data_5HLE # _model_server_result.job_id j6lAA_EVF7AKWdpHgHxC0A _model_server_result.datetime_utc '2025-02-27 02:34:42' _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 5hle # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5HLE # _exptl.entry_id 5HLE _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 5HLE _cell.length_a 112.858 _cell.length_b 112.858 _cell.length_c 72.11 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HLE _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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,D _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 metalc ? metalc1 A OG1 THR 108 A THR 108 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc2 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? # _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 5HLE _atom_sites.fract_transf_matrix[1][1] 0.008861 _atom_sites.fract_transf_matrix[1][2] 0.005116 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010231 _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] 0.013868 _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 1 401 1 ADP ADP . C 3 MG A 1 402 701 MG MG . D 4 HOH A 1 501 2 HOH HOH . D 4 HOH A 2 502 1 HOH HOH . D 4 HOH A 3 503 3 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 -50.16 -1.518 -2.887 1 36.16 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -49.88 -2.682 -3.801 1 41.06 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -48.969 -1.067 -2.082 1 31.91 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -50.943 -0.401 -3.51 1 32.84 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -52.791 -2.227 -2.324 1 38.83 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -52.986 -2.991 -3.613 1 41.1 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -53.341 -0.827 -2.236 1 33.27 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -51.237 -2.175 -1.902 1 32.41 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -53.428 -3.13 -1.147 1 42.24 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -53.208 -4.539 -1.008 1 35.16 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -54.545 -5.251 -0.76 1 36.56 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -54.941 -5.211 0.615 1 40.58 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -55.707 -4.631 -1.5 1 40.19 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -56.621 -5.699 -1.744 1 43.68 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -56.314 -3.668 -0.498 1 37.21 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -57.68 -3.322 -0.767 1 39.21 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -56.104 -4.401 0.813 1 37.31 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -55.774 -3.417 1.876 1 40.55 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -54.656 -2.661 1.886 1 37.8 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -54.625 -1.853 2.97 1 37.84 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -55.739 -2.095 3.68 1 35.11 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -56.313 -1.574 4.942 1 40.58 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -55.647 -0.617 5.651 1 41.49 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -57.508 -2.088 5.349 1 41.28 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -58.155 -3.034 4.637 1 37.26 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -57.683 -3.539 3.474 1 39.26 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -56.501 -3.121 2.96 1 36.2 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #