data_5YGI # _model_server_result.job_id ud4idAOJ-LknIjCCQuEkAQ _model_server_result.datetime_utc '2024-11-21 17:28:05' _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 5ygi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":506}' # _entry.id 5YGI # _exptl.entry_id 5YGI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 368.26 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(4-hexoxypyridin-2-yl)amino]-phosphono-methyl]phosphonic acid' _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 _cell.angle_gamma 90 _cell.entry_id 5YGI _cell.length_a 111.743 _cell.length_b 111.743 _cell.length_c 66.191 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YGI _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD2 ASP 98 A ASP 103 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc2 A OD1 ASP 98 A ASP 103 1_555 F MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc3 A OD2 ASP 102 A ASP 107 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc4 A OD2 ASP 102 A ASP 107 1_555 F MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc5 A OD2 ASP 238 A ASP 243 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc6 D MG MG . A MG 503 1_555 G O7 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc7 D MG MG . A MG 503 1_555 G O3 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc8 D MG MG . A MG 503 1_555 H O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc9 D MG MG . A MG 503 1_555 H O HOH . A HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc10 D MG MG . A MG 503 1_555 H O HOH . A HOH 635 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 E MG MG . A MG 504 1_555 G O9 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc12 E MG MG . A MG 504 1_555 G O4 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc13 E MG MG . A MG 504 1_555 H O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc14 E MG MG . A MG 504 1_555 H O HOH . A HOH 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc15 F MG MG . A MG 505 1_555 G O9 T93 . A T93 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc16 F MG MG . A MG 505 1_555 H O HOH . A HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc17 F MG MG . A MG 505 1_555 H O HOH . A HOH 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc18 F MG MG . A MG 505 1_555 H O HOH . A HOH 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? # _chem_comp.formula 'C12 H22 N2 O7 P2' _chem_comp.formula_weight 368.26 _chem_comp.id T93 _chem_comp.mon_nstd_flag . _chem_comp.name '[[(4-hexoxypyridin-2-yl)amino]-phosphono-methyl]phosphonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C22 C21 T93 sing 294 n n C21 C20 T93 sing 295 n n C20 C19 T93 sing 296 n n C19 C18 T93 sing 297 n n C18 C17 T93 sing 298 n n O1 P2 T93 doub 299 n n C17 O16 T93 sing 300 n n O4 P2 T93 sing 301 n n O16 C15 T93 sing 302 n n C23 C15 T93 doub 303 n y C23 C11 T93 sing 304 n y P2 O3 T93 sing 305 n n P2 C5 T93 sing 306 n n N10 C11 T93 sing 307 n n N10 C5 T93 sing 308 n n C15 C14 T93 sing 309 n y C11 N12 T93 doub 310 n y C5 P6 T93 sing 311 n n C14 C13 T93 doub 312 n y N12 C13 T93 sing 313 n y O9 P6 T93 doub 314 n n P6 O8 T93 sing 315 n n P6 O7 T93 sing 316 n n O3 H1 T93 sing 317 n n O4 H2 T93 sing 318 n n C5 H051 T93 sing 319 n n O7 H3 T93 sing 320 n n O8 H4 T93 sing 321 n n N10 H101 T93 sing 322 n n C13 H131 T93 sing 323 n n C14 H141 T93 sing 324 n n C17 H171 T93 sing 325 n n C17 H172 T93 sing 326 n n C18 H182 T93 sing 327 n n C18 H181 T93 sing 328 n n C19 H192 T93 sing 329 n n C19 H191 T93 sing 330 n n C20 H202 T93 sing 331 n n C20 H201 T93 sing 332 n n C21 H212 T93 sing 333 n n C21 H211 T93 sing 334 n n C22 H223 T93 sing 335 n n C22 H221 T93 sing 336 n n C22 H222 T93 sing 337 n n C23 H231 T93 sing 338 n n # _atom_sites.entry_id 5YGI _atom_sites.fract_transf_matrix[1][1] 0.008949 _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] 0.008949 _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] 0.015108 _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 PO4 A 1 501 501 PO4 PO4 . C 2 PO4 A 1 502 502 PO4 PO4 . D 3 MG A 1 503 601 MG MG . E 3 MG A 1 504 602 MG MG . F 3 MG A 1 505 603 MG MG . G 4 T93 A 1 506 701 T93 T93 . H 5 HOH A 1 601 835 HOH HOH . H 5 HOH A 2 602 851 HOH HOH . H 5 HOH A 3 603 820 HOH HOH . H 5 HOH A 4 604 838 HOH HOH . H 5 HOH A 5 605 810 HOH HOH . H 5 HOH A 6 606 832 HOH HOH . H 5 HOH A 7 607 837 HOH HOH . H 5 HOH A 8 608 815 HOH HOH . H 5 HOH A 9 609 812 HOH HOH . H 5 HOH A 10 610 850 HOH HOH . H 5 HOH A 11 611 831 HOH HOH . H 5 HOH A 12 612 808 HOH HOH . H 5 HOH A 13 613 806 HOH HOH . H 5 HOH A 14 614 849 HOH HOH . H 5 HOH A 15 615 846 HOH HOH . H 5 HOH A 16 616 814 HOH HOH . H 5 HOH A 17 617 809 HOH HOH . H 5 HOH A 18 618 852 HOH HOH . H 5 HOH A 19 619 821 HOH HOH . H 5 HOH A 20 620 834 HOH HOH . H 5 HOH A 21 621 853 HOH HOH . H 5 HOH A 22 622 825 HOH HOH . H 5 HOH A 23 623 848 HOH HOH . H 5 HOH A 24 624 804 HOH HOH . H 5 HOH A 25 625 807 HOH HOH . H 5 HOH A 26 626 818 HOH HOH . H 5 HOH A 27 627 816 HOH HOH . H 5 HOH A 28 628 822 HOH HOH . H 5 HOH A 29 629 802 HOH HOH . H 5 HOH A 30 630 844 HOH HOH . H 5 HOH A 31 631 847 HOH HOH . H 5 HOH A 32 632 841 HOH HOH . H 5 HOH A 33 633 803 HOH HOH . H 5 HOH A 34 634 805 HOH HOH . H 5 HOH A 35 635 819 HOH HOH . H 5 HOH A 36 636 827 HOH HOH . H 5 HOH A 37 637 801 HOH HOH . H 5 HOH A 38 638 829 HOH HOH . H 5 HOH A 39 639 833 HOH HOH . H 5 HOH A 40 640 823 HOH HOH . H 5 HOH A 41 641 817 HOH HOH . H 5 HOH A 42 642 811 HOH HOH . H 5 HOH A 43 643 813 HOH HOH . H 5 HOH A 44 644 845 HOH HOH . H 5 HOH A 45 645 840 HOH HOH . H 5 HOH A 46 646 839 HOH HOH . H 5 HOH A 47 647 842 HOH HOH . H 5 HOH A 48 648 843 HOH HOH . H 5 HOH A 49 649 828 HOH HOH . H 5 HOH A 50 650 826 HOH HOH . H 5 HOH A 51 651 824 HOH HOH . H 5 HOH A 52 652 830 HOH HOH . H 5 HOH A 53 653 836 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O1 T93 . . . G 4 -14.343 35.554 -10.384 1 39.73 ? O1 T93 506 A 1 HETATM 2 P P2 T93 . . . G 4 -15.372 35.559 -9.28 1 40.81 ? P2 T93 506 A 1 HETATM 3 O O3 T93 . . . G 4 -15.231 36.772 -8.377 1 42.44 -1 O3 T93 506 A 1 HETATM 4 O O4 T93 . . . G 4 -16.721 35.599 -9.93 1 41.17 -1 O4 T93 506 A 1 HETATM 5 C C5 T93 . . . G 4 -15.175 34.011 -8.32 1 40.23 ? C5 T93 506 A 1 HETATM 6 P P6 T93 . . . G 4 -16.372 34.063 -6.912 1 42.04 ? P6 T93 506 A 1 HETATM 7 O O7 T93 . . . G 4 -16.131 35.26 -6.029 1 43.74 -1 O7 T93 506 A 1 HETATM 8 O O8 T93 . . . G 4 -16.242 32.772 -6.119 1 41.9 -1 O8 T93 506 A 1 HETATM 9 O O9 T93 . . . G 4 -17.74 34.157 -7.538 1 42.18 ? O9 T93 506 A 1 HETATM 10 N N10 T93 . . . G 4 -15.475 32.908 -9.24 1 38.9 ? N10 T93 506 A 1 HETATM 11 C C11 T93 . . . G 4 -15.12 31.565 -8.877 1 38.27 ? C11 T93 506 A 1 HETATM 12 N N12 T93 . . . G 4 -14.066 31.396 -8.042 1 38.67 ? N12 T93 506 A 1 HETATM 13 C C13 T93 . . . G 4 -13.733 30.137 -7.679 1 38.5 ? C13 T93 506 A 1 HETATM 14 C C14 T93 . . . G 4 -14.444 29.05 -8.161 1 37.84 ? C14 T93 506 A 1 HETATM 15 C C15 T93 . . . G 4 -15.482 29.215 -9.01 1 37.25 ? C15 T93 506 A 1 HETATM 16 O O16 T93 . . . G 4 -16.144 28.056 -9.466 1 36.66 ? O16 T93 506 A 1 HETATM 17 C C17 T93 . . . G 4 -17.298 28.166 -10.23 1 36.27 ? C17 T93 506 A 1 HETATM 18 C C18 T93 . . . G 4 -17.804 26.754 -10.476 1 35.89 ? C18 T93 506 A 1 HETATM 19 C C19 T93 . . . G 4 -19.123 26.796 -11.245 1 35.71 ? C19 T93 506 A 1 HETATM 20 C C20 T93 . . . G 4 -19.699 25.372 -11.251 1 35.58 ? C20 T93 506 A 1 HETATM 21 C C21 T93 . . . G 4 -19.139 24.607 -12.43 1 35.3 ? C21 T93 506 A 1 HETATM 22 C C22 T93 . . . G 4 -20.105 23.48 -12.746 1 35.49 ? C22 T93 506 A 1 HETATM 23 C C23 T93 . . . G 4 -15.837 30.47 -9.381 1 37.5 ? C23 T93 506 A 1 HETATM 24 H H051 T93 . . . G 4 -14.267 33.935 -7.988 1 18.68 ? H051 T93 506 A 1 HETATM 25 H H101 T93 . . . G 4 -15.862 33.065 -9.993 1 18.68 ? H101 T93 506 A 1 HETATM 26 H H131 T93 . . . G 4 -13.018 29.999 -7.101 1 18.68 ? H131 T93 506 A 1 HETATM 27 H H141 T93 . . . G 4 -14.189 28.19 -7.914 1 18.68 ? H141 T93 506 A 1 HETATM 28 H H171 T93 . . . G 4 -17.966 28.678 -9.748 1 18.68 ? H171 T93 506 A 1 HETATM 29 H H172 T93 . . . G 4 -17.096 28.597 -11.075 1 18.68 ? H172 T93 506 A 1 HETATM 30 H H182 T93 . . . G 4 -17.147 26.262 -10.992 1 18.68 ? H182 T93 506 A 1 HETATM 31 H H181 T93 . . . G 4 -17.943 26.31 -9.625 1 18.68 ? H181 T93 506 A 1 HETATM 32 H H192 T93 . . . G 4 -19.742 27.4 -10.805 1 18.68 ? H192 T93 506 A 1 HETATM 33 H H191 T93 . . . G 4 -18.965 27.091 -12.155 1 18.68 ? H191 T93 506 A 1 HETATM 34 H H202 T93 . . . G 4 -19.455 24.921 -10.427 1 18.68 ? H202 T93 506 A 1 HETATM 35 H H201 T93 . . . G 4 -20.665 25.414 -11.322 1 18.68 ? H201 T93 506 A 1 HETATM 36 H H212 T93 . . . G 4 -19.058 25.196 -13.196 1 18.68 ? H212 T93 506 A 1 HETATM 37 H H211 T93 . . . G 4 -18.27 24.242 -12.202 1 18.68 ? H211 T93 506 A 1 HETATM 38 H H223 T93 . . . G 4 -21.004 23.835 -12.819 1 18.68 ? H223 T93 506 A 1 HETATM 39 H H221 T93 . . . G 4 -20.074 22.819 -12.036 1 18.68 ? H221 T93 506 A 1 HETATM 40 H H222 T93 . . . G 4 -19.852 23.064 -13.586 1 18.68 ? H222 T93 506 A 1 HETATM 41 H H231 T93 . . . G 4 -16.555 30.603 -9.956 1 18.68 ? H231 T93 506 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 41 #