data_1D9Z # _model_server_result.job_id gvz-saz8Kew_LQ8HyJNtHQ _model_server_result.datetime_utc '2024-10-19 09:18:03' _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 1d9z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":700}' # _entry.id 1D9Z # _exptl.entry_id 1D9Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 1D9Z _cell.length_a 153.443 _cell.length_b 153.443 _cell.length_c 80.741 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D9Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 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 _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 NE2 HIS 402 A HIS 403 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc2 A NE2 HIS 580 A HIS 581 1_555 D ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc3 E O1B ATP . A ATP 700 1_555 B MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? # _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 1D9Z _atom_sites.fract_transf_matrix[1][1] 0.00652 _atom_sites.fract_transf_matrix[1][2] 0.00376 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00753 _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] 0.01239 _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 MG A 1 703 703 MG WAT . C 3 ZN A 1 701 701 ZN WAT . D 3 ZN A 1 702 702 ZN WAT . E 4 ATP A 1 700 700 ATP ATP . # 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 4 46.238 40.973 66.6 1 100.89 ? PG ATP 700 A 1 HETATM 2 O O1G ATP . . . E 4 45.557 40.728 67.877 1 100.89 ? O1G ATP 700 A 1 HETATM 3 O O2G ATP . . . E 4 47.425 41.85 66.735 1 100.45 ? O2G ATP 700 A 1 HETATM 4 O O3G ATP . . . E 4 46.652 39.676 65.976 1 100.89 ? O3G ATP 700 A 1 HETATM 5 P PB ATP . . . E 4 45.599 41.938 64.095 1 98.96 ? PB ATP 700 A 1 HETATM 6 O O1B ATP . . . E 4 46.402 40.83 63.48 1 100.89 ? O1B ATP 700 A 1 HETATM 7 O O2B ATP . . . E 4 46.217 43.246 63.903 1 98.43 ? O2B ATP 700 A 1 HETATM 8 O O3B ATP . . . E 4 45.164 41.626 65.584 1 100.24 ? O3B ATP 700 A 1 HETATM 9 P PA ATP . . . E 4 44.401 42.139 61.743 1 100.67 ? PA ATP 700 A 1 HETATM 10 O O1A ATP . . . E 4 45.556 43.023 61.501 1 100.89 ? O1A ATP 700 A 1 HETATM 11 O O2A ATP . . . E 4 44.565 40.829 61.084 1 100.29 ? O2A ATP 700 A 1 HETATM 12 O O3A ATP . . . E 4 44.194 41.934 63.343 1 98.85 ? O3A ATP 700 A 1 HETATM 13 O O5' ATP . . . E 4 42.946 42.749 61.636 1 100.89 ? O5' ATP 700 A 1 HETATM 14 C C5' ATP . . . E 4 41.847 42.078 62.299 1 99.43 ? C5' ATP 700 A 1 HETATM 15 C C4' ATP . . . E 4 40.575 42.419 61.548 1 100.44 ? C4' ATP 700 A 1 HETATM 16 O O4' ATP . . . E 4 40.504 43.771 61.061 1 100.89 ? O4' ATP 700 A 1 HETATM 17 C C3' ATP . . . E 4 40.018 41.559 60.437 1 100.34 ? C3' ATP 700 A 1 HETATM 18 O O3' ATP . . . E 4 38.742 40.982 60.788 1 99.67 ? O3' ATP 700 A 1 HETATM 19 C C2' ATP . . . E 4 40.017 42.532 59.231 1 99.82 ? C2' ATP 700 A 1 HETATM 20 O O2' ATP . . . E 4 38.93 42.256 58.329 1 99.73 ? O2' ATP 700 A 1 HETATM 21 C C1' ATP . . . E 4 39.789 43.907 59.875 1 98.61 ? C1' ATP 700 A 1 HETATM 22 N N9 ATP . . . E 4 39.961 45.074 59.03 1 94.02 ? N9 ATP 700 A 1 HETATM 23 C C8 ATP . . . E 4 41.125 45.758 58.867 1 93.3 ? C8 ATP 700 A 1 HETATM 24 N N7 ATP . . . E 4 41.154 46.88 58.253 1 90.52 ? N7 ATP 700 A 1 HETATM 25 C C5 ATP . . . E 4 39.889 47.025 57.93 1 87.24 ? C5 ATP 700 A 1 HETATM 26 C C6 ATP . . . E 4 39.349 48.087 57.239 1 82.58 ? C6 ATP 700 A 1 HETATM 27 N N6 ATP . . . E 4 40.06 49.123 56.793 1 73.63 ? N6 ATP 700 A 1 HETATM 28 N N1 ATP . . . E 4 38.019 47.994 57.024 1 83.02 ? N1 ATP 700 A 1 HETATM 29 C C2 ATP . . . E 4 37.313 46.898 57.497 1 83.82 ? C2 ATP 700 A 1 HETATM 30 N N3 ATP . . . E 4 37.766 45.858 58.156 1 86.99 ? N3 ATP 700 A 1 HETATM 31 C C4 ATP . . . E 4 39.102 45.963 58.365 1 89.92 ? C4 ATP 700 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #