data_1OYY # _model_server_result.job_id ljmQIi9OlMeOCvuZSRuWhg _model_server_result.datetime_utc '2025-01-19 21:53:40' _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 1oyy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":527}' # _entry.id 1OYY # _exptl.entry_id 1OYY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 110.78 _cell.angle_gamma 90 _cell.entry_id 1OYY _cell.length_a 66.591 _cell.length_b 54.534 _cell.length_c 78.686 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1OYY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 E _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 OE2 GLU 10 A GLU 10 1_555 C MN MN . A MN 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc2 A OE1 GLU 10 A GLU 10 1_555 C MN MN . A MN 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc3 A OD2 ASP 35 A ASP 35 1_555 C MN MN . A MN 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc4 A SG CYS 380 A CYS 380 1_555 B ZN ZN . A ZN 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc5 A SG CYS 397 A CYS 397 1_555 B ZN ZN . A ZN 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc6 A SG CYS 400 A CYS 400 1_555 B ZN ZN . A ZN 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc7 A SG CYS 403 A CYS 403 1_555 B ZN ZN . A ZN 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc8 D MN MN . A MN 526 1_555 E O2B AGS . A AGS 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc9 D MN MN . A MN 526 1_555 F O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc10 D MN MN . A MN 526 1_555 F O HOH . A HOH 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc11 D MN MN . A MN 526 1_555 F O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 PG S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 1OYY _atom_sites.fract_transf_matrix[1][1] 0.015017 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005698 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018337 _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] 0.013593 _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 ZN A 1 524 101 ZN ZN . C 3 MN A 1 525 102 MN MN . D 3 MN A 1 526 103 MN MN . E 4 AGS A 1 527 104 AGS AGS . F 5 HOH A 1 528 1 HOH WAT . F 5 HOH A 2 529 2 HOH WAT . F 5 HOH A 3 530 3 HOH WAT . F 5 HOH A 4 531 4 HOH WAT . F 5 HOH A 5 532 5 HOH WAT . F 5 HOH A 6 533 6 HOH WAT . F 5 HOH A 7 534 7 HOH WAT . F 5 HOH A 8 535 8 HOH WAT . F 5 HOH A 9 536 9 HOH WAT . F 5 HOH A 10 537 10 HOH WAT . F 5 HOH A 11 538 11 HOH WAT . F 5 HOH A 12 539 12 HOH WAT . F 5 HOH A 13 540 13 HOH WAT . F 5 HOH A 14 541 14 HOH WAT . F 5 HOH A 15 542 15 HOH WAT . F 5 HOH A 16 543 16 HOH WAT . F 5 HOH A 17 544 17 HOH WAT . F 5 HOH A 18 545 18 HOH WAT . F 5 HOH A 19 546 19 HOH WAT . F 5 HOH A 20 547 20 HOH WAT . F 5 HOH A 21 548 21 HOH WAT . F 5 HOH A 22 549 22 HOH WAT . F 5 HOH A 23 550 23 HOH WAT . F 5 HOH A 24 551 24 HOH WAT . F 5 HOH A 25 552 25 HOH WAT . F 5 HOH A 26 553 26 HOH WAT . F 5 HOH A 27 554 27 HOH WAT . F 5 HOH A 28 555 28 HOH WAT . F 5 HOH A 29 556 29 HOH WAT . F 5 HOH A 30 557 30 HOH WAT . F 5 HOH A 31 558 31 HOH WAT . F 5 HOH A 32 559 32 HOH WAT . F 5 HOH A 33 560 33 HOH WAT . F 5 HOH A 34 561 34 HOH WAT . F 5 HOH A 35 562 35 HOH WAT . F 5 HOH A 36 563 36 HOH WAT . F 5 HOH A 37 564 37 HOH WAT . F 5 HOH A 38 565 39 HOH WAT . F 5 HOH A 39 566 40 HOH WAT . F 5 HOH A 40 567 41 HOH WAT . F 5 HOH A 41 568 42 HOH WAT . F 5 HOH A 42 569 43 HOH WAT . F 5 HOH A 43 570 44 HOH WAT . # 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 P PG AGS . . . E 4 12.695 -6.201 16.674 1 94.77 ? PG AGS 527 A 1 HETATM 2 S S1G AGS . . . E 4 13.362 -6.11 18.003 1 94.6 ? S1G AGS 527 A 1 HETATM 3 O O2G AGS . . . E 4 11.26 -5.908 16.867 1 86.74 ? O2G AGS 527 A 1 HETATM 4 O O3G AGS . . . E 4 13.218 -5.103 15.803 1 98.54 ? O3G AGS 527 A 1 HETATM 5 P PB AGS . . . E 4 13.16 -8.478 14.744 1 69.84 ? PB AGS 527 A 1 HETATM 6 O O1B AGS . . . E 4 11.894 -9.142 14.41 1 75.01 ? O1B AGS 527 A 1 HETATM 7 O O2B AGS . . . E 4 13.721 -7.952 13.486 1 76.13 ? O2B AGS 527 A 1 HETATM 8 O O3B AGS . . . E 4 13.099 -7.593 16.043 1 81.72 ? O3B AGS 527 A 1 HETATM 9 P PA AGS . . . E 4 15.305 -10.366 14.242 1 73.17 ? PA AGS 527 A 1 HETATM 10 O O1A AGS . . . E 4 15.124 -10.008 12.82 1 65.11 ? O1A AGS 527 A 1 HETATM 11 O O2A AGS . . . E 4 16.695 -10.173 14.706 1 68.31 ? O2A AGS 527 A 1 HETATM 12 O O3A AGS . . . E 4 14.277 -9.549 15.201 1 78.17 ? O3A AGS 527 A 1 HETATM 13 O O5' AGS . . . E 4 14.814 -11.838 14.598 1 51.16 ? O5' AGS 527 A 1 HETATM 14 C C5' AGS . . . E 4 15.08 -12.222 15.963 1 66.43 ? C5' AGS 527 A 1 HETATM 15 C C4' AGS . . . E 4 15.34 -13.666 16.203 1 64.44 ? C4' AGS 527 A 1 HETATM 16 O O4' AGS . . . E 4 14.503 -14.571 15.468 1 68.48 ? O4' AGS 527 A 1 HETATM 17 C C3' AGS . . . E 4 16.768 -14.168 16.026 1 65.09 ? C3' AGS 527 A 1 HETATM 18 O O3' AGS . . . E 4 16.918 -15.151 17.104 1 73.74 ? O3' AGS 527 A 1 HETATM 19 C C2' AGS . . . E 4 16.677 -14.944 14.709 1 67.76 ? C2' AGS 527 A 1 HETATM 20 O O2' AGS . . . E 4 17.273 -14.711 13.467 1 66.94 ? O2' AGS 527 A 1 HETATM 21 C C1' AGS . . . E 4 15.298 -15.543 14.856 1 66 ? C1' AGS 527 A 1 HETATM 22 N N9 AGS . . . E 4 14.764 -16.099 13.64 1 62.1 ? N9 AGS 527 A 1 HETATM 23 C C8 AGS . . . E 4 14.312 -15.398 12.565 1 56.79 ? C8 AGS 527 A 1 HETATM 24 N N7 AGS . . . E 4 13.507 -15.997 11.794 1 52.14 ? N7 AGS 527 A 1 HETATM 25 C C5 AGS . . . E 4 13.387 -17.191 12.324 1 60.99 ? C5 AGS 527 A 1 HETATM 26 C C6 AGS . . . E 4 12.657 -18.276 11.905 1 61.6 ? C6 AGS 527 A 1 HETATM 27 N N6 AGS . . . E 4 11.87 -18.384 10.843 1 63.69 ? N6 AGS 527 A 1 HETATM 28 N N1 AGS . . . E 4 12.731 -19.383 12.68 1 65.74 ? N1 AGS 527 A 1 HETATM 29 C C2 AGS . . . E 4 13.514 -19.361 13.814 1 65.22 ? C2 AGS 527 A 1 HETATM 30 N N3 AGS . . . E 4 14.27 -18.384 14.271 1 66.84 ? N3 AGS 527 A 1 HETATM 31 C C4 AGS . . . E 4 14.149 -17.319 13.468 1 60.78 ? C4 AGS 527 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #