data_5LPB # _model_server_result.job_id JQUbBUZLouy1K7-HFAUxeA _model_server_result.datetime_utc '2024-11-23 05:33:24' _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 5lpb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1201}' # _entry.id 5LPB # _exptl.entry_id 5LPB _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 5LPB _cell.length_a 116.141 _cell.length_b 116.141 _cell.length_c 49.743 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LPB _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C TPO 175 A TPO 1039 1_555 A N HIS 176 A HIS 1040 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C LEU 177 A LEU 1041 1_555 A N SEP 178 A SEP 1042 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 A C SEP 178 A SEP 1042 1_555 A N VAL 179 A VAL 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 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 ? covale ? covale7 A C GLN 195 A GLN 1059 1_555 A N SEP 196 A SEP 1060 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 A C SEP 196 A SEP 1060 1_555 A N PHE 197 A PHE 1061 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _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 5LPB _atom_sites.fract_transf_matrix[1][1] 0.00861 _atom_sites.fract_transf_matrix[1][2] 0.004971 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009942 _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] 0.020103 _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 1201 1201 ADP ADP . C 3 HOH A 1 1301 1309 HOH HOH . C 3 HOH A 2 1302 1313 HOH HOH . C 3 HOH A 3 1303 1325 HOH HOH . C 3 HOH A 4 1304 1307 HOH HOH . C 3 HOH A 5 1305 1317 HOH HOH . C 3 HOH A 6 1306 1308 HOH HOH . C 3 HOH A 7 1307 1303 HOH HOH . C 3 HOH A 8 1308 1304 HOH HOH . C 3 HOH A 9 1309 1323 HOH HOH . C 3 HOH A 10 1310 1302 HOH HOH . C 3 HOH A 11 1311 1301 HOH HOH . C 3 HOH A 12 1312 1305 HOH HOH . C 3 HOH A 13 1313 1319 HOH HOH . C 3 HOH A 14 1314 1316 HOH HOH . C 3 HOH A 15 1315 1321 HOH HOH . C 3 HOH A 16 1316 1315 HOH HOH . C 3 HOH A 17 1317 1322 HOH HOH . C 3 HOH A 18 1318 1306 HOH HOH . C 3 HOH A 19 1319 1318 HOH HOH . C 3 HOH A 20 1320 1320 HOH HOH . C 3 HOH A 21 1321 1310 HOH HOH . C 3 HOH A 22 1322 1324 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 PA ADP . . . B 2 37.772 32.287 19.902 1 146.75 ? PA ADP 1201 A 1 HETATM 2 O O5' ADP . . . B 2 37.335 31.895 21.403 1 104.53 ? O5' ADP 1201 A 1 HETATM 3 C C5' ADP . . . B 2 38.019 32.434 22.534 1 103.28 ? C5' ADP 1201 A 1 HETATM 4 C C4' ADP . . . B 2 37.361 31.958 23.827 1 103.84 ? C4' ADP 1201 A 1 HETATM 5 O O4' ADP . . . B 2 36.04 32.504 23.955 1 105.55 ? O4' ADP 1201 A 1 HETATM 6 C C3' ADP . . . B 2 37.206 30.445 23.876 1 101.33 ? C3' ADP 1201 A 1 HETATM 7 O O3' ADP . . . B 2 38.309 29.804 24.53 1 103.74 ? O3' ADP 1201 A 1 HETATM 8 C C2' ADP . . . B 2 35.902 30.231 24.622 1 94.58 ? C2' ADP 1201 A 1 HETATM 9 O O2' ADP . . . B 2 36.142 29.979 26.01 1 98.68 ? O2' ADP 1201 A 1 HETATM 10 C C1' ADP . . . B 2 35.119 31.524 24.445 1 86.41 ? C1' ADP 1201 A 1 HETATM 11 N N9 ADP . . . B 2 34.124 31.206 23.397 1 66.09 ? N9 ADP 1201 A 1 HETATM 12 C C8 ADP . . . B 2 34.303 31.389 22.073 1 63.26 ? C8 ADP 1201 A 1 HETATM 13 N N7 ADP . . . B 2 33.22 30.976 21.366 1 63.86 ? N7 ADP 1201 A 1 HETATM 14 C C5 ADP . . . B 2 32.325 30.503 22.257 1 56.68 ? C5 ADP 1201 A 1 HETATM 15 C C6 ADP . . . B 2 30.975 29.91 22.181 1 52.47 ? C6 ADP 1201 A 1 HETATM 16 N N6 ADP . . . B 2 30.362 29.743 20.982 1 58.39 ? N6 ADP 1201 A 1 HETATM 17 N N1 ADP . . . B 2 30.38 29.554 23.34 1 61.99 ? N1 ADP 1201 A 1 HETATM 18 C C2 ADP . . . B 2 30.986 29.715 24.532 1 63.44 ? C2 ADP 1201 A 1 HETATM 19 N N3 ADP . . . B 2 32.217 30.242 24.672 1 69.43 ? N3 ADP 1201 A 1 HETATM 20 C C4 ADP . . . B 2 32.925 30.65 23.592 1 63.28 ? C4 ADP 1201 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #