data_5LPZ # _model_server_result.job_id ttItX45dJFkb3bB5yNUVuA _model_server_result.datetime_utc '2024-12-03 17:48:59' _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 5lpz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1200}' # _entry.id 5LPZ # _exptl.entry_id 5LPZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 5LPZ _cell.length_a 116.833 _cell.length_b 116.833 _cell.length_c 50.558 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LPZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _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 _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 covale ? covale1 A C ASP 174 A ASP 1038 1_555 A N TPO 175 A TPO 1039 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C TPO 175 A TPO 1039 1_555 A N HIS 176 A HIS 1040 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C LEU 177 A LEU 1041 1_555 A N SEP 178 A SEP 1042 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C SEP 178 A SEP 1042 1_555 A N VAL 179 A VAL 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C VAL 179 A VAL 1043 1_555 A N SEP 180 A SEP 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C SEP 180 A SEP 1044 1_555 A N THR 181 A THR 1045 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 5LPZ _atom_sites.fract_transf_matrix[1][1] 0.008559 _atom_sites.fract_transf_matrix[1][2] 0.004942 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009883 _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] 0.019779 _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 ADP A 1 1200 1200 ADP ADP . C 3 HOH A 1 1301 5 HOH HOH . C 3 HOH A 2 1302 12 HOH HOH . C 3 HOH A 3 1303 2 HOH HOH . C 3 HOH A 4 1304 16 HOH HOH . C 3 HOH A 5 1305 15 HOH HOH . C 3 HOH A 6 1306 1 HOH HOH . C 3 HOH A 7 1307 8 HOH HOH . C 3 HOH A 8 1308 4 HOH HOH . C 3 HOH A 9 1309 11 HOH HOH . C 3 HOH A 10 1310 9 HOH HOH . C 3 HOH A 11 1311 18 HOH HOH . C 3 HOH A 12 1312 3 HOH HOH . C 3 HOH A 13 1313 14 HOH HOH . C 3 HOH A 14 1314 6 HOH HOH . C 3 HOH A 15 1315 7 HOH HOH . C 3 HOH A 16 1316 10 HOH HOH . C 3 HOH A 17 1317 13 HOH HOH . C 3 HOH A 18 1318 19 HOH HOH . C 3 HOH A 19 1319 17 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 PB ADP . . . B 2 40.484 30.87 20.832 1 190.71 ? PB ADP 1200 A 1 HETATM 2 O O1B ADP . . . B 2 39.411 30.331 19.916 1 193 ? O1B ADP 1200 A 1 HETATM 3 O O2B ADP . . . B 2 41.338 29.815 21.492 1 193.05 ? O2B ADP 1200 A 1 HETATM 4 O O3B ADP . . . B 2 41.274 32.044 20.295 1 193.14 ? O3B ADP 1200 A 1 HETATM 5 P PA ADP . . . B 2 38.732 32.811 21.857 1 171.12 ? PA ADP 1200 A 1 HETATM 6 O O1A ADP . . . B 2 37.987 32.741 20.544 1 173.81 ? O1A ADP 1200 A 1 HETATM 7 O O2A ADP . . . B 2 39.572 34.023 22.187 1 175.7 ? O2A ADP 1200 A 1 HETATM 8 O O3A ADP . . . B 2 39.64 31.495 22.047 1 182.91 ? O3A ADP 1200 A 1 HETATM 9 O O5' ADP . . . B 2 37.669 32.6 23.042 1 155.51 ? O5' ADP 1200 A 1 HETATM 10 C C5' ADP . . . B 2 37.543 33.532 24.11 1 136.4 ? C5' ADP 1200 A 1 HETATM 11 C C4' ADP . . . B 2 36.775 32.817 25.209 1 117.36 ? C4' ADP 1200 A 1 HETATM 12 O O4' ADP . . . B 2 35.388 32.802 24.874 1 106.15 ? O4' ADP 1200 A 1 HETATM 13 C C3' ADP . . . B 2 37.242 31.373 25.317 1 109.7 ? C3' ADP 1200 A 1 HETATM 14 O O3' ADP . . . B 2 37.771 31.126 26.622 1 110.05 ? O3' ADP 1200 A 1 HETATM 15 C C2' ADP . . . B 2 36.019 30.51 25.077 1 101.86 ? C2' ADP 1200 A 1 HETATM 16 O O2' ADP . . . B 2 35.823 29.603 26.167 1 101.07 ? O2' ADP 1200 A 1 HETATM 17 C C1' ADP . . . B 2 34.852 31.481 24.962 1 94.74 ? C1' ADP 1200 A 1 HETATM 18 N N9 ADP . . . B 2 34.081 31.18 23.734 1 75.89 ? N9 ADP 1200 A 1 HETATM 19 C C8 ADP . . . B 2 34.474 31.43 22.472 1 69.43 ? C8 ADP 1200 A 1 HETATM 20 N N7 ADP . . . B 2 33.536 31.029 21.577 1 63.84 ? N7 ADP 1200 A 1 HETATM 21 C C5 ADP . . . B 2 32.516 30.509 22.279 1 61.17 ? C5 ADP 1200 A 1 HETATM 22 C C6 ADP . . . B 2 31.208 29.903 21.963 1 56.02 ? C6 ADP 1200 A 1 HETATM 23 N N6 ADP . . . B 2 30.793 29.766 20.681 1 53.79 ? N6 ADP 1200 A 1 HETATM 24 N N1 ADP . . . B 2 30.446 29.488 22.996 1 55.11 ? N1 ADP 1200 A 1 HETATM 25 C C2 ADP . . . B 2 30.848 29.614 24.274 1 56.72 ? C2 ADP 1200 A 1 HETATM 26 N N3 ADP . . . B 2 32.019 30.153 24.635 1 60.23 ? N3 ADP 1200 A 1 HETATM 27 C C4 ADP . . . B 2 32.88 30.608 23.698 1 65.16 ? C4 ADP 1200 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #