data_3U9D # _model_server_result.job_id Y3EkuICSuTyZ-dTaum9dNA _model_server_result.datetime_utc '2024-11-28 22:10:48' _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 3u9d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 3U9D # _exptl.entry_id 3U9D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 90.03 _cell.angle_gamma 90 _cell.entry_id 3U9D _cell.length_a 45.698 _cell.length_b 75.738 _cell.length_c 128.518 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U9D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F 1 1 C,D,G,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 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 E O1B ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc2 E O3G ATP . A ATP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc3 C OD1 ASP 11 C ASP 11 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? metalc ? metalc4 G O3G ATP . C ATP 501 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc5 G O1B ATP . C ATP 501 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc6 G O1G ATP . C ATP 501 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 3U9D _atom_sites.fract_transf_matrix[1][1] 0.021883 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000011 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013203 _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] 0.007781 _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 E 3 ATP A 1 501 501 ATP ATP . F 4 MG A 1 502 502 MG MG . G 3 ATP C 1 501 501 ATP ATP . H 4 MG C 1 502 502 MG MG . # 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 ATP . . . E 3 -14.398 3.004 -13.744 1 34.5 ? PG ATP 501 A 1 HETATM 2 O O1G ATP . . . E 3 -13.945 2.553 -15.122 1 35.17 ? O1G ATP 501 A 1 HETATM 3 O O2G ATP . . . E 3 -15.891 3.232 -13.611 1 35.11 ? O2G ATP 501 A 1 HETATM 4 O O3G ATP . . . E 3 -13.685 2.272 -12.629 1 36.1 ? O3G ATP 501 A 1 HETATM 5 P PB ATP . . . E 3 -12.359 4.586 -14.364 1 22.37 ? PB ATP 501 A 1 HETATM 6 O O1B ATP . . . E 3 -11.407 3.58 -13.763 1 23.38 ? O1B ATP 501 A 1 HETATM 7 O O2B ATP . . . E 3 -12.645 4.511 -15.839 1 24.75 ? O2B ATP 501 A 1 HETATM 8 O O3B ATP . . . E 3 -13.752 4.438 -13.592 1 26.65 ? O3B ATP 501 A 1 HETATM 9 P PA ATP . . . E 3 -10.892 6.992 -13.534 1 20.2 ? PA ATP 501 A 1 HETATM 10 O O1A ATP . . . E 3 -10.419 6.695 -12.159 1 19.08 ? O1A ATP 501 A 1 HETATM 11 O O2A ATP . . . E 3 -9.93 6.946 -14.708 1 21.33 ? O2A ATP 501 A 1 HETATM 12 O O3A ATP . . . E 3 -12.198 6.118 -13.866 1 22.05 ? O3A ATP 501 A 1 HETATM 13 O O5' ATP . . . E 3 -11.551 8.477 -13.466 1 22.3 ? O5' ATP 501 A 1 HETATM 14 C C5' ATP . . . E 3 -12.28 9.054 -14.558 1 22.87 ? C5' ATP 501 A 1 HETATM 15 C C4' ATP . . . E 3 -13.428 9.878 -13.978 1 23.87 ? C4' ATP 501 A 1 HETATM 16 O O4' ATP . . . E 3 -12.904 10.737 -12.978 1 24.84 ? O4' ATP 501 A 1 HETATM 17 C C3' ATP . . . E 3 -14.113 10.784 -14.983 1 24.98 ? C3' ATP 501 A 1 HETATM 18 O O3' ATP . . . E 3 -15.505 10.727 -14.703 1 26.97 ? O3' ATP 501 A 1 HETATM 19 C C2' ATP . . . E 3 -13.647 12.2 -14.695 1 24.16 ? C2' ATP 501 A 1 HETATM 20 O O2' ATP . . . E 3 -14.71 13.149 -14.782 1 21.66 ? O2' ATP 501 A 1 HETATM 21 C C1' ATP . . . E 3 -13.131 12.123 -13.269 1 23.65 ? C1' ATP 501 A 1 HETATM 22 N N9 ATP . . . E 3 -11.907 12.966 -13.22 1 21.62 ? N9 ATP 501 A 1 HETATM 23 C C8 ATP . . . E 3 -10.862 12.882 -14.059 1 20.99 ? C8 ATP 501 A 1 HETATM 24 N N7 ATP . . . E 3 -9.923 13.835 -13.766 1 20.5 ? N7 ATP 501 A 1 HETATM 25 C C5 ATP . . . E 3 -10.386 14.54 -12.724 1 20.67 ? C5 ATP 501 A 1 HETATM 26 C C6 ATP . . . E 3 -9.896 15.676 -11.921 1 22.05 ? C6 ATP 501 A 1 HETATM 27 N N6 ATP . . . E 3 -8.687 16.251 -12.183 1 22.26 ? N6 ATP 501 A 1 HETATM 28 N N1 ATP . . . E 3 -10.697 16.12 -10.934 1 21.19 ? N1 ATP 501 A 1 HETATM 29 C C2 ATP . . . E 3 -11.878 15.545 -10.671 1 20.57 ? C2 ATP 501 A 1 HETATM 30 N N3 ATP . . . E 3 -12.374 14.514 -11.359 1 20.11 ? N3 ATP 501 A 1 HETATM 31 C C4 ATP . . . E 3 -11.693 13.977 -12.38 1 19.96 ? C4 ATP 501 A 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #