data_5YL1 # _model_server_result.job_id E3BLuQvLjc43FPIpM05wSw _model_server_result.datetime_utc '2024-10-15 13:14:00' _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 5yl1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5YL1 # _exptl.entry_id 5YL1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5YL1 _cell.length_a 196.981 _cell.length_b 200.319 _cell.length_c 419.29 _cell.Z_PDB 240 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YL1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 1 (1-60) A,B,C 2 1 A,B,C 3 (1-5) A,B,C 4 (1,2,6,10,23,24) A,B,C 5 P A,B,C 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' ? ? -0.996576 -0.02086 0.080006 0.017737 -0.999061 -0.039538 0.080755 -0.037983 0.99601 55.06985 -2.025 47.29374 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' ? ? 0.313223 -0.816078 -0.485704 0.755963 0.523816 -0.392604 0.574815 -0.244202 0.780995 10.78739 -58.44395 -40.44539 3 'point symmetry operation' ? ? -0.798005 -0.564479 -0.211071 0.407096 -0.246667 -0.879448 0.444365 -0.78773 0.426638 81.50555 -65.02393 -51.56019 4 'point symmetry operation' ? ? -0.798005 0.407096 0.444365 -0.564479 -0.246667 -0.78773 -0.211071 -0.879448 0.426638 114.42439 -10.64663 -17.98413 5 'point symmetry operation' ? ? 0.313223 0.755963 0.574815 -0.816078 0.523816 -0.244202 -0.485704 -0.392604 0.780995 64.05119 29.54037 13.88183 6 'point symmetry operation' ? ? -0.986957 -0.006135 0.160866 -0.006135 -0.997115 -0.075663 0.160866 -0.075663 0.984072 109.83443 -1.74873 -8.97192 7 'point symmetry operation' ? ? -0.221307 0.762937 0.607413 -0.799195 -0.498821 0.335358 0.558847 -0.411225 0.720128 93.03999 59.52064 -42.6157 8 'point symmetry operation' ? ? 0.856583 0.431911 0.282345 -0.434648 0.30902 0.845924 0.278113 -0.847325 0.452431 21.49656 66.48879 -41.67945 9 'point symmetry operation' ? ? 0.757106 -0.541746 -0.365106 0.583716 0.31 0.75045 -0.293371 -0.781288 0.550928 -5.92526 9.52596 -7.45704 10 'point symmetry operation' ? ? -0.382265 -0.812473 -0.440184 0.848551 -0.497236 0.180878 -0.365834 -0.304375 0.879501 48.67054 -32.64715 12.75732 11 'point symmetry operation' ? ? -0.999371 -0.035442 -0.001403 -0.035442 0.996244 0.079001 -0.001403 0.079001 -0.996874 102.12416 5.8902 -103.02187 12 'point symmetry operation' ? ? -0.340625 0.797342 0.498218 0.787433 0.531479 -0.312216 -0.513735 0.285965 -0.808888 93.47163 -55.91181 -67.3352 13 'point symmetry operation' ? ? 0.782452 0.573971 0.241509 0.468955 -0.287966 -0.834959 -0.409696 0.766572 -0.494486 23.04676 -65.85152 -56.87416 14 'point symmetry operation' ? ? 0.817805 -0.396864 -0.416766 -0.550751 -0.329646 -0.766816 0.166936 0.85664 -0.488159 -11.82567 -10.19258 -86.09556 15 'point symmetry operation' ? ? -0.283422 -0.773501 -0.566893 -0.862485 0.46404 -0.201957 0.419275 0.431698 -0.798652 37.04685 34.14624 -114.61641 16 'point symmetry operation' ? ? 0.986328 0.041576 -0.159463 0.041576 -0.99913 -0.003338 -0.159463 -0.003338 -0.987198 -7.5666 -0.45345 -94.3702 17 'point symmetry operation' ? ? 0.248709 -0.744201 -0.619927 -0.744201 -0.556474 0.369462 -0.619927 0.369462 -0.692235 7.09299 58.52314 -55.9677 18 'point symmetry operation' ? ? -0.84103 -0.441402 -0.312783 -0.441403 0.225613 0.868483 -0.312783 0.868483 -0.384583 78.34312 68.07468 -56.25019 19 'point symmetry operation' ? ? -0.776906 0.531514 0.337506 0.531514 0.266313 0.804096 0.337506 0.804096 -0.489407 107.71854 15.00127 -94.82727 20 'point symmetry operation' ? ? 0.352463 0.830011 0.432263 0.830011 -0.490619 0.265281 0.432263 0.265281 -0.861844 54.62342 -27.35145 -118.38673 21 'point symmetry operation' ? ? -0.096723 -0.043196 -0.994374 0.993282 0.05958 -0.099205 0.06353 -0.997288 0.037143 4.77946 -55.00572 -52.00149 22 'point symmetry operation' ? ? -0.634531 0.299134 -0.712663 0.299134 -0.75516 -0.583311 -0.712663 -0.583311 0.389691 46.47845 -43.7605 5.46704 23 'point symmetry operation' ? ? -0.382265 0.848551 -0.365834 -0.812473 -0.497236 -0.304375 -0.440184 0.180878 0.879501 50.97487 27.19317 16.10906 24 'point symmetry operation' ? ? 0.311453 0.845779 -0.433191 -0.805336 0.47691 0.352123 0.504411 0.239195 0.829672 12.05482 59.79972 -34.78235 25 'point symmetry operation' ? ? 0.487927 0.294649 -0.82165 0.310681 0.821041 0.478925 0.815723 -0.488952 0.309066 -16.49552 8.99802 -76.87698 26 'point symmetry operation' ? ? -0.064234 0.118903 -0.990826 -0.996651 -0.057995 0.057652 -0.050608 0.991211 0.12223 3.15292 54.87668 -43.61298 27 'point symmetry operation' ? ? -0.499775 0.356665 -0.789313 -0.322877 0.768887 0.551873 0.803726 0.530663 -0.269112 35.58521 45.18312 -107.03281 28 'point symmetry operation' ? ? -0.340625 0.787433 -0.513735 0.797342 0.531479 0.285965 0.498218 -0.312216 -0.808888 41.27313 -25.55738 -118.49242 29 'point symmetry operation' ? ? 0.193276 0.815901 -0.544931 0.815901 -0.442129 -0.372596 -0.544931 -0.372596 -0.751147 12.35616 -59.58385 -62.15503 30 'point symmetry operation' ? ? 0.364095 0.402726 -0.83979 -0.292847 -0.806444 -0.513701 -0.884124 0.432966 -0.175685 -11.20342 -9.87286 -15.87698 31 'point symmetry operation' ? ? 0.099588 -0.118163 0.987988 -0.994629 0.016315 0.102209 -0.028197 -0.99286 -0.115903 97.08949 57.00357 -55.21435 32 'point symmetry operation' ? ? 0.509777 -0.384435 0.769635 -0.240456 0.795281 0.556515 -0.82602 -0.468761 0.312976 65.11011 41.18671 7.19591 33 'point symmetry operation' ? ? 0.311453 -0.805336 0.504411 0.845779 0.47691 0.239195 -0.433191 0.352123 0.829672 61.949 -30.39502 13.02314 34 'point symmetry operation' ? ? -0.221307 -0.799195 0.558847 0.762937 -0.498821 -0.411225 0.607413 0.335358 0.720128 91.97469 -58.81811 -45.78569 35 'point symmetry operation' ? ? -0.352247 -0.374498 0.857714 -0.374498 -0.783484 -0.495887 0.857714 -0.495887 0.135731 113.69271 -4.80281 -87.95878 36 'point symmetry operation' ? ? 0.06137 0.042456 0.997212 0.997998 -0.0179 -0.060656 0.015275 0.998938 -0.04347 99.37014 -53.18651 -55.53518 37 'point symmetry operation' ? ? 0.62453 -0.271364 0.732342 0.264198 -0.809008 -0.525076 0.734957 0.521409 -0.433555 57.21823 -38.92131 -111.99414 38 'point symmetry operation' ? ? 0.411437 -0.830648 0.375157 -0.830648 -0.511153 -0.220785 0.375157 -0.220785 -0.900284 50.19501 32.44725 -117.00377 39 'point symmetry operation' ? ? -0.283422 -0.862485 0.419275 -0.773501 0.46404 0.431698 -0.566893 -0.201957 -0.798652 88.00632 62.29025 -63.64093 40 'point symmetry operation' ? ? -0.499775 -0.322877 0.803726 0.356665 0.768887 0.530663 -0.789313 0.551873 -0.269112 118.39823 9.36568 -25.65125 41 'point symmetry operation' ? ? -0.096723 0.993282 0.06353 -0.043196 0.05958 -0.997288 -0.994374 -0.099205 0.037143 58.40211 -48.3768 1.22722 42 'point symmetry operation' ? ? 0.757106 0.583716 -0.293371 -0.541746 0.31 -0.781288 -0.365106 0.75045 0.550928 -3.26208 -11.98913 -5.20381 43 'point symmetry operation' ? ? 0.509777 -0.240456 -0.82602 -0.384435 0.795281 -0.468761 0.769635 0.556515 0.312976 -17.34405 -4.35125 -75.28415 44 'point symmetry operation' ? ? -0.49691 -0.340256 -0.798314 0.211338 0.844782 -0.491609 0.841675 -0.413 -0.347872 35.61701 -36.01846 -112.16515 45 'point symmetry operation' ? ? -0.871748 0.422235 -0.248542 0.422235 0.390093 -0.818257 -0.248542 -0.818257 -0.518346 82.43071 -63.22774 -64.87852 46 'point symmetry operation' ? ? 0.099588 -0.994629 -0.028197 -0.118163 0.016315 -0.99286 0.987988 0.102209 -0.115903 45.47162 -44.27782 -108.14899 47 'point symmetry operation' ? ? -0.736917 -0.595388 0.320104 -0.595388 0.347434 -0.724433 0.320104 -0.724433 -0.610517 105.8164 -6.34939 -98.77691 48 'point symmetry operation' ? ? -0.49691 0.211338 0.841675 -0.340256 0.844782 -0.413 -0.798314 -0.491609 -0.347872 119.71711 -3.77754 -28.29252 49 'point symmetry operation' ? ? 0.487927 0.310681 0.815723 0.294649 0.821041 -0.488952 -0.82165 0.478925 0.309066 67.96344 -40.11648 5.89715 50 'point symmetry operation' ? ? 0.856583 -0.434648 0.278113 0.431911 0.30902 -0.847325 0.282345 0.845924 0.452431 22.07721 -65.14702 -43.45687 51 'point symmetry operation' ? ? 0.06137 0.997998 0.015275 0.042456 -0.0179 0.998938 0.997212 -0.060656 -0.04347 47.83002 50.30529 -104.73324 52 'point symmetry operation' ? ? 0.782452 0.468955 -0.409696 0.573971 -0.287966 0.766572 0.241509 -0.834959 -0.494486 -10.45272 11.40699 -88.67281 53 'point symmetry operation' ? ? 0.364095 -0.292847 -0.884124 0.402726 -0.806444 0.432966 -0.83979 -0.513701 -0.175685 -12.84936 3.42419 -17.26956 54 'point symmetry operation' ? ? -0.615546 -0.234623 -0.752366 -0.234623 -0.856815 0.459152 -0.752366 0.459152 0.472361 43.95218 37.38886 10.79965 55 'point symmetry operation' ? ? -0.802641 0.563163 -0.196507 -0.457282 -0.369468 0.808941 0.382963 0.739149 0.554075 81.4541 66.36297 -43.25588 56 'point symmetry operation' ? ? -0.064234 -0.996651 -0.050608 0.118903 -0.057995 0.991211 -0.990826 0.057652 0.12223 52.68824 46.03735 5.29102 57 'point symmetry operation' ? ? -0.802641 -0.457282 0.382963 0.563163 -0.369468 0.739149 -0.196507 0.808941 0.554075 112.2904 10.61955 -13.71047 58 'point symmetry operation' ? ? -0.376961 0.321965 0.868469 0.321965 -0.833619 0.448795 0.868469 0.448795 0.21058 114.8683 8.39262 -85.51777 59 'point symmetry operation' ? ? 0.62453 0.264198 0.734957 -0.271364 -0.809008 0.521409 0.732342 -0.525076 -0.433555 56.85937 42.43409 -110.89564 60 'point symmetry operation' ? ? 0.817805 -0.550751 0.166936 -0.396864 -0.329646 0.85664 -0.416766 -0.766816 -0.488159 18.42998 65.69981 -54.77272 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OE1 GLU 53 A GLU 118 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc2 A OE2 GLU 53 A GLU 118 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc3 A OE1 GLN 183 A GLN 248 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YL1 _atom_sites.fract_transf_matrix[1][1] 0.005077 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004992 _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] 0.002385 _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 CA A 1 301 251 CA CA . C 2 CA A 1 302 252 CA CA . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _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 43.38 _atom_site.Cartn_y 2.22 _atom_site.Cartn_z 22.613 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 53.37 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 301 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #