data_4GBT # _model_server_result.job_id VH9a3p90KxtNJzRXMcjNpw _model_server_result.datetime_utc '2024-11-05 00:41:39' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4gbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 4GBT # _exptl.entry_id 4GBT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.12 _cell.angle_gamma 90 _cell.entry_id 4GBT _cell.length_a 255.2 _cell.length_b 350.1 _cell.length_c 272.1 _cell.Z_PDB 122 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GBT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 60-MERIC 60 'complete icosahedral assembly' 1 ? monomeric 1 'icosahedral asymmetric unit' 2 ? pentameric 5 'icosahedral pentamer' 3 ? hexameric 6 'icosahedral 23 hexamer' 4 ? monomeric 1 'icosahedral asymmetric unit, std point frame' 5 ? 60-meric 60 'crystal asymmetric unit, crystal frame' 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 (1-60) A,B,C,D 2 1 A,B,C,D 3 (1-5) A,B,C,D 4 (1,2,6,10,23,24) A,B,C,D 5 P A,B,C,D 6 (X0)(1-60) # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] P 'transform to point frame' ? ? -0.024395 -0.607697 -0.793794 0.448624 -0.716243 0.53454 -0.893388 -0.343074 0.2901 55.49975 -64.99169 37.37611 X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.498821 -0.259911 -0.826816 0.744021 0.617708 0.254693 0.444533 -0.742215 0.501505 88.21116 -64.85176 5.46772 3 'point symmetry operation' ? ? -0.312104 0.323477 -0.893283 0.943941 -0.000853 -0.330112 -0.107546 -0.946236 -0.305077 144.54761 -37.88764 95.55655 4 'point symmetry operation' ? ? -0.312104 0.943941 -0.107546 0.323477 -0.000853 -0.946236 -0.893283 -0.330112 -0.305077 91.15428 43.62886 145.76679 5 'point symmetry operation' ? ? 0.498821 0.744021 0.444533 -0.259911 0.617708 -0.742215 -0.826816 0.254693 0.501505 1.81895 67.04471 86.7096 6 'point symmetry operation' ? ? 0.596284 0.612997 -0.518344 0.612997 -0.7646 -0.199052 -0.518344 -0.199052 -0.831684 61.02148 -25.64559 157.59204 7 'point symmetry operation' ? ? 0.5231 0.608396 -0.596842 -0.351588 -0.483885 -0.8014 -0.776371 0.629055 -0.039215 71.03226 76.92488 120.22975 8 'point symmetry operation' ? ? 0.448276 0.682837 -0.576873 -0.891649 0.387293 -0.234449 0.063328 0.619466 0.782465 74.45665 72.90982 10.73542 9 'point symmetry operation' ? ? 0.475216 0.733446 -0.486032 -0.26084 0.644995 0.718293 0.840317 -0.214568 0.497823 66.56226 -32.14209 -19.57352 10 'point symmetry operation' ? ? 0.566689 0.690282 -0.44986 0.669083 -0.066914 0.740169 0.480824 -0.72044 -0.499775 58.25888 -93.05268 71.18886 11 'point symmetry operation' ? ? -0.597474 -0.642647 0.479614 -0.642647 0.026008 -0.765721 0.479614 -0.765721 -0.428534 69.4906 93.09966 66.42509 12 'point symmetry operation' ? ? -0.562971 -0.597655 0.570852 -0.641604 0.751426 0.153962 -0.520969 -0.279585 -0.806489 61.08592 30.53762 156.04768 13 'point symmetry operation' ? ? -0.471727 -0.646549 0.599539 0.307473 0.516649 0.799084 -0.826398 0.561292 -0.044921 53.30586 -73.94844 123.81431 14 'point symmetry operation' ? ? -0.449839 -0.721759 0.526032 0.892991 -0.353869 0.278108 -0.014581 0.594845 0.803708 56.9022 -75.96234 14.27041 15 'point symmetry operation' ? ? -0.527554 -0.719347 0.451914 0.305785 -0.657102 -0.688994 0.79258 -0.225294 0.566622 66.90492 27.27907 -21.19808 16 'point symmetry operation' ? ? -0.99881 0.02965 0.03873 0.02965 -0.261408 0.964773 0.03873 0.964773 0.260218 125.09633 -67.45411 47.79566 17 'point symmetry operation' ? ? -0.45895 0.249171 0.852806 0.249171 -0.885249 0.392744 0.852806 0.392744 0.344199 35.27907 -42.61077 -9.93236 18 'point symmetry operation' ? ? 0.335555 -0.359765 0.870616 -0.359765 -0.903088 -0.234522 0.870616 -0.234522 -0.432467 -16.70171 38.92623 41.70651 19 'point symmetry operation' ? ? 0.286727 -0.955628 0.067546 -0.955628 -0.290273 -0.050165 0.067546 -0.050165 -0.996454 40.98967 64.47553 131.3491 20 'point symmetry operation' ? ? -0.537956 -0.714957 -0.446588 -0.714957 0.106308 0.69104 -0.446588 0.69104 -0.568352 128.62567 -1.27114 135.1124 21 'point symmetry operation' ? ? -0.389945 0.375625 -0.840743 0.406471 0.889469 0.208869 0.826271 -0.26029 -0.499524 145.95158 -40.16769 49.09698 22 'point symmetry operation' ? ? -0.288778 0.95739 -0.003555 0.95739 0.28876 -0.004786 -0.003555 -0.004786 -0.999982 82.59723 -60.85399 136.13238 23 'point symmetry operation' ? ? 0.566689 0.669083 0.480824 0.690282 -0.066914 -0.72044 -0.44986 0.740169 -0.499775 -4.98405 4.84568 130.66151 24 'point symmetry operation' ? ? 0.994231 -0.090865 -0.057001 -0.025718 0.313976 -0.949083 0.104136 0.945073 0.309828 4.2421 66.1366 40.24494 25 'point symmetry operation' ? ? 0.402998 -0.272232 -0.873775 -0.201123 0.905053 -0.374738 0.892828 0.326755 0.309983 97.52544 38.31681 -10.16471 26 'point symmetry operation' ? ? 0.433534 -0.358886 0.826589 0.679348 -0.472498 -0.561456 0.59206 0.804951 0.038964 -19.97098 -5.25905 27.47155 27 'point symmetry operation' ? ? 0.316683 -0.947874 -0.03532 -0.262262 -0.051715 -0.96361 0.911554 0.314422 -0.264968 46.06548 82.23945 27.70842 28 'point symmetry operation' ? ? -0.562971 -0.641604 -0.520969 -0.597655 0.751426 -0.279585 0.570852 0.153962 -0.806489 135.27862 57.1901 86.27806 29 'point symmetry operation' ? ? -0.989776 0.136669 0.040793 0.136669 0.827011 0.545321 0.040793 0.545321 -0.837234 124.37891 -45.78975 122.2392 30 'point symmetry operation' ? ? -0.373903 0.311398 0.873629 0.9259 0.070584 0.371115 0.0539 0.947654 -0.314715 28.42939 -84.38544 85.89478 31 'point symmetry operation' ? ? -0.411645 0.904141 -0.11436 -0.714294 -0.39802 -0.575643 -0.56598 -0.155274 0.809665 97.9782 84.76164 49.10119 32 'point symmetry operation' ? ? 0.416526 0.750365 0.513281 -0.908332 0.367043 0.200528 -0.037927 -0.549755 0.834464 2.40611 44.41779 13.67228 33 'point symmetry operation' ? ? 0.994231 -0.025718 0.104136 -0.090865 0.313976 0.945073 -0.057001 -0.949083 0.309828 -6.70768 -58.41424 50.54191 34 'point symmetry operation' ? ? 0.5231 -0.351588 -0.776371 0.608396 -0.483885 0.629055 -0.596842 -0.8014 -0.039215 83.23178 -81.62408 108.7575 35 'point symmetry operation' ? ? -0.345779 0.223096 -0.911408 0.223096 -0.923922 -0.310799 -0.911408 -0.310799 0.269701 147.93121 6.86348 107.86708 36 'point symmetry operation' ? ? 0.368056 -0.920879 0.128514 -0.371525 -0.018951 0.928229 -0.852352 -0.389386 -0.349105 31.64962 -39.33494 146.14307 37 'point symmetry operation' ? ? -0.444431 -0.759881 -0.474406 0.213204 -0.604089 0.767868 -0.870072 0.240119 0.430486 124.5396 -65.80329 94.2997 38 'point symmetry operation' ? ? -0.997949 -0.001761 -0.063991 -0.001761 -0.998487 0.054951 -0.063991 0.054951 0.996436 132.02152 -3.62158 4.3313 39 'point symmetry operation' ? ? -0.527554 0.305785 0.79258 -0.719347 -0.657102 -0.225294 0.451914 -0.688994 0.566622 43.75562 61.27719 0.57115 40 'point symmetry operation' ? ? 0.316683 -0.262262 0.911554 -0.947874 -0.051715 0.314422 -0.03532 -0.96361 -0.264968 -18.27762 39.20512 88.21564 41 'point symmetry operation' ? ? -0.389945 0.406471 0.826271 0.375625 0.889469 -0.26029 -0.840743 0.208869 -0.499524 32.6726 -6.31565 155.62273 42 'point symmetry operation' ? ? 0.475216 -0.26084 0.840317 0.733446 0.644995 -0.214568 -0.486032 0.718293 0.497823 -23.56741 -32.28817 65.18299 43 'point symmetry operation' ? ? 0.416526 -0.908332 -0.037927 0.750365 0.367043 -0.549755 0.513281 0.200528 0.834464 39.86245 -10.59231 -21.55107 44 'point symmetry operation' ? ? -0.484906 -0.641194 -0.594757 0.403002 0.439734 -0.802635 0.77618 -0.628891 0.045172 135.30429 28.78898 15.28406 45 'point symmetry operation' ? ? -0.983333 0.171399 -0.060653 0.171399 0.762611 -0.623736 -0.060653 -0.623736 -0.779278 130.86072 31.4321 124.78349 46 'point symmetry operation' ? ? -0.411645 -0.714294 -0.56598 0.904141 -0.39802 -0.155274 -0.11436 -0.575643 0.809665 128.66721 -47.22512 20.24171 47 'point symmetry operation' ? ? -0.988384 0.085845 -0.125413 0.085844 -0.365609 -0.926801 -0.125413 -0.926801 0.353993 135.58411 57.49346 51.9124 48 'point symmetry operation' ? ? -0.484906 0.403002 0.77618 -0.641194 0.439734 -0.628891 -0.594757 -0.802635 0.045172 42.14474 83.7088 102.88982 49 'point symmetry operation' ? ? 0.402998 -0.201123 0.892828 -0.272232 0.905053 0.326755 -0.873775 -0.374738 0.309983 -22.52086 -4.8078 102.72491 50 'point symmetry operation' ? ? 0.448276 -0.891649 0.063328 0.682837 0.387293 0.619466 -0.576873 -0.234449 0.782465 30.95296 -85.72942 51.64557 51 'point symmetry operation' ? ? 0.368056 -0.371525 -0.852352 -0.920879 -0.018951 -0.389386 0.128514 0.92823 -0.349105 98.3026 85.30618 83.46369 52 'point symmetry operation' ? ? -0.471727 0.307473 -0.826398 -0.646549 0.516649 0.561292 0.599539 0.799084 -0.044921 150.20287 3.17428 32.69392 53 'point symmetry operation' ? ? -0.373903 0.9259 0.0539 0.311398 0.070584 0.947654 0.873629 0.371115 -0.314715 84.13259 -84.29516 33.51238 54 'point symmetry operation' ? ? 0.52634 0.629112 0.572001 0.629112 -0.740699 0.235762 0.572001 0.235762 -0.785641 -8.60137 -56.22236 84.78798 55 'point symmetry operation' ? ? 0.984895 -0.172741 0.011906 -0.132478 -0.796034 -0.590575 0.111494 0.580077 -0.806895 0.15618 48.59704 115.65959 56 'point symmetry operation' ? ? 0.433534 0.679348 0.59206 -0.358886 -0.472498 0.804951 0.826589 -0.561456 0.038964 -4.034 -31.76545 12.48466 57 'point symmetry operation' ? ? 0.984895 -0.132478 0.111494 -0.172741 -0.796034 0.580077 0.011906 -0.590575 -0.806895 -6.61115 -28.37961 122.02347 58 'point symmetry operation' ? ? 0.442283 -0.42057 -0.792153 -0.42057 -0.877362 0.230992 -0.792153 0.230992 -0.564921 89.46863 11.17864 156.96166 59 'point symmetry operation' ? ? -0.444431 0.213204 -0.870072 -0.759881 -0.604089 0.240119 -0.474406 0.767868 0.430486 151.42635 32.24115 69.01584 60 'point symmetry operation' ? ? -0.449839 0.892991 -0.014581 -0.721759 -0.353869 0.594845 0.526032 0.278108 0.803708 93.63855 5.70024 -20.27586 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4GBT _atom_sites.fract_transf_matrix[1][1] 0.003918 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000008 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.002856 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.003675 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code B 2 NA A 1 601 1 NA NA . C 3 CL A 1 602 1 CL CL . D 4 HOH A 1 701 1 HOH HOH . D 4 HOH A 2 702 2 HOH HOH . D 4 HOH A 3 703 3 HOH HOH . D 4 HOH A 4 704 4 HOH HOH . D 4 HOH A 5 705 9 HOH HOH . D 4 HOH A 6 706 10 HOH HOH . D 4 HOH A 7 707 11 HOH HOH . D 4 HOH A 8 708 12 HOH HOH . D 4 HOH A 9 709 16 HOH HOH . D 4 HOH A 10 710 27 HOH HOH . D 4 HOH A 11 711 34 HOH HOH . D 4 HOH A 12 712 37 HOH HOH . D 4 HOH A 13 713 45 HOH HOH . D 4 HOH A 14 714 49 HOH HOH . D 4 HOH A 15 715 62 HOH HOH . D 4 HOH A 16 716 63 HOH HOH . D 4 HOH A 17 717 65 HOH HOH . D 4 HOH A 18 718 67 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id B _atom_site.label_entity_id 2 _atom_site.Cartn_x -41.643 _atom_site.Cartn_y -61.995 _atom_site.Cartn_z 86.168 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 28.53 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 601 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 1 #