 2019 HOH HOH A . E 5 HOH 20 2020 2020 HOH HOH A . E 5 HOH 21 2021 2021 HOH HOH A . E 5 HOH 22 2022 2022 HOH HOH A . E 5 HOH 23 2023 2023 HOH HOH A . E 5 HOH 24 2024 2024 HOH HOH A . E 5 HOH 25 2025 2025 HOH HOH A . E 5 HOH 26 2026 2026 HOH HOH A . E 5 HOH 27 2027 2027 HOH HOH A . E 5 HOH 28 2028 2028 HOH HOH A . E 5 HOH 29 2029 2029 HOH HOH A . E 5 HOH 30 2030 2030 HOH HOH A . E 5 HOH 31 2031 2031 HOH HOH A . E 5 HOH 32 2032 2032 HOH HOH A . E 5 HOH 33 2033 2033 HOH HOH A . E 5 HOH 34 2034 2034 HOH HOH A . E 5 HOH 35 2035 2035 HOH HOH A . E 5 HOH 36 2036 2036 HOH HOH A . E 5 HOH 37 2037 2037 HOH HOH A . E 5 HOH 38 2038 2038 HOH HOH A . E 5 HOH 39 2039 2039 HOH HOH A . E 5 HOH 40 2040 2040 HOH HOH A . E 5 HOH 41 2041 2041 HOH HOH A . E 5 HOH 42 2042 2042 HOH HOH A . E 5 HOH 43 2043 2043 HOH HOH A . E 5 HOH 44 2044 2044 HOH HOH A . E 5 HOH 45 2045 2045 HOH HOH A . E 5 HOH 46 2046 2046 HOH HOH A . E 5 HOH 47 2047 2047 HOH HOH A . E 5 HOH 48 2048 2048 HOH HOH A . E 5 HOH 49 2049 2049 HOH HOH A . E 5 HOH 50 2050 2050 HOH HOH A . E 5 HOH 51 2051 2051 HOH HOH A . E 5 HOH 52 2052 2052 HOH HOH A . E 5 HOH 53 2053 2053 HOH HOH A . E 5 HOH 54 2054 2054 HOH HOH A . E 5 HOH 55 2055 2055 HOH HOH A . E 5 HOH 56 2056 2056 HOH HOH A . E 5 HOH 57 2057 2057 HOH HOH A . E 5 HOH 58 2058 2058 HOH HOH A . E 5 HOH 59 2059 2059 HOH HOH A . E 5 HOH 60 2060 2060 HOH HOH A . E 5 HOH 61 2061 2061 HOH HOH A . E 5 HOH 62 2062 2062 HOH HOH A . E 5 HOH 63 2063 2063 HOH HOH A . E 5 HOH 64 2064 2064 HOH HOH A . E 5 HOH 65 2065 2065 HOH HOH A . E 5 HOH 66 2066 2066 HOH HOH A . E 5 HOH 67 2067 2067 HOH HOH A . E 5 HOH 68 2068 2068 HOH HOH A . E 5 HOH 69 2069 2069 HOH HOH A . E 5 HOH 70 2070 2070 HOH HOH A . E 5 HOH 71 2071 2071 HOH HOH A . E 5 HOH 72 2072 2072 HOH HOH A . E 5 HOH 73 2073 2073 HOH HOH A . E 5 HOH 74 2074 2074 HOH HOH A . E 5 HOH 75 2075 2075 HOH HOH A . E 5 HOH 76 2076 2076 HOH HOH A . E 5 HOH 77 2077 2077 HOH HOH A . E 5 HOH 78 2078 2078 HOH HOH A . E 5 HOH 79 2079 2079 HOH HOH A . E 5 HOH 80 2080 2080 HOH HOH A . E 5 HOH 81 2081 2081 HOH HOH A . E 5 HOH 82 2082 2082 HOH HOH A . E 5 HOH 83 2083 2083 HOH HOH A . E 5 HOH 84 2084 2084 HOH HOH A . E 5 HOH 85 2085 2085 HOH HOH A . E 5 HOH 86 2086 2086 HOH HOH A . E 5 HOH 87 2087 2087 HOH HOH A . E 5 HOH 88 2088 2088 HOH HOH A . E 5 HOH 89 2089 2089 HOH HOH A . E 5 HOH 90 2090 2090 HOH HOH A . E 5 HOH 91 2091 2091 HOH HOH A . E 5 HOH 92 2092 2092 HOH HOH A . E 5 HOH 93 2093 2093 HOH HOH A . E 5 HOH 94 2094 2094 HOH HOH A . E 5 HOH 95 2095 2095 HOH HOH A . E 5 HOH 96 2096 2096 HOH HOH A . E 5 HOH 97 2097 2097 HOH HOH A . E 5 HOH 98 2098 2098 HOH HOH A . E 5 HOH 99 2099 2099 HOH HOH A . E 5 HOH 100 2100 2100 HOH HOH A . E 5 HOH 101 2101 2101 HOH HOH A . E 5 HOH 102 2102 2102 HOH HOH A . E 5 HOH 103 2103 2103 HOH HOH A . E 5 HOH 104 2104 2104 HOH HOH A . E 5 HOH 105 2105 2105 HOH HOH A . E 5 HOH 106 2106 2106 HOH HOH A . E 5 HOH 107 2107 2107 HOH HOH A . E 5 HOH 108 2108 2108 HOH HOH A . E 5 HOH 109 2109 2109 HOH HOH A . E 5 HOH 110 2110 2110 HOH HOH A . E 5 HOH 111 2111 2111 HOH HOH A . E 5 HOH 112 2112 2112 HOH HOH A . E 5 HOH 113 2113 2113 HOH HOH A . E 5 HOH 114 2114 2114 HOH HOH A . E 5 HOH 115 2115 2115 HOH HOH A . E 5 HOH 116 2116 2116 HOH HOH A . E 5 HOH 117 2117 2117 HOH HOH A . E 5 HOH 118 2118 2118 HOH HOH A . E 5 HOH 119 2119 2119 HOH HOH A . E 5 HOH 120 2120 2120 HOH HOH A . E 5 HOH 121 2121 2121 HOH HOH A . E 5 HOH 122 2122 2122 HOH HOH A . E 5 HOH 123 2123 2123 HOH HOH A . E 5 HOH 124 2124 2124 HOH HOH A . E 5 HOH 125 2125 2125 HOH HOH A . E 5 HOH 126 2126 2126 HOH HOH A . E 5 HOH 127 2127 2127 HOH HOH A . E 5 HOH 128 2128 2128 HOH HOH A . E 5 HOH 129 2129 2129 HOH HOH A . E 5 HOH 130 2130 2130 HOH HOH A . E 5 HOH 131 2131 2131 HOH HOH A . E 5 HOH 132 2132 2132 HOH HOH A . E 5 HOH 133 2133 2133 HOH HOH A . E 5 HOH 134 2134 2134 HOH HOH A . E 5 HOH 135 2135 2135 HOH HOH A . E 5 HOH 136 2136 2136 HOH HOH A . E 5 HOH 137 2137 2137 HOH HOH A . E 5 HOH 138 2138 2138 HOH HOH A . E 5 HOH 139 2139 2139 HOH HOH A . E 5 HOH 140 2140 2140 HOH HOH A . E 5 HOH 141 2141 2141 HOH HOH A . E 5 HOH 142 2142 2142 HOH HOH A . E 5 HOH 143 2143 2143 HOH HOH A . E 5 HOH 144 2144 2144 HOH HOH A . E 5 HOH 145 2145 2145 HOH HOH A . E 5 HOH 146 2146 2146 HOH HOH A . E 5 HOH 147 2147 2147 HOH HOH A . E 5 HOH 148 2148 2148 HOH HOH A . E 5 HOH 149 2149 2149 HOH HOH A . E 5 HOH 150 2150 2150 HOH HOH A . E 5 HOH 151 2151 2151 HOH HOH A . E 5 HOH 152 2152 2152 HOH HOH A . E 5 HOH 153 2153 2153 HOH HOH A . E 5 HOH 154 2154 2154 HOH HOH A . E 5 HOH 155 2155 2155 HOH HOH A . E 5 HOH 156 2156 2156 HOH HOH A . E 5 HOH 157 2157 2157 HOH HOH A . E 5 HOH 158 2158 2158 HOH HOH A . E 5 HOH 159 2159 2159 HOH HOH A . E 5 HOH 160 2160 2160 HOH HOH A . E 5 HOH 161 2161 2161 HOH HOH A . E 5 HOH 162 2162 2162 HOH HOH A . E 5 HOH 163 2163 2163 HOH HOH A . E 5 HOH 164 2164 2164 HOH HOH A . E 5 HOH 165 2165 2165 HOH HOH A . E 5 HOH 166 2166 2166 HOH HOH A . E 5 HOH 167 2167 2167 HOH HOH A . E 5 HOH 168 2168 2168 HOH HOH A . E 5 HOH 169 2169 2169 HOH HOH A . E 5 HOH 170 2170 2170 HOH HOH A . E 5 HOH 171 2171 2171 HOH HOH A . E 5 HOH 172 2172 2172 HOH HOH A . E 5 HOH 173 2173 2173 HOH HOH A . E 5 HOH 174 2174 2174 HOH HOH A . E 5 HOH 175 2175 2175 HOH HOH A . E 5 HOH 176 2176 2176 HOH HOH A . E 5 HOH 177 2177 2177 HOH HOH A . E 5 HOH 178 2178 2178 HOH HOH A . E 5 HOH 179 2179 2179 HOH HOH A . E 5 HOH 180 2180 2180 HOH HOH A . E 5 HOH 181 2181 2181 HOH HOH A . E 5 HOH 182 2182 2182 HOH HOH A . E 5 HOH 183 2183 2183 HOH HOH A . E 5 HOH 184 2184 2184 HOH HOH A . E 5 HOH 185 2185 2185 HOH HOH A . E 5 HOH 186 2186 2186 HOH HOH A . E 5 HOH 187 2187 2187 HOH HOH A . E 5 HOH 188 2188 2188 HOH HOH A . E 5 HOH 189 2189 2189 HOH HOH A . E 5 HOH 190 2190 2190 HOH HOH A . E 5 HOH 191 2191 2191 HOH HOH A . E 5 HOH 192 2192 2192 HOH HOH A . E 5 HOH 193 2193 2193 HOH HOH A . E 5 HOH 194 2194 2194 HOH HOH A . E 5 HOH 195 2195 2195 HOH HOH A . E 5 HOH 196 2196 2196 HOH HOH A . E 5 HOH 197 2197 2197 HOH HOH A . E 5 HOH 198 2198 2198 HOH HOH A . E 5 HOH 199 2199 2199 HOH HOH A . E 5 HOH 200 2200 2200 HOH HOH A . E 5 HOH 201 2201 2201 HOH HOH A . E 5 HOH 202 2202 2202 HOH HOH A . E 5 HOH 203 2203 2203 HOH HOH A . E 5 HOH 204 2204 2204 HOH HOH A . E 5 HOH 205 2205 2205 HOH HOH A . E 5 HOH 206 2206 2206 HOH HOH A . E 5 HOH 207 2207 2207 HOH HOH A . E 5 HOH 208 2208 2208 HOH HOH A . E 5 HOH 209 2209 2209 HOH HOH A . E 5 HOH 210 2210 2210 HOH HOH A . E 5 HOH 211 2211 2211 HOH HOH A . E 5 HOH 212 2212 2212 HOH HOH A . E 5 HOH 213 2213 2213 HOH HOH A . E 5 HOH 214 2214 2214 HOH HOH A . E 5 HOH 215 2215 2215 HOH HOH A . E 5 HOH 216 2216 2216 HOH HOH A . E 5 HOH 217 2217 2217 HOH HOH A . E 5 HOH 218 2218 2218 HOH HOH A . E 5 HOH 219 2219 2219 HOH HOH A . E 5 HOH 220 2220 2220 HOH HOH A . E 5 HOH 221 2221 2221 HOH HOH A . E 5 HOH 222 2222 2222 HOH HOH A . E 5 HOH 223 2223 2223 HOH HOH A . E 5 HOH 224 2224 2224 HOH HOH A . E 5 HOH 225 2225 2225 HOH HOH A . E 5 HOH 226 2226 2226 HOH HOH A . E 5 HOH 227 2227 2227 HOH HOH A . E 5 HOH 228 2228 2228 HOH HOH A . E 5 HOH 229 2229 2229 HOH HOH A . E 5 HOH 230 2230 2230 HOH HOH A . E 5 HOH 231 2231 2231 HOH HOH A . E 5 HOH 232 2232 2232 HOH HOH A . E 5 HOH 233 2233 2233 HOH HOH A . E 5 HOH 234 2234 2234 HOH HOH A . E 5 HOH 235 2235 2235 HOH HOH A . E 5 HOH 236 2236 2236 HOH HOH A . E 5 HOH 237 2237 2237 HOH HOH A . E 5 HOH 238 2238 2238 HOH HOH A . E 5 HOH 239 2239 2239 HOH HOH A . E 5 HOH 240 2240 2240 HOH HOH A . E 5 HOH 241 2241 2241 HOH HOH A . E 5 HOH 242 2242 2242 HOH HOH A . E 5 HOH 243 2243 2243 HOH HOH A . E 5 HOH 244 2244 2244 HOH HOH A . E 5 HOH 245 2245 2245 HOH HOH A . E 5 HOH 246 2246 2246 HOH HOH A . E 5 HOH 247 2247 2247 HOH HOH A . E 5 HOH 248 2248 2248 HOH HOH A . E 5 HOH 249 2249 2249 HOH HOH A . E 5 HOH 250 2250 2250 HOH HOH A . E 5 HOH 251 2251 2251 HOH HOH A . E 5 HOH 252 2252 2252 HOH HOH A . E 5 HOH 253 2253 2253 HOH HOH A . E 5 HOH 254 2254 2254 HOH HOH A . E 5 HOH 255 2255 2255 HOH HOH A . E 5 HOH 256 2256 2256 HOH HOH A . E 5 HOH 257 2257 2257 HOH HOH A . E 5 HOH 258 2258 2258 HOH HOH A . E 5 HOH 259 2259 2259 HOH HOH A . E 5 HOH 260 2260 2260 HOH HOH A . E 5 HOH 261 2261 2261 HOH HOH A . E 5 HOH 262 2262 2262 HOH HOH A . E 5 HOH 263 2263 2263 HOH HOH A . E 5 HOH 264 2264 2264 HOH HOH A . E 5 HOH 265 2265 2265 HOH HOH A . E 5 HOH 266 2266 2266 HOH HOH A . E 5 HOH 267 2267 2267 HOH HOH A . E 5 HOH 268 2268 2268 HOH HOH A . E 5 HOH 269 2269 2269 HOH HOH A . E 5 HOH 270 2270 2270 HOH HOH A . E 5 HOH 271 2271 2271 HOH HOH A . E 5 HOH 272 2272 2272 HOH HOH A . E 5 HOH 273 2273 2273 HOH HOH A . E 5 HOH 274 2274 2274 HOH HOH A . E 5 HOH 275 2275 2275 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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,B,C,D,E # _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 2014-09-17 2 'Structure model' 1 1 2014-12-03 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 25.4816 _pdbx_refine_tls.origin_y 40.6344 _pdbx_refine_tls.origin_z 8.8525 _pdbx_refine_tls.T[1][1] 0.0030 _pdbx_refine_tls.T[2][2] 0.0145 _pdbx_refine_tls.T[3][3] 0.0218 _pdbx_refine_tls.T[1][2] 0.0028 _pdbx_refine_tls.T[1][3] 0.0031 _pdbx_refine_tls.T[2][3] 0.0038 _pdbx_refine_tls.L[1][1] 0.0081 _pdbx_refine_tls.L[2][2] 0.4489 _pdbx_refine_tls.L[3][3] 0.4018 _pdbx_refine_tls.L[1][2] 0.0258 _pdbx_refine_tls.L[1][3] -0.0496 _pdbx_refine_tls.L[2][3] -0.0335 _pdbx_refine_tls.S[1][1] -0.0024 _pdbx_refine_tls.S[1][2] -0.0020 _pdbx_refine_tls.S[1][3] 0.0050 _pdbx_refine_tls.S[2][1] 0.0060 _pdbx_refine_tls.S[2][2] 0.0050 _pdbx_refine_tls.S[2][3] 0.0088 _pdbx_refine_tls.S[3][1] 0.0306 _pdbx_refine_tls.S[3][2] 0.0170 _pdbx_refine_tls.S[3][3] -0.0026 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 43 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 168 _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.6.0117 ? 1 SCALA 'data scaling' . ? 2 PHASER phasing . ? 3 # _pdbx_entry_details.entry_id 4UYD _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'ADDITION OF HIS AFFINITY TAG AT THE N-TERMINUS' # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 2089 ? 5.92 . 2 1 O ? A HOH 2096 ? 6.23 . 3 1 O ? A HOH 2141 ? 7.07 . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A GLN 123 ? CD ? A GLN 93 CD 2 1 Y 1 A GLN 123 ? OE1 ? A GLN 93 OE1 3 1 Y 1 A GLN 123 ? NE2 ? A GLN 93 NE2 4 1 Y 1 A THR 169 ? CA ? A THR 139 CA 5 1 Y 1 A THR 169 ? C ? A THR 139 C 6 1 Y 1 A THR 169 ? O ? A THR 139 O 7 1 Y 1 A THR 169 ? CB ? A THR 139 CB 8 1 Y 1 A THR 169 ? OG1 ? A THR 139 OG1 9 1 Y 1 A THR 169 ? CG2 ? A THR 139 CG2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 31 ? A GLY 1 2 1 Y 1 A SER 32 ? A SER 2 3 1 Y 1 A SER 33 ? A SER 3 4 1 Y 1 A HIS 34 ? A HIS 4 5 1 Y 1 A HIS 35 ? A HIS 5 6 1 Y 1 A HIS 36 ? A HIS 6 7 1 Y 1 A HIS 37 ? A HIS 7 8 1 Y 1 A HIS 38 ? A HIS 8 9 1 Y 1 A HIS 39 ? A HIS 9 10 1 Y 1 A SER 40 ? A SER 10 11 1 Y 1 A SER 41 ? A SER 11 12 1 Y 1 A GLY 42 ? A GLY 12 13 1 Y 1 A GLU 170 ? A GLU 140 14 1 Y 1 A ILE 171 ? A ILE 141 15 1 Y 1 A MET 172 ? A MET 142 16 1 Y 1 A ILE 173 ? A ILE 143 17 1 Y 1 A VAL 174 ? A VAL 144 18 1 Y 1 A GLN 175 ? A GLN 145 19 1 Y 1 A ALA 176 ? A ALA 146 20 1 Y 1 A LYS 177 ? A LYS 147 21 1 Y 1 A GLY 178 ? A GLY 148 22 1 Y 1 A ARG 179 ? A ARG 149 23 1 Y 1 A GLY 180 ? A GLY 150 24 1 Y 1 A ARG 181 ? A ARG 151 25 1 Y 1 A GLY 182 ? A GLY 152 26 1 Y 1 A ARG 183 ? A ARG 153 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'DIMETHYL SULFOXIDE' DMS 3 1,2-ETHANEDIOL EDO 4 1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide V1T 5 water HOH #