data_7KGL # _entry.id 7KGL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.342 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 7KGL WWPDB D_1000252436 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2021-06-02 _pdbx_database_PDB_obs_spr.pdb_id 7MFV _pdbx_database_PDB_obs_spr.replace_pdb_id 7KGL _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB . 7KGJ unspecified PDB . 7KGK unspecified PDB . 7KLW unspecified # _pdbx_database_status.status_code OBS _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7KGL _pdbx_database_status.recvd_initial_deposition_date 2020-10-16 _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.status_code_nmr_data ? _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 'Jiang, J.' 1 0000-0003-0964-5481 'Ahmad, J.' 2 0000-0002-3269-1518 'Natarajan, K.' 3 0000-0002-6295-2571 'Boyd, L.F.' 4 0000-0002-5126-6250 'Margulies, D.H.' 5 0000-0001-8530-7375 # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biorxiv _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Synthetic nanobody-SARS-CoV-2 receptor-binding domain structures identify distinct epitopes.' _citation.year 2021 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1101/2021.01.27.428466 _citation.pdbx_database_id_PubMed 33532775 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ahmad, J.' 1 0000-0002-3269-1518 primary 'Jiang, J.' 2 0000-0003-0964-5481 primary 'Boyd, L.F.' 3 0000-0002-5126-6250 primary 'Natarajan, K.' 4 0000-0002-6295-2571 primary 'Margulies, D.H.' 5 0000-0001-8530-7375 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 7KGL _cell.details ? _cell.formula_units_Z ? _cell.length_a 69.320 _cell.length_a_esd ? _cell.length_b 69.320 _cell.length_b_esd ? _cell.length_c 106.570 _cell.length_c_esd ? _cell.volume 443488.850 _cell.volume_esd ? _cell.Z_PDB 12 _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 7KGL _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall 'P 6c 2c' _symmetry.space_group_name_H-M 'P 63 2 2' _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 'SB16, Sybody-16, Synthetic Nanobody' 12873.515 1 ? ? ? ? 2 non-polymer syn 1,2-ETHANEDIOL 62.068 1 ? ? ? ? 3 water nat water 18.015 63 ? ? ? ? # _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 ;QVQLVESGGGLVQAGGSLRLSCAASGFPVAYKTMWWYRQAPGKEREWVAAIESYGIKWTRYADSVKGRFTISRDNAKNTV YLQMNSLKPEDTAVYYCIVWVGAQYHGQGTQVTVSA ; _entity_poly.pdbx_seq_one_letter_code_can ;QVQLVESGGGLVQAGGSLRLSCAASGFPVAYKTMWWYRQAPGKEREWVAAIESYGIKWTRYADSVKGRFTISRDNAKNTV YLQMNSLKPEDTAVYYCIVWVGAQYHGQGTQVTVSA ; _entity_poly.pdbx_strand_id B _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 GLN n 1 2 VAL n 1 3 GLN n 1 4 LEU n 1 5 VAL n 1 6 GLU n 1 7 SER n 1 8 GLY n 1 9 GLY n 1 10 GLY n 1 11 LEU n 1 12 VAL n 1 13 GLN n 1 14 ALA n 1 15 GLY n 1 16 GLY n 1 17 SER n 1 18 LEU n 1 19 ARG n 1 20 LEU n 1 21 SER n 1 22 CYS n 1 23 ALA n 1 24 ALA n 1 25 SER n 1 26 GLY n 1 27 PHE n 1 28 PRO n 1 29 VAL n 1 30 ALA n 1 31 TYR n 1 32 LYS n 1 33 THR n 1 34 MET n 1 35 TRP n 1 36 TRP n 1 37 TYR n 1 38 ARG n 1 39 GLN n 1 40 ALA n 1 41 PRO n 1 42 GLY n 1 43 LYS n 1 44 GLU n 1 45 ARG n 1 46 GLU n 1 47 TRP n 1 48 VAL n 1 49 ALA n 1 50 ALA n 1 51 ILE n 1 52 GLU n 1 53 SER n 1 54 TYR n 1 55 GLY n 1 56 ILE n 1 57 LYS n 1 58 TRP n 1 59 THR n 1 60 ARG n 1 61 TYR n 1 62 ALA n 1 63 ASP n 1 64 SER n 1 65 VAL n 1 66 LYS n 1 67 GLY n 1 68 ARG n 1 69 PHE n 1 70 THR n 1 71 ILE n 1 72 SER n 1 73 ARG n 1 74 ASP n 1 75 ASN n 1 76 ALA n 1 77 LYS n 1 78 ASN n 1 79 THR n 1 80 VAL n 1 81 TYR n 1 82 LEU n 1 83 GLN n 1 84 MET n 1 85 ASN n 1 86 SER n 1 87 LEU n 1 88 LYS n 1 89 PRO n 1 90 GLU n 1 91 ASP n 1 92 THR n 1 93 ALA n 1 94 VAL n 1 95 TYR n 1 96 TYR n 1 97 CYS n 1 98 ILE n 1 99 VAL n 1 100 TRP n 1 101 VAL n 1 102 GLY n 1 103 ALA n 1 104 GLN n 1 105 TYR n 1 106 HIS n 1 107 GLY n 1 108 GLN n 1 109 GLY n 1 110 THR n 1 111 GLN n 1 112 VAL n 1 113 THR n 1 114 VAL n 1 115 SER n 1 116 ALA 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 116 _entity_src_gen.gene_src_common_name ? _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 'synthetic construct' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 32630 _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 MC1061' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 1211845 _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 pET21b _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7KGL _struct_ref.pdbx_db_accession 7KGL _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7KGL _struct_ref_seq.pdbx_strand_id B _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 116 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7KGL _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 116 _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 116 # 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 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 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 7KGL _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 2.87 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 57.15 _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, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '20% PEG 4000, 0.1M MES pH 6.0, 0.2M LiSO4' _exptl_crystal_grow.pdbx_pH_range 5.5-7.5 # _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.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2020-10-06 _diffrn_detector.pdbx_frequency ? # _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 1.0000 _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 22-ID' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.0000 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 22-ID _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 23.17 _reflns.entry_id 7KGL _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.10 _reflns.d_resolution_low 39.85 _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 9278 _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 98.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.1 _reflns.pdbx_Rmerge_I_obs 0.055 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 17.8 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _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 ? _reflns.pdbx_Rpim_I_all 0.025 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.10 _reflns_shell.d_res_low 2.18 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.7 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 823 _reflns_shell.percent_possible_all 98.4 _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 0.714 _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 0.311 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.891 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 36.86 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _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 7KGL _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 2.10 _refine.ls_d_res_low 39.85 _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 8914 _refine.ls_number_reflns_R_free 438 _refine.ls_number_reflns_R_work 8476 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 95.07 _refine.ls_percent_reflns_R_free 4.91 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2260 _refine.ls_R_factor_R_free 0.2588 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2243 _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _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 2.53 _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 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 7BZ5 _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _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 29.6815 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.3281 _refine.overall_SU_R_Cruickshank_DPI ? _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 2.10 _refine_hist.d_res_low 39.85 _refine_hist.number_atoms_solvent 63 _refine_hist.number_atoms_total 974 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 907 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # 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' ? 0.0027 ? 940 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.5706 ? 1276 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0463 ? 134 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0045 ? 161 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 19.2632 ? 329 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _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_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.10 2.40 . . 132 2670 92.29 . . . 0.3626 . 0.2893 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.41 3.03 . . 147 2776 95.18 . . . 0.2830 . 0.2548 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.03 39.85 . . 159 3030 97.55 . . . 0.2169 . 0.1904 . . . . . . . . . . . # _struct.entry_id 7KGL _struct.title 'Crystal structure of synthetic nanobody' _struct.pdbx_descriptor 'SB16, Sybody-16, Nanobody' _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 7KGL _struct_keywords.text 'SARS-CoV-2, Spike Protein, RBD, Antibody, Nanobody, Sybody, VIRAL PROTEIN, epitope, neutralization' _struct_keywords.pdbx_keywords 'VIRAL PROTEIN' # 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 ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id LYS _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 88 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id THR _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 92 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id LYS _struct_conf.beg_auth_asym_id B _struct_conf.beg_auth_seq_id 88 _struct_conf.end_auth_comp_id THR _struct_conf.end_auth_asym_id B _struct_conf.end_auth_seq_id 92 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 22 SG ? ? ? 1_555 A CYS 97 SG A ? B CYS 22 B CYS 97 1_555 ? ? ? ? ? ? ? 2.031 ? ? disulf2 disulf ? ? A CYS 22 SG ? ? ? 1_555 A CYS 97 SG B ? B CYS 22 B CYS 97 1_555 ? ? ? ? ? ? ? 2.031 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 6 ? AA3 ? 4 ? # 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 ? parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? anti-parallel AA2 5 6 ? anti-parallel AA3 1 2 ? parallel AA3 2 3 ? anti-parallel AA3 3 4 ? 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 LEU A 4 ? SER A 7 ? LEU B 4 SER B 7 AA1 2 LEU A 18 ? ALA A 24 ? LEU B 18 ALA B 24 AA1 3 THR A 79 ? MET A 84 ? THR B 79 MET B 84 AA1 4 PHE A 69 ? ASP A 74 ? PHE B 69 ASP B 74 AA2 1 GLY A 10 ? GLN A 13 ? GLY B 10 GLN B 13 AA2 2 THR A 110 ? SER A 115 ? THR B 110 SER B 115 AA2 3 ALA A 93 ? TRP A 100 ? ALA B 93 TRP B 100 AA2 4 MET A 34 ? GLN A 39 ? MET B 34 GLN B 39 AA2 5 GLU A 46 ? ILE A 51 ? GLU B 46 ILE B 51 AA2 6 THR A 59 ? TYR A 61 ? THR B 59 TYR B 61 AA3 1 GLY A 10 ? GLN A 13 ? GLY B 10 GLN B 13 AA3 2 THR A 110 ? SER A 115 ? THR B 110 SER B 115 AA3 3 ALA A 93 ? TRP A 100 ? ALA B 93 TRP B 100 AA3 4 GLN A 104 ? HIS A 106 ? GLN B 104 HIS B 106 # 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 N VAL A 5 ? N VAL B 5 O ALA A 23 ? O ALA B 23 AA1 2 3 N LEU A 18 ? N LEU B 18 O MET A 84 ? O MET B 84 AA1 3 4 O TYR A 81 ? O TYR B 81 N SER A 72 ? N SER B 72 AA2 1 2 N GLY A 10 ? N GLY B 10 O THR A 113 ? O THR B 113 AA2 2 3 O THR A 110 ? O THR B 110 N TYR A 95 ? N TYR B 95 AA2 3 4 O TYR A 96 ? O TYR B 96 N TYR A 37 ? N TYR B 37 AA2 4 5 N TRP A 36 ? N TRP B 36 O ALA A 49 ? O ALA B 49 AA2 5 6 N ALA A 50 ? N ALA B 50 O ARG A 60 ? O ARG B 60 AA3 1 2 N GLY A 10 ? N GLY B 10 O THR A 113 ? O THR B 113 AA3 2 3 O THR A 110 ? O THR B 110 N TYR A 95 ? N TYR B 95 AA3 3 4 N VAL A 99 ? N VAL B 99 O TYR A 105 ? O TYR B 105 # _atom_sites.entry_id 7KGL _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.014426 _atom_sites.fract_transf_matrix[1][2] 0.008329 _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] 0.016658 _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] 0.009384 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? S ? ? 9.55732 6.39887 ? ? 1.23737 29.19336 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # 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 GLN 1 1 1 GLN GLN B . n A 1 2 VAL 2 2 2 VAL VAL B . n A 1 3 GLN 3 3 3 GLN GLN B . n A 1 4 LEU 4 4 4 LEU LEU B . n A 1 5 VAL 5 5 5 VAL VAL B . n A 1 6 GLU 6 6 6 GLU GLU B . n A 1 7 SER 7 7 7 SER SER B . n A 1 8 GLY 8 8 8 GLY GLY B . n A 1 9 GLY 9 9 9 GLY GLY B . n A 1 10 GLY 10 10 10 GLY GLY B . n A 1 11 LEU 11 11 11 LEU LEU B . n A 1 12 VAL 12 12 12 VAL VAL B . n A 1 13 GLN 13 13 13 GLN GLN B . n A 1 14 ALA 14 14 14 ALA ALA B . n A 1 15 GLY 15 15 15 GLY GLY B . n A 1 16 GLY 16 16 16 GLY GLY B . n A 1 17 SER 17 17 17 SER SER B . n A 1 18 LEU 18 18 18 LEU LEU B . n A 1 19 ARG 19 19 19 ARG ARG B . n A 1 20 LEU 20 20 20 LEU LEU B . n A 1 21 SER 21 21 21 SER SER B . n A 1 22 CYS 22 22 22 CYS CYS B . n A 1 23 ALA 23 23 23 ALA ALA B . n A 1 24 ALA 24 24 24 ALA ALA B . n A 1 25 SER 25 25 25 SER SER B . n A 1 26 GLY 26 26 26 GLY GLY B . n A 1 27 PHE 27 27 27 PHE PHE B . n A 1 28 PRO 28 28 28 PRO PRO B . n A 1 29 VAL 29 29 29 VAL VAL B . n A 1 30 ALA 30 30 30 ALA ALA B . n A 1 31 TYR 31 31 31 TYR TYR B . n A 1 32 LYS 32 32 32 LYS LYS B . n A 1 33 THR 33 33 33 THR THR B . n A 1 34 MET 34 34 34 MET MET B . n A 1 35 TRP 35 35 35 TRP TRP B . n A 1 36 TRP 36 36 36 TRP TRP B . n A 1 37 TYR 37 37 37 TYR TYR B . n A 1 38 ARG 38 38 38 ARG ARG B . n A 1 39 GLN 39 39 39 GLN GLN B . n A 1 40 ALA 40 40 40 ALA ALA B . n A 1 41 PRO 41 41 41 PRO PRO B . n A 1 42 GLY 42 42 42 GLY GLY B . n A 1 43 LYS 43 43 43 LYS LYS B . n A 1 44 GLU 44 44 44 GLU GLU B . n A 1 45 ARG 45 45 45 ARG ARG B . n A 1 46 GLU 46 46 46 GLU GLU B . n A 1 47 TRP 47 47 47 TRP TRP B . n A 1 48 VAL 48 48 48 VAL VAL B . n A 1 49 ALA 49 49 49 ALA ALA B . n A 1 50 ALA 50 50 50 ALA ALA B . n A 1 51 ILE 51 51 51 ILE ILE B . n A 1 52 GLU 52 52 52 GLU GLU B . n A 1 53 SER 53 53 53 SER SER B . n A 1 54 TYR 54 54 54 TYR TYR B . n A 1 55 GLY 55 55 55 GLY GLY B . n A 1 56 ILE 56 56 56 ILE ILE B . n A 1 57 LYS 57 57 57 LYS LYS B . n A 1 58 TRP 58 58 58 TRP TRP B . n A 1 59 THR 59 59 59 THR THR B . n A 1 60 ARG 60 60 60 ARG ARG B . n A 1 61 TYR 61 61 61 TYR TYR B . n A 1 62 ALA 62 62 62 ALA ALA B . n A 1 63 ASP 63 63 63 ASP ASP B . n A 1 64 SER 64 64 64 SER SER B . n A 1 65 VAL 65 65 65 VAL VAL B . n A 1 66 LYS 66 66 66 LYS LYS B . n A 1 67 GLY 67 67 67 GLY GLY B . n A 1 68 ARG 68 68 68 ARG ARG B . n A 1 69 PHE 69 69 69 PHE PHE B . n A 1 70 THR 70 70 70 THR THR B . n A 1 71 ILE 71 71 71 ILE ILE B . n A 1 72 SER 72 72 72 SER SER B . n A 1 73 ARG 73 73 73 ARG ARG B . n A 1 74 ASP 74 74 74 ASP ASP B . n A 1 75 ASN 75 75 75 ASN ASN B . n A 1 76 ALA 76 76 76 ALA ALA B . n A 1 77 LYS 77 77 77 LYS LYS B . n A 1 78 ASN 78 78 78 ASN ASN B . n A 1 79 THR 79 79 79 THR THR B . n A 1 80 VAL 80 80 80 VAL VAL B . n A 1 81 TYR 81 81 81 TYR TYR B . n A 1 82 LEU 82 82 82 LEU LEU B . n A 1 83 GLN 83 83 83 GLN GLN B . n A 1 84 MET 84 84 84 MET MET B . n A 1 85 ASN 85 85 85 ASN ASN B . n A 1 86 SER 86 86 86 SER SER B . n A 1 87 LEU 87 87 87 LEU LEU B . n A 1 88 LYS 88 88 88 LYS LYS B . n A 1 89 PRO 89 89 89 PRO PRO B . n A 1 90 GLU 90 90 90 GLU GLU B . n A 1 91 ASP 91 91 91 ASP ASP B . n A 1 92 THR 92 92 92 THR THR B . n A 1 93 ALA 93 93 93 ALA ALA B . n A 1 94 VAL 94 94 94 VAL VAL B . n A 1 95 TYR 95 95 95 TYR TYR B . n A 1 96 TYR 96 96 96 TYR TYR B . n A 1 97 CYS 97 97 97 CYS CYS B . n A 1 98 ILE 98 98 98 ILE ILE B . n A 1 99 VAL 99 99 99 VAL VAL B . n A 1 100 TRP 100 100 100 TRP TRP B . n A 1 101 VAL 101 101 101 VAL VAL B . n A 1 102 GLY 102 102 102 GLY GLY B . n A 1 103 ALA 103 103 103 ALA ALA B . n A 1 104 GLN 104 104 104 GLN GLN B . n A 1 105 TYR 105 105 105 TYR TYR B . n A 1 106 HIS 106 106 106 HIS HIS B . n A 1 107 GLY 107 107 107 GLY GLY B . n A 1 108 GLN 108 108 108 GLN GLN B . n A 1 109 GLY 109 109 109 GLY GLY B . n A 1 110 THR 110 110 110 THR THR B . n A 1 111 GLN 111 111 111 GLN GLN B . n A 1 112 VAL 112 112 112 VAL VAL B . n A 1 113 THR 113 113 113 THR THR B . n A 1 114 VAL 114 114 114 VAL VAL B . n A 1 115 SER 115 115 115 SER SER B . n A 1 116 ALA 116 116 116 ALA ALA B . 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 EDO 1 201 1 EDO EDO B . C 3 HOH 1 301 51 HOH HOH B . C 3 HOH 2 302 7 HOH HOH B . C 3 HOH 3 303 63 HOH HOH B . C 3 HOH 4 304 34 HOH HOH B . C 3 HOH 5 305 33 HOH HOH B . C 3 HOH 6 306 15 HOH HOH B . C 3 HOH 7 307 59 HOH HOH B . C 3 HOH 8 308 22 HOH HOH B . C 3 HOH 9 309 56 HOH HOH B . C 3 HOH 10 310 11 HOH HOH B . C 3 HOH 11 311 52 HOH HOH B . C 3 HOH 12 312 47 HOH HOH B . C 3 HOH 13 313 46 HOH HOH B . C 3 HOH 14 314 29 HOH HOH B . C 3 HOH 15 315 1 HOH HOH B . C 3 HOH 16 316 13 HOH HOH B . C 3 HOH 17 317 45 HOH HOH B . C 3 HOH 18 318 10 HOH HOH B . C 3 HOH 19 319 27 HOH HOH B . C 3 HOH 20 320 9 HOH HOH B . C 3 HOH 21 321 6 HOH HOH B . C 3 HOH 22 322 17 HOH HOH B . C 3 HOH 23 323 30 HOH HOH B . C 3 HOH 24 324 20 HOH HOH B . C 3 HOH 25 325 55 HOH HOH B . C 3 HOH 26 326 36 HOH HOH B . C 3 HOH 27 327 24 HOH HOH B . C 3 HOH 28 328 8 HOH HOH B . C 3 HOH 29 329 19 HOH HOH B . C 3 HOH 30 330 35 HOH HOH B . C 3 HOH 31 331 18 HOH HOH B . C 3 HOH 32 332 2 HOH HOH B . C 3 HOH 33 333 31 HOH HOH B . C 3 HOH 34 334 50 HOH HOH B . C 3 HOH 35 335 4 HOH HOH B . C 3 HOH 36 336 16 HOH HOH B . C 3 HOH 37 337 38 HOH HOH B . C 3 HOH 38 338 14 HOH HOH B . C 3 HOH 39 339 25 HOH HOH B . C 3 HOH 40 340 49 HOH HOH B . C 3 HOH 41 341 60 HOH HOH B . C 3 HOH 42 342 37 HOH HOH B . C 3 HOH 43 343 21 HOH HOH B . C 3 HOH 44 344 43 HOH HOH B . C 3 HOH 45 345 39 HOH HOH B . C 3 HOH 46 346 53 HOH HOH B . C 3 HOH 47 347 62 HOH HOH B . C 3 HOH 48 348 12 HOH HOH B . C 3 HOH 49 349 26 HOH HOH B . C 3 HOH 50 350 48 HOH HOH B . C 3 HOH 51 351 41 HOH HOH B . C 3 HOH 52 352 3 HOH HOH B . C 3 HOH 53 353 23 HOH HOH B . C 3 HOH 54 354 32 HOH HOH B . C 3 HOH 55 355 5 HOH HOH B . C 3 HOH 56 356 58 HOH HOH B . C 3 HOH 57 357 40 HOH HOH B . C 3 HOH 58 358 54 HOH HOH B . C 3 HOH 59 359 61 HOH HOH B . C 3 HOH 60 360 44 HOH HOH B . C 3 HOH 61 361 42 HOH HOH B . C 3 HOH 62 362 28 HOH HOH B . C 3 HOH 63 363 57 HOH HOH B . # _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 # _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_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 B HOH 305 ? C HOH . 2 1 B HOH 354 ? C HOH . # 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 2021-02-03 2 'Structure model' 1 1 2021-02-10 3 'Structure model' 1 2 2021-06-02 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 3 'Structure model' repository Obsolete ? ? # 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' Advisory 3 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' pdbx_database_PDB_obs_spr 4 3 'Structure model' pdbx_database_status # 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_CSD' 4 2 'Structure model' '_citation.pdbx_database_id_DOI' 5 2 'Structure model' '_citation.pdbx_database_id_PubMed' 6 2 'Structure model' '_citation.title' 7 2 'Structure model' '_citation.year' 8 2 'Structure model' '_citation_author.identifier_ORCID' 9 2 'Structure model' '_citation_author.name' 10 3 'Structure model' '_pdbx_database_status.status_code' 11 3 'Structure model' '_pdbx_database_status.status_code_sf' # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined 10.8524250255 17.0324740077 9.74167246797 0.16235042863 ? -0.0549534465628 ? 0.0145365780696 ? 0.460055964759 ? 0.113259292114 ? 0.210582987509 ? 1.67034941686 ? -1.11978541647 ? 0.290344678364 ? 2.72030106487 ? 1.45780844742 ? 3.17932421966 ? -0.117461083335 ? -1.04341249535 ? -0.611377435752 ? 0.0661424922132 ? 0.400856144641 ? 0.648267973138 ? 0.299211290001 ? -0.397955369223 ? 0.264456398054 ? 2 'X-RAY DIFFRACTION' ? refined 19.0287375704 15.9161318093 17.3224686402 0.219214837368 ? 0.0400768157606 ? 0.0236344053612 ? 0.618614012654 ? 0.159250133869 ? 0.138120649092 ? 3.94536699725 ? -0.00218638582876 ? 0.583470697592 ? 2.64591180809 ? 0.250140238008 ? 3.47960904395 ? -0.283402699831 ? -1.58744991082 ? -0.585882887237 ? 0.647911331116 ? 0.139708339126 ? 0.278486179848 ? 0.490305128724 ? -0.234182965792 ? 0.028394656404 ? 3 'X-RAY DIFFRACTION' ? refined 25.6419203922 24.3220832584 15.2043619504 0.0633546800786 ? 0.0296407801458 ? 0.0234905910023 ? 0.394298341866 ? -0.0395457188847 ? 0.113037975568 ? 3.16387419826 ? 1.67699474968 ? 0.148138117779 ? 6.4248927694 ? -1.36071685101 ? 3.08348163598 ? 0.0752175581419 ? -0.989812563208 ? 0.0876172646424 ? 0.81456015547 ? 0.226042832502 ? 0.0953513354182 ? -0.663428176052 ? -0.123788182108 ? -0.0996499760766 ? 4 'X-RAY DIFFRACTION' ? refined 23.9202039044 20.9999254397 7.22174583994 0.138319651319 ? -0.0478133648924 ? 0.00184105834506 ? 0.154903562232 ? 0.00866863143072 ? 0.105497192296 ? 6.44292726288 ? -2.89438973178 ? -1.23103438587 ? 7.94459323954 ? 3.43351134227 ? 7.09895987652 ? -0.166989787575 ? -0.61359618609 ? 0.186391645107 ? -0.132096926741 ? 0.0749705204872 ? -0.102578976888 ? -0.00274009125842 ? 0.038435992448 ? 0.0496976021271 ? 5 'X-RAY DIFFRACTION' ? refined 15.6911229439 15.3733050743 11.5180271381 0.147636229676 ? 0.0711664721154 ? -0.0780786355967 ? 0.45054616418 ? 0.178390854597 ? 0.261152349709 ? 2.55008174809 ? -0.434951731144 ? 0.41073554349 ? 2.14531922416 ? -1.03318283807 ? 1.87269709383 ? -0.637362434517 ? -1.18945887405 ? -0.551026545319 ? -0.250714145903 ? 0.639916419496 ? 0.247073934225 ? 0.399032951952 ? -0.412523632317 ? 0.102572977303 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_PDB_ins_code _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 A 1 B 1 ? A 24 B 24 ? ? ;chain 'B' and (resid 1 through 24 ) ; 2 'X-RAY DIFFRACTION' 2 A 25 B 25 ? A 45 B 45 ? ? ;chain 'B' and (resid 25 through 45 ) ; 3 'X-RAY DIFFRACTION' 3 A 46 B 46 ? A 58 B 58 ? ? ;chain 'B' and (resid 46 through 58 ) ; 4 'X-RAY DIFFRACTION' 4 A 59 B 59 ? A 74 B 74 ? ? ;chain 'B' and (resid 59 through 74 ) ; 5 'X-RAY DIFFRACTION' 5 A 75 B 75 ? A 117 B 116 ? ? ;chain 'B' and (resid 75 through 116 ) ; # 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 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.18.2_3874 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.18.2_3874 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _pdbx_entry_details.entry_id 7KGL _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N # 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 SER B 25 ? ? -127.86 -76.74 2 1 PRO B 41 ? ? -49.34 -73.54 3 1 VAL B 101 ? ? -118.87 76.51 4 1 ALA B 103 ? ? -79.64 -161.24 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-ETHANEDIOL EDO 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 ? # _space_group.name_H-M_alt 'P 63 2 2' _space_group.name_Hall 'P 6c 2c' _space_group.IT_number 182 _space_group.crystal_system hexagonal _space_group.id 1 # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 x-y,x,z+1/2 3 y,-x+y,z+1/2 4 -y,x-y,z 5 -x+y,-x,z 6 x-y,-y,-z 7 -x,-x+y,-z 8 -x,-y,z+1/2 9 y,x,-z 10 -y,-x,-z+1/2 11 -x+y,y,-z+1/2 12 x,x-y,-z+1/2 #