data_5VAR # _entry.id 5VAR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.298 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5VAR WWPDB D_1000227137 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5VAR _pdbx_database_status.recvd_initial_deposition_date 2017-03-27 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Judge, R.A.' 1 ? 'Upadhyay, A.K.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Bioorg. Med. Chem. Lett.' _citation.journal_id_ASTM BMCLE8 _citation.journal_id_CSD 1127 _citation.journal_id_ISSN 1464-3405 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 28 _citation.language ? _citation.page_first 1708 _citation.page_last 1713 _citation.title 'Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain - A fragment based approach.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.bmcl.2018.04.050 _citation.pdbx_database_id_PubMed 29691138 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Upadhyay, A.K.' 1 ? primary 'Judge, R.A.' 2 ? primary 'Li, L.' 3 ? primary 'Pithawalla, R.' 4 ? primary 'Simanis, J.' 5 ? primary 'Bodelle, P.M.' 6 ? primary 'Marin, V.L.' 7 ? primary 'Henry, R.F.' 8 ? primary 'Petros, A.M.' 9 ? primary 'Sun, C.' 10 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 101.610 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 5VAR _cell.details ? _cell.formula_units_Z ? _cell.length_a 33.270 _cell.length_a_esd ? _cell.length_b 39.840 _cell.length_b_esd ? _cell.length_c 44.300 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 2 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VAR _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? # 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 'Lysine-specific demethylase 4A' 13542.895 1 1.14.11.- ? ? ? 2 non-polymer syn '(1R,2S,3R,4S)-3-[(dimethylamino)methyl]-1-phenylbicyclo[2.2.1]heptan-2-ol' 245.360 1 ? ? ? ? 3 water nat water 18.015 74 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'JmjC domain-containing histone demethylation protein 3A,Jumonji domain-containing protein 2A' # _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 ;GSHMQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQV YGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP ; _entity_poly.pdbx_seq_one_letter_code_can ;GSHMQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQV YGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP ; _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 HIS n 1 4 MET n 1 5 GLN n 1 6 SER n 1 7 ILE n 1 8 THR n 1 9 ALA n 1 10 GLY n 1 11 GLN n 1 12 LYS n 1 13 VAL n 1 14 ILE n 1 15 SER n 1 16 LYS n 1 17 HIS n 1 18 LYS n 1 19 ASN n 1 20 GLY n 1 21 ARG n 1 22 PHE n 1 23 TYR n 1 24 GLN n 1 25 CYS n 1 26 GLU n 1 27 VAL n 1 28 VAL n 1 29 ARG n 1 30 LEU n 1 31 THR n 1 32 THR n 1 33 GLU n 1 34 THR n 1 35 PHE n 1 36 TYR n 1 37 GLU n 1 38 VAL n 1 39 ASN n 1 40 PHE n 1 41 ASP n 1 42 ASP n 1 43 GLY n 1 44 SER n 1 45 PHE n 1 46 SER n 1 47 ASP n 1 48 ASN n 1 49 LEU n 1 50 TYR n 1 51 PRO n 1 52 GLU n 1 53 ASP n 1 54 ILE n 1 55 VAL n 1 56 SER n 1 57 GLN n 1 58 ASP n 1 59 CYS n 1 60 LEU n 1 61 GLN n 1 62 PHE n 1 63 GLY n 1 64 PRO n 1 65 PRO n 1 66 ALA n 1 67 GLU n 1 68 GLY n 1 69 GLU n 1 70 VAL n 1 71 VAL n 1 72 GLN n 1 73 VAL n 1 74 ARG n 1 75 TRP n 1 76 THR n 1 77 ASP n 1 78 GLY n 1 79 GLN n 1 80 VAL n 1 81 TYR n 1 82 GLY n 1 83 ALA n 1 84 LYS n 1 85 PHE n 1 86 VAL n 1 87 ALA n 1 88 SER n 1 89 HIS n 1 90 PRO n 1 91 ILE n 1 92 GLN n 1 93 MET n 1 94 TYR n 1 95 GLN n 1 96 VAL n 1 97 GLU n 1 98 PHE n 1 99 GLU n 1 100 ASP n 1 101 GLY n 1 102 SER n 1 103 GLN n 1 104 LEU n 1 105 VAL n 1 106 VAL n 1 107 LYS n 1 108 ARG n 1 109 ASP n 1 110 ASP n 1 111 VAL n 1 112 TYR n 1 113 THR n 1 114 LEU n 1 115 ASP n 1 116 GLU n 1 117 GLU n 1 118 LEU n 1 119 PRO 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 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 119 _entity_src_gen.gene_src_common_name Human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677' _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 KDM4A_HUMAN _struct_ref.pdbx_db_accession O75164 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAK FVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP ; _struct_ref.pdbx_align_begin 897 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5VAR _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 5 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 119 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O75164 _struct_ref_seq.db_align_beg 897 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1011 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 897 _struct_ref_seq.pdbx_auth_seq_align_end 1011 # 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 5VAR GLY A 1 ? UNP O75164 ? ? 'expression tag' 893 1 1 5VAR SER A 2 ? UNP O75164 ? ? 'expression tag' 894 2 1 5VAR HIS A 3 ? UNP O75164 ? ? 'expression tag' 895 3 1 5VAR MET A 4 ? UNP O75164 ? ? 'expression tag' 896 4 # 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 92Y non-polymer . '(1R,2S,3R,4S)-3-[(dimethylamino)methyl]-1-phenylbicyclo[2.2.1]heptan-2-ol' ? 'C16 H23 N O' 245.360 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 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 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5VAR _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.12 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 42.08 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '18%(w/v) PEG 8000, 0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-10-21 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 17-ID' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.000 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 17-ID _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 23.670 _reflns.entry_id 5VAR _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.830 _reflns.d_resolution_low 39.840 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 9890 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 97.200 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.900 _reflns.pdbx_Rmerge_I_obs 0.086 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 10.700 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects 0 _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.099 _reflns.pdbx_Rpim_I_all 0.049 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 38231 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.997 _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 1.830 1.930 ? ? ? ? ? ? ? 95.200 ? ? ? ? 0.654 ? ? ? ? ? ? ? ? 3.700 ? ? ? ? 0.763 0.386 ? 1 1 0.731 ? 5.780 39.840 ? ? ? ? ? ? ? 98.100 ? ? ? ? 0.052 ? ? ? ? ? ? ? ? 3.600 ? ? ? ? 0.061 0.030 ? 2 1 0.998 ? # _refine.aniso_B[1][1] 3.6585 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 2.1971 _refine.aniso_B[2][2] 2.0638 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] -5.7223 _refine.B_iso_max 87.540 _refine.B_iso_mean 28.5500 _refine.B_iso_min 11.480 _refine.correlation_coeff_Fo_to_Fc 0.9360 _refine.correlation_coeff_Fo_to_Fc_free 0.9190 _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5VAR _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.8300 _refine.ls_d_res_low 32.5900 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 9841 _refine.ls_number_reflns_R_free 494 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.8000 _refine.ls_percent_reflns_R_free 5.0200 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1960 _refine.ls_R_factor_R_free 0.2430 _refine.ls_R_factor_R_free_error 0.0000 _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1940 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 2GFA _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI 0.1400 _refine.pdbx_overall_SU_R_free_Blow_DPI 0.1420 _refine.pdbx_overall_SU_R_Blow_DPI 0.1480 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI 0.1450 _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_analyze.entry_id 5VAR _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_coordinate_error_obs 0.260 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_sigma_a_free_details ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_sigma_a_obs_details ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.RG_d_res_high ? _refine_analyze.RG_d_res_low ? _refine_analyze.RG_free ? _refine_analyze.RG_work ? _refine_analyze.RG_free_work_ratio ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.8300 _refine_hist.d_res_low 32.5900 _refine_hist.pdbx_number_atoms_ligand 18 _refine_hist.number_atoms_solvent 74 _refine_hist.number_atoms_total 961 _refine_hist.pdbx_number_residues_total 108 _refine_hist.pdbx_B_iso_mean_ligand 34.58 _refine_hist.pdbx_B_iso_mean_solvent 43.26 _refine_hist.pdbx_number_atoms_protein 869 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? ? ? 318 ? t_dihedral_angle_d 2.000 SINUSOIDAL 'X-RAY DIFFRACTION' ? ? ? 30 ? t_trig_c_planes 2.000 HARMONIC 'X-RAY DIFFRACTION' ? ? ? 139 ? t_gen_planes 5.000 HARMONIC 'X-RAY DIFFRACTION' ? ? ? 932 ? t_it 20.000 HARMONIC 'X-RAY DIFFRACTION' ? ? ? ? ? t_nbd ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? t_improper_torsion ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? t_pseud_angle ? ? 'X-RAY DIFFRACTION' ? ? ? 113 ? t_chiral_improper_torsion 5.000 SEMIHARMONIC 'X-RAY DIFFRACTION' ? ? ? ? ? t_sum_occupancies ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? t_utility_distance ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? t_utility_angle ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? t_utility_torsion ? ? 'X-RAY DIFFRACTION' ? ? ? 1054 ? t_ideal_dist_contact 4.000 SEMIHARMONIC 'X-RAY DIFFRACTION' ? 0.010 ? 932 ? t_bond_d 2.000 HARMONIC 'X-RAY DIFFRACTION' ? 1.030 ? 1287 ? t_angle_deg 2.000 HARMONIC 'X-RAY DIFFRACTION' ? 3.670 ? ? ? t_omega_torsion ? ? 'X-RAY DIFFRACTION' ? 16.110 ? ? ? t_other_torsion ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.8300 _refine_ls_shell.d_res_low 2.0500 _refine_ls_shell.number_reflns_all 2702 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 137 _refine_ls_shell.number_reflns_R_work 2565 _refine_ls_shell.percent_reflns_obs 94.8400 _refine_ls_shell.percent_reflns_R_free 5.0700 _refine_ls_shell.R_factor_all 0.2140 _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.2740 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.2110 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 5 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 5VAR _struct.title 'Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine competitive inhibitor' _struct.pdbx_descriptor 'KDM4A tandem TUDOR domain,Lysine-specific demethylase 4A (E.C.1.14.11.-)' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 5VAR _struct_keywords.text 'KDM4A tandem TUDOR domain, OXIDOREDUCTASE' _struct_keywords.pdbx_keywords OXIDOREDUCTASE # 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 ? # 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 AA1 TYR A 50 ? ILE A 54 ? TYR A 942 ILE A 946 5 ? 5 HELX_P HELX_P2 AA2 ASP A 58 ? GLY A 63 ? ASP A 950 GLY A 955 1 ? 6 HELX_P HELX_P3 AA3 LYS A 107 ? ASP A 109 ? LYS A 999 ASP A 1001 5 ? 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 5 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 PHE A 45 ? LEU A 49 ? PHE A 937 LEU A 941 AA1 2 PHE A 22 ? PHE A 40 ? PHE A 914 PHE A 932 AA1 3 VAL A 80 ? GLU A 97 ? VAL A 972 GLU A 989 AA1 4 GLN A 103 ? VAL A 106 ? GLN A 995 VAL A 998 AA2 1 VAL A 70 ? ARG A 74 ? VAL A 962 ARG A 966 AA2 2 VAL A 80 ? GLU A 97 ? VAL A 972 GLU A 989 AA2 3 PHE A 22 ? PHE A 40 ? PHE A 914 PHE A 932 AA2 4 LYS A 12 ? LYS A 16 ? LYS A 904 LYS A 908 AA2 5 VAL A 111 ? TYR A 112 ? VAL A 1003 TYR A 1004 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 O LEU A 49 ? O LEU A 941 N TYR A 36 ? N TYR A 928 AA1 2 3 N GLU A 33 ? N GLU A 925 O ILE A 91 ? O ILE A 983 AA1 3 4 N TYR A 94 ? N TYR A 986 O VAL A 106 ? O VAL A 998 AA2 1 2 N VAL A 71 ? N VAL A 963 O ALA A 83 ? O ALA A 975 AA2 2 3 O ILE A 91 ? O ILE A 983 N GLU A 33 ? N GLU A 925 AA2 3 4 O CYS A 25 ? O CYS A 917 N VAL A 13 ? N VAL A 905 AA2 4 5 N ILE A 14 ? N ILE A 906 O TYR A 112 ? O TYR A 1004 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id 92Y _struct_site.pdbx_auth_seq_id 1101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'binding site for residue 92Y A 1101' # 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 6 ASP A 42 ? ASP A 934 . ? 1_555 ? 2 AC1 6 SER A 44 ? SER A 936 . ? 1_555 ? 3 AC1 6 PHE A 45 ? PHE A 937 . ? 1_555 ? 4 AC1 6 TRP A 75 ? TRP A 967 . ? 1_555 ? 5 AC1 6 TYR A 81 ? TYR A 973 . ? 1_555 ? 6 AC1 6 GLY A 101 ? GLY A 993 . ? 1_655 ? # _atom_sites.entry_id 5VAR _atom_sites.fract_transf_matrix[1][1] 0.030057 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.006175 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.025100 _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] 0.023045 _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 1 893 ? ? ? A . n A 1 2 SER 2 894 ? ? ? A . n A 1 3 HIS 3 895 ? ? ? A . n A 1 4 MET 4 896 ? ? ? A . n A 1 5 GLN 5 897 897 GLN GLN A . n A 1 6 SER 6 898 898 SER SER A . n A 1 7 ILE 7 899 899 ILE ILE A . n A 1 8 THR 8 900 900 THR THR A . n A 1 9 ALA 9 901 901 ALA ALA A . n A 1 10 GLY 10 902 902 GLY GLY A . n A 1 11 GLN 11 903 903 GLN GLN A . n A 1 12 LYS 12 904 904 LYS LYS A . n A 1 13 VAL 13 905 905 VAL VAL A . n A 1 14 ILE 14 906 906 ILE ILE A . n A 1 15 SER 15 907 907 SER SER A . n A 1 16 LYS 16 908 908 LYS LYS A . n A 1 17 HIS 17 909 909 HIS HIS A . n A 1 18 LYS 18 910 910 LYS LYS A . n A 1 19 ASN 19 911 911 ASN ASN A . n A 1 20 GLY 20 912 912 GLY GLY A . n A 1 21 ARG 21 913 913 ARG ARG A . n A 1 22 PHE 22 914 914 PHE PHE A . n A 1 23 TYR 23 915 915 TYR TYR A . n A 1 24 GLN 24 916 916 GLN GLN A . n A 1 25 CYS 25 917 917 CYS CYS A . n A 1 26 GLU 26 918 918 GLU GLU A . n A 1 27 VAL 27 919 919 VAL VAL A . n A 1 28 VAL 28 920 920 VAL VAL A . n A 1 29 ARG 29 921 921 ARG ARG A . n A 1 30 LEU 30 922 922 LEU LEU A . n A 1 31 THR 31 923 923 THR THR A . n A 1 32 THR 32 924 924 THR THR A . n A 1 33 GLU 33 925 925 GLU GLU A . n A 1 34 THR 34 926 926 THR THR A . n A 1 35 PHE 35 927 927 PHE PHE A . n A 1 36 TYR 36 928 928 TYR TYR A . n A 1 37 GLU 37 929 929 GLU GLU A . n A 1 38 VAL 38 930 930 VAL VAL A . n A 1 39 ASN 39 931 931 ASN ASN A . n A 1 40 PHE 40 932 932 PHE PHE A . n A 1 41 ASP 41 933 933 ASP ASP A . n A 1 42 ASP 42 934 934 ASP ASP A . n A 1 43 GLY 43 935 935 GLY GLY A . n A 1 44 SER 44 936 936 SER SER A . n A 1 45 PHE 45 937 937 PHE PHE A . n A 1 46 SER 46 938 938 SER SER A . n A 1 47 ASP 47 939 939 ASP ASP A . n A 1 48 ASN 48 940 940 ASN ASN A . n A 1 49 LEU 49 941 941 LEU LEU A . n A 1 50 TYR 50 942 942 TYR TYR A . n A 1 51 PRO 51 943 943 PRO PRO A . n A 1 52 GLU 52 944 944 GLU GLU A . n A 1 53 ASP 53 945 945 ASP ASP A . n A 1 54 ILE 54 946 946 ILE ILE A . n A 1 55 VAL 55 947 947 VAL VAL A . n A 1 56 SER 56 948 948 SER SER A . n A 1 57 GLN 57 949 949 GLN GLN A . n A 1 58 ASP 58 950 950 ASP ASP A . n A 1 59 CYS 59 951 951 CYS CYS A . n A 1 60 LEU 60 952 952 LEU LEU A . n A 1 61 GLN 61 953 953 GLN GLN A . n A 1 62 PHE 62 954 954 PHE PHE A . n A 1 63 GLY 63 955 955 GLY GLY A . n A 1 64 PRO 64 956 956 PRO PRO A . n A 1 65 PRO 65 957 957 PRO PRO A . n A 1 66 ALA 66 958 958 ALA ALA A . n A 1 67 GLU 67 959 959 GLU GLU A . n A 1 68 GLY 68 960 960 GLY GLY A . n A 1 69 GLU 69 961 961 GLU GLU A . n A 1 70 VAL 70 962 962 VAL VAL A . n A 1 71 VAL 71 963 963 VAL VAL A . n A 1 72 GLN 72 964 964 GLN GLN A . n A 1 73 VAL 73 965 965 VAL VAL A . n A 1 74 ARG 74 966 966 ARG ARG A . n A 1 75 TRP 75 967 967 TRP TRP A . n A 1 76 THR 76 968 968 THR THR A . n A 1 77 ASP 77 969 969 ASP ASP A . n A 1 78 GLY 78 970 970 GLY GLY A . n A 1 79 GLN 79 971 971 GLN GLN A . n A 1 80 VAL 80 972 972 VAL VAL A . n A 1 81 TYR 81 973 973 TYR TYR A . n A 1 82 GLY 82 974 974 GLY GLY A . n A 1 83 ALA 83 975 975 ALA ALA A . n A 1 84 LYS 84 976 976 LYS LYS A . n A 1 85 PHE 85 977 977 PHE PHE A . n A 1 86 VAL 86 978 978 VAL VAL A . n A 1 87 ALA 87 979 979 ALA ALA A . n A 1 88 SER 88 980 980 SER SER A . n A 1 89 HIS 89 981 981 HIS HIS A . n A 1 90 PRO 90 982 982 PRO PRO A . n A 1 91 ILE 91 983 983 ILE ILE A . n A 1 92 GLN 92 984 984 GLN GLN A . n A 1 93 MET 93 985 985 MET MET A . n A 1 94 TYR 94 986 986 TYR TYR A . n A 1 95 GLN 95 987 987 GLN GLN A . n A 1 96 VAL 96 988 988 VAL VAL A . n A 1 97 GLU 97 989 989 GLU GLU A . n A 1 98 PHE 98 990 990 PHE PHE A . n A 1 99 GLU 99 991 991 GLU GLU A . n A 1 100 ASP 100 992 992 ASP ASP A . n A 1 101 GLY 101 993 993 GLY GLY A . n A 1 102 SER 102 994 994 SER SER A . n A 1 103 GLN 103 995 995 GLN GLN A . n A 1 104 LEU 104 996 996 LEU LEU A . n A 1 105 VAL 105 997 997 VAL VAL A . n A 1 106 VAL 106 998 998 VAL VAL A . n A 1 107 LYS 107 999 999 LYS LYS A . n A 1 108 ARG 108 1000 1000 ARG ARG A . n A 1 109 ASP 109 1001 1001 ASP ASP A . n A 1 110 ASP 110 1002 1002 ASP ASP A . n A 1 111 VAL 111 1003 1003 VAL VAL A . n A 1 112 TYR 112 1004 1004 TYR TYR A . n A 1 113 THR 113 1005 ? ? ? A . n A 1 114 LEU 114 1006 ? ? ? A . n A 1 115 ASP 115 1007 ? ? ? A . n A 1 116 GLU 116 1008 ? ? ? A . n A 1 117 GLU 117 1009 ? ? ? A . n A 1 118 LEU 118 1010 ? ? ? A . n A 1 119 PRO 119 1011 ? ? ? 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 92Y 1 1101 1 92Y LIG A . C 3 HOH 1 1201 1 HOH HOH A . C 3 HOH 2 1202 5 HOH HOH A . C 3 HOH 3 1203 12 HOH HOH A . C 3 HOH 4 1204 38 HOH HOH A . C 3 HOH 5 1205 1 HOH HOH A . C 3 HOH 6 1206 13 HOH HOH A . C 3 HOH 7 1207 4 HOH HOH A . C 3 HOH 8 1208 49 HOH HOH A . C 3 HOH 9 1209 8 HOH HOH A . C 3 HOH 10 1210 6 HOH HOH A . C 3 HOH 11 1211 17 HOH HOH A . C 3 HOH 12 1212 21 HOH HOH A . C 3 HOH 13 1213 19 HOH HOH A . C 3 HOH 14 1214 3 HOH HOH A . C 3 HOH 15 1215 18 HOH HOH A . C 3 HOH 16 1216 39 HOH HOH A . C 3 HOH 17 1217 27 HOH HOH A . C 3 HOH 18 1218 24 HOH HOH A . C 3 HOH 19 1219 3 HOH HOH A . C 3 HOH 20 1220 7 HOH HOH A . C 3 HOH 21 1221 9 HOH HOH A . C 3 HOH 22 1222 41 HOH HOH A . C 3 HOH 23 1223 20 HOH HOH A . C 3 HOH 24 1224 10 HOH HOH A . C 3 HOH 25 1225 2 HOH HOH A . C 3 HOH 26 1226 7 HOH HOH A . C 3 HOH 27 1227 4 HOH HOH A . C 3 HOH 28 1228 22 HOH HOH A . C 3 HOH 29 1229 43 HOH HOH A . C 3 HOH 30 1230 9 HOH HOH A . C 3 HOH 31 1231 32 HOH HOH A . C 3 HOH 32 1232 11 HOH HOH A . C 3 HOH 33 1233 42 HOH HOH A . C 3 HOH 34 1234 5 HOH HOH A . C 3 HOH 35 1235 59 HOH HOH A . C 3 HOH 36 1236 31 HOH HOH A . C 3 HOH 37 1237 2 HOH HOH A . C 3 HOH 38 1238 13 HOH HOH A . C 3 HOH 39 1239 28 HOH HOH A . C 3 HOH 40 1240 12 HOH HOH A . C 3 HOH 41 1241 23 HOH HOH A . C 3 HOH 42 1242 14 HOH HOH A . C 3 HOH 43 1243 52 HOH HOH A . C 3 HOH 44 1244 26 HOH HOH A . C 3 HOH 45 1245 45 HOH HOH A . C 3 HOH 46 1246 36 HOH HOH A . C 3 HOH 47 1247 37 HOH HOH A . C 3 HOH 48 1248 51 HOH HOH A . C 3 HOH 49 1249 11 HOH HOH A . C 3 HOH 50 1250 30 HOH HOH A . C 3 HOH 51 1251 15 HOH HOH A . C 3 HOH 52 1252 6 HOH HOH A . C 3 HOH 53 1253 33 HOH HOH A . C 3 HOH 54 1254 58 HOH HOH A . C 3 HOH 55 1255 48 HOH HOH A . C 3 HOH 56 1256 53 HOH HOH A . C 3 HOH 57 1257 46 HOH HOH A . C 3 HOH 58 1258 34 HOH HOH A . C 3 HOH 59 1259 25 HOH HOH A . C 3 HOH 60 1260 16 HOH HOH A . C 3 HOH 61 1261 40 HOH HOH A . C 3 HOH 62 1262 47 HOH HOH A . C 3 HOH 63 1263 29 HOH HOH A . C 3 HOH 64 1264 60 HOH HOH A . C 3 HOH 65 1265 56 HOH HOH A . C 3 HOH 66 1266 57 HOH HOH A . C 3 HOH 67 1267 10 HOH HOH A . C 3 HOH 68 1268 8 HOH HOH A . C 3 HOH 69 1269 54 HOH HOH A . C 3 HOH 70 1270 35 HOH HOH A . C 3 HOH 71 1271 44 HOH HOH A . C 3 HOH 72 1272 61 HOH HOH A . C 3 HOH 73 1273 50 HOH HOH A . C 3 HOH 74 1274 55 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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 6950 ? # _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 2018-03-28 2 'Structure model' 1 1 2018-05-09 3 'Structure model' 1 2 2018-05-16 4 'Structure model' 1 3 2018-09-05 # _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 ? # 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' 'Data collection' 2 2 'Structure model' 'Database references' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' # 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' citation 4 4 'Structure model' pdbx_related_exp_data_set # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 'Structure model' '_citation.title' 9 2 'Structure model' '_citation.year' 10 3 'Structure model' '_citation.journal_volume' 11 3 'Structure model' '_citation.page_first' 12 3 'Structure model' '_citation.page_last' # _phasing.method MR # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? 0.5.12 1 ? phasing ? ? ? ? ? ? ? ? ? ? ? MOLREP ? ? ? . 2 ? refinement ? ? ? ? ? ? ? ? ? ? ? BUSTER ? ? ? 2.11.7 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.22 4 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 5 # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 1274 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 5.91 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # 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 893 ? A GLY 1 2 1 Y 1 A SER 894 ? A SER 2 3 1 Y 1 A HIS 895 ? A HIS 3 4 1 Y 1 A MET 896 ? A MET 4 5 1 Y 1 A THR 1005 ? A THR 113 6 1 Y 1 A LEU 1006 ? A LEU 114 7 1 Y 1 A ASP 1007 ? A ASP 115 8 1 Y 1 A GLU 1008 ? A GLU 116 9 1 Y 1 A GLU 1009 ? A GLU 117 10 1 Y 1 A LEU 1010 ? A LEU 118 11 1 Y 1 A PRO 1011 ? A PRO 119 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '(1R,2S,3R,4S)-3-[(dimethylamino)methyl]-1-phenylbicyclo[2.2.1]heptan-2-ol' 92Y 3 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #