data_3ORM # _model_server_result.job_id 3rteOoNAz_kEguwV_DWbAQ _model_server_result.datetime_utc '2024-12-03 20:33:14' _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 3orm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":340}' # _entry.id 3ORM # _exptl.entry_id 3ORM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _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 90 _cell.angle_gamma 90 _cell.entry_id 3ORM _cell.length_a 40.458 _cell.length_b 51.076 _cell.length_c 134.746 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ORM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 2 _struct_asym.id B _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 159 A ASP 156 1_555 C MN MN . A MN 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc2 A OD1 ASP 159 A ASP 156 1_555 C MN MN . A MN 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc3 B O2B AGS . A AGS 340 1_555 C MN MN . A MN 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc4 B S1G AGS . A AGS 340 1_555 C MN MN . A MN 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? # _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 3ORM _atom_sites.fract_transf_matrix[1][1] 0.024717 _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] 0.019579 _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] 0.007421 _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 AGS A 1 340 340 AGS AGS . C 3 MN A 1 341 341 MN MN . D 4 HOH A 1 309 309 HOH HOH . D 4 HOH A 2 310 310 HOH HOH . D 4 HOH A 3 311 311 HOH HOH . D 4 HOH A 4 312 312 HOH HOH . D 4 HOH A 5 313 313 HOH HOH . D 4 HOH A 6 314 314 HOH HOH . D 4 HOH A 7 315 315 HOH HOH . D 4 HOH A 8 316 316 HOH HOH . D 4 HOH A 9 317 317 HOH HOH . D 4 HOH A 10 318 318 HOH HOH . D 4 HOH A 11 319 319 HOH HOH . D 4 HOH A 12 320 320 HOH HOH . D 4 HOH A 13 321 321 HOH HOH . D 4 HOH A 14 322 322 HOH HOH . D 4 HOH A 15 323 323 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 P PG AGS . . . B 2 1.769 11.56 9.297 1 56.05 ? PG AGS 340 A 1 HETATM 2 S S1G AGS . . . B 2 -0.211 11.203 9.382 1 50.35 ? S1G AGS 340 A 1 HETATM 3 O O2G AGS . . . B 2 2.344 10.641 8.264 1 52.7 ? O2G AGS 340 A 1 HETATM 4 O O3G AGS . . . B 2 2.407 11.262 10.675 1 58.47 ? O3G AGS 340 A 1 HETATM 5 P PB AGS . . . B 2 0.991 14.186 9.043 1 45.31 ? PB AGS 340 A 1 HETATM 6 O O1B AGS . . . B 2 0.124 14.189 7.747 1 58.4 ? O1B AGS 340 A 1 HETATM 7 O O2B AGS . . . B 2 0.1 13.952 10.229 1 42.85 ? O2B AGS 340 A 1 HETATM 8 O O3B AGS . . . B 2 2.069 13.056 8.911 1 65.88 ? O3B AGS 340 A 1 HETATM 9 P PA AGS . . . B 2 2.435 16.067 10.519 1 41.96 ? PA AGS 340 A 1 HETATM 10 O O1A AGS . . . B 2 1.451 16.674 11.559 1 45.65 ? O1A AGS 340 A 1 HETATM 11 O O2A AGS . . . B 2 3.229 14.979 11.194 1 58.53 ? O2A AGS 340 A 1 HETATM 12 O O3A AGS . . . B 2 1.711 15.583 9.195 1 74.57 ? O3A AGS 340 A 1 HETATM 13 O O5' AGS . . . B 2 3.429 17.174 10.051 1 46.37 ? O5' AGS 340 A 1 HETATM 14 C C5' AGS . . . B 2 4.335 16.845 9.045 1 51.61 ? C5' AGS 340 A 1 HETATM 15 C C4' AGS . . . B 2 5.515 17.777 8.961 1 53.48 ? C4' AGS 340 A 1 HETATM 16 O O4' AGS . . . B 2 5.421 19.214 8.712 1 47.05 ? O4' AGS 340 A 1 HETATM 17 C C3' AGS . . . B 2 6.909 17.473 9.514 1 55.86 ? C3' AGS 340 A 1 HETATM 18 O O3' AGS . . . B 2 7.298 16.304 10.133 1 58.19 ? O3' AGS 340 A 1 HETATM 19 C C2' AGS . . . B 2 7.54 18.837 9.678 1 52.54 ? C2' AGS 340 A 1 HETATM 20 O O2' AGS . . . B 2 8.876 19.133 9.45 1 50.82 ? O2' AGS 340 A 1 HETATM 21 C C1' AGS . . . B 2 6.355 19.824 9.651 1 52.26 ? C1' AGS 340 A 1 HETATM 22 N N9 AGS . . . B 2 5.618 20.371 10.784 1 57.6 ? N9 AGS 340 A 1 HETATM 23 C C8 AGS . . . B 2 4.531 19.816 11.313 1 53.66 ? C8 AGS 340 A 1 HETATM 24 N N7 AGS . . . B 2 4.103 20.612 12.367 1 53.07 ? N7 AGS 340 A 1 HETATM 25 C C5 AGS . . . B 2 4.956 21.673 12.462 1 56.36 ? C5 AGS 340 A 1 HETATM 26 C C6 AGS . . . B 2 4.987 22.743 13.318 1 50.69 ? C6 AGS 340 A 1 HETATM 27 N N6 AGS . . . B 2 3.995 22.853 14.341 1 36.34 ? N6 AGS 340 A 1 HETATM 28 N N1 AGS . . . B 2 5.944 23.662 13.201 1 55.96 ? N1 AGS 340 A 1 HETATM 29 C C2 AGS . . . B 2 6.885 23.542 12.237 1 57.74 ? C2 AGS 340 A 1 HETATM 30 N N3 AGS . . . B 2 6.855 22.476 11.386 1 61.84 ? N3 AGS 340 A 1 HETATM 31 C C4 AGS . . . B 2 5.893 21.554 11.501 1 60.67 ? C4 AGS 340 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #