data_4J9V # _model_server_result.job_id 0lrA4RI3yj9DR6UdloWo6g _model_server_result.datetime_utc '2025-03-04 23:22:39' _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 4j9v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4J9V # _exptl.entry_id 4J9V _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 4 _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 120 _cell.entry_id 4J9V _cell.length_a 109.324 _cell.length_b 109.324 _cell.length_c 337.656 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J9V _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_444 -y-1,-x-1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -54.662 -94.677361 -56.276 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 F N N ? 2 G 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 GLN 84 A GLN 84 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc2 A O ALA 116 A ALA 116 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc3 B OE1 GLN 84 B GLN 84 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc4 B O ALA 116 B ALA 116 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? # _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 4J9V _atom_sites.fract_transf_matrix[1][1] 0.009147 _atom_sites.fract_transf_matrix[1][2] 0.005281 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010562 _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] 0.002962 _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 C 2 AGS A 1 501 1 AGS AGS . D 2 AGS A 1 502 1 AGS AGS . E 3 MG B 1 501 1 MG MG . F 2 AGS B 1 502 1 AGS AGS . G 2 AGS B 1 503 1 AGS AGS . H 4 SO4 B 1 504 1 SO4 SO4 . I 3 MG B 1 505 1 MG MG . J 5 HOH A 1 601 2 HOH HOH . J 5 HOH A 2 602 14 HOH HOH . J 5 HOH A 3 603 15 HOH HOH . J 5 HOH A 4 604 17 HOH HOH . J 5 HOH A 5 605 18 HOH HOH . K 5 HOH B 1 601 1 HOH HOH . K 5 HOH B 2 602 3 HOH HOH . K 5 HOH B 3 603 4 HOH HOH . K 5 HOH B 4 604 8 HOH HOH . K 5 HOH B 5 605 20 HOH HOH . K 5 HOH B 6 606 21 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 . . . C 2 -42.944 -32.629 -13.218 1 52.4 ? PG AGS 501 A 1 HETATM 2 S S1G AGS . . . C 2 -44.044 -34.033 -14.3 1 70.28 ? S1G AGS 501 A 1 HETATM 3 O O2G AGS . . . C 2 -41.404 -32.719 -13.682 1 24.53 ? O2G AGS 501 A 1 HETATM 4 O O3G AGS . . . C 2 -43.022 -32.859 -11.764 1 47.99 ? O3G AGS 501 A 1 HETATM 5 P PB AGS . . . C 2 -44.4 -30.838 -14.855 1 67 ? PB AGS 501 A 1 HETATM 6 O O1B AGS . . . C 2 -43.822 -29.538 -15.353 1 73.48 ? O1B AGS 501 A 1 HETATM 7 O O2B AGS . . . C 2 -44.494 -32.019 -15.791 1 65.61 ? O2B AGS 501 A 1 HETATM 8 O O3B AGS . . . C 2 -43.538 -31.173 -13.532 1 70.43 ? O3B AGS 501 A 1 HETATM 9 P PA AGS . . . C 2 -47.049 -31.597 -14.173 1 66.43 ? PA AGS 501 A 1 HETATM 10 O O1A AGS . . . C 2 -48.241 -31.201 -15.018 1 66.91 ? O1A AGS 501 A 1 HETATM 11 O O2A AGS . . . C 2 -46.453 -32.986 -14.289 1 62.79 ? O2A AGS 501 A 1 HETATM 12 O O3A AGS . . . C 2 -45.877 -30.497 -14.312 1 80.06 ? O3A AGS 501 A 1 HETATM 13 O O5' AGS . . . C 2 -47.458 -31.303 -12.639 1 72.74 ? O5' AGS 501 A 1 HETATM 14 C C5' AGS . . . C 2 -46.819 -31.909 -11.517 1 68.29 ? C5' AGS 501 A 1 HETATM 15 C C4' AGS . . . C 2 -47.921 -32.444 -10.614 1 63.1 ? C4' AGS 501 A 1 HETATM 16 O O4' AGS . . . C 2 -48.624 -31.42 -9.91 1 60.48 ? O4' AGS 501 A 1 HETATM 17 C C3' AGS . . . C 2 -48.936 -33.151 -11.484 1 62.5 ? C3' AGS 501 A 1 HETATM 18 O O3' AGS . . . C 2 -48.933 -34.534 -11.127 1 66.98 ? O3' AGS 501 A 1 HETATM 19 C C2' AGS . . . C 2 -50.275 -32.481 -11.234 1 58.47 ? C2' AGS 501 A 1 HETATM 20 O O2' AGS . . . C 2 -51.305 -33.433 -10.973 1 56.85 ? O2' AGS 501 A 1 HETATM 21 C C1' AGS . . . C 2 -50.038 -31.598 -10.026 1 59.38 ? C1' AGS 501 A 1 HETATM 22 N N9 AGS . . . C 2 -50.635 -30.261 -10.225 1 63.7 ? N9 AGS 501 A 1 HETATM 23 C C8 AGS . . . C 2 -50.527 -29.547 -11.352 1 69.4 ? C8 AGS 501 A 1 HETATM 24 N N7 AGS . . . C 2 -51.159 -28.359 -11.244 1 67.74 ? N7 AGS 501 A 1 HETATM 25 C C5 AGS . . . C 2 -51.689 -28.299 -10.017 1 64.28 ? C5 AGS 501 A 1 HETATM 26 C C6 AGS . . . C 2 -52.485 -27.31 -9.266 1 67.46 ? C6 AGS 501 A 1 HETATM 27 N N6 AGS . . . C 2 -52.836 -26.129 -9.831 1 72.36 ? N6 AGS 501 A 1 HETATM 28 N N1 AGS . . . C 2 -52.837 -27.628 -8.008 1 63.34 ? N1 AGS 501 A 1 HETATM 29 C C2 AGS . . . C 2 -52.485 -28.799 -7.447 1 62.99 ? C2 AGS 501 A 1 HETATM 30 N N3 AGS . . . C 2 -51.764 -29.743 -8.071 1 64.9 ? N3 AGS 501 A 1 HETATM 31 C C4 AGS . . . C 2 -51.343 -29.554 -9.343 1 63.42 ? C4 AGS 501 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #