data_5LTK # _model_server_result.job_id 8SA25i2wCRvYIx12eIxmWg _model_server_result.datetime_utc '2024-10-19 11:39:06' _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 5ltk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 5LTK # _exptl.entry_id 5LTK _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 5LTK _cell.length_a 184.342 _cell.length_b 184.342 _cell.length_c 82.317 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LTK _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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,E,F,G _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 68 A THR 126 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc2 B O3B ADP . A ADP 801 1_555 C BE BEF . A BEF 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? metalc ? metalc3 B O1B ADP . A ADP 801 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc4 B O3B ADP . A ADP 801 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc5 D MG MG . A MG 803 1_555 G O HOH . A HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc6 D MG MG . A MG 803 1_555 G O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc7 D MG MG . A MG 803 1_555 G O HOH . A HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? # _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 5LTK _atom_sites.fract_transf_matrix[1][1] 0.005425 _atom_sites.fract_transf_matrix[1][2] 0.003132 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006264 _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] 0.012148 _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 1 801 1 ADP ADP . C 3 BEF A 1 802 1 BEF BEF . D 4 MG A 1 803 1 MG MG . E 5 SO4 A 1 804 1 SO4 SO4 . F 5 SO4 A 1 805 2 SO4 SO4 . G 6 HOH A 1 901 4 HOH HOH . G 6 HOH A 2 902 1 HOH HOH . G 6 HOH A 3 903 2 HOH HOH . G 6 HOH A 4 904 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 -75.221 -44.865 -5.32 1 63.69 ? PB ADP 801 A 1 HETATM 2 O O1B ADP . . . B 2 -74.802 -44.031 -6.507 1 96.82 ? O1B ADP 801 A 1 HETATM 3 O O2B ADP . . . B 2 -76.288 -45.882 -5.639 1 64.06 ? O2B ADP 801 A 1 HETATM 4 O O3B ADP . . . B 2 -75.462 -44.098 -4.04 1 76.64 ? O3B ADP 801 A 1 HETATM 5 P PA ADP . . . B 2 -72.518 -45.523 -5.744 1 62.3 ? PA ADP 801 A 1 HETATM 6 O O1A ADP . . . B 2 -72.66 -45.897 -7.199 1 69.75 ? O1A ADP 801 A 1 HETATM 7 O O2A ADP . . . B 2 -71.979 -44.16 -5.384 1 85.59 ? O2A ADP 801 A 1 HETATM 8 O O3A ADP . . . B 2 -73.933 -45.777 -5.016 1 129.36 ? O3A ADP 801 A 1 HETATM 9 O O5' ADP . . . B 2 -71.618 -46.647 -5.028 1 98.23 ? O5' ADP 801 A 1 HETATM 10 C C5' ADP . . . B 2 -71.698 -47.998 -5.473 1 84.1 ? C5' ADP 801 A 1 HETATM 11 C C4' ADP . . . B 2 -70.781 -48.879 -4.638 1 80.82 ? C4' ADP 801 A 1 HETATM 12 O O4' ADP . . . B 2 -69.451 -48.815 -5.153 1 76.56 ? O4' ADP 801 A 1 HETATM 13 C C3' ADP . . . B 2 -70.716 -48.441 -3.183 1 79.25 ? C3' ADP 801 A 1 HETATM 14 O O3' ADP . . . B 2 -71.57 -49.236 -2.356 1 77.44 ? O3' ADP 801 A 1 HETATM 15 C C2' ADP . . . B 2 -69.271 -48.649 -2.786 1 81.74 ? C2' ADP 801 A 1 HETATM 16 O O2' ADP . . . B 2 -69.152 -49.86 -2.034 1 110.8 ? O2' ADP 801 A 1 HETATM 17 C C1' ADP . . . B 2 -68.501 -48.785 -4.088 1 68.93 ? C1' ADP 801 A 1 HETATM 18 N N9 ADP . . . B 2 -67.654 -47.582 -4.242 1 61.51 ? N9 ADP 801 A 1 HETATM 19 C C8 ADP . . . B 2 -68.042 -46.43 -4.818 1 79.17 ? C8 ADP 801 A 1 HETATM 20 N N7 ADP . . . B 2 -67.043 -45.514 -4.802 1 86.79 ? N7 ADP 801 A 1 HETATM 21 C C5 ADP . . . B 2 -65.985 -46.085 -4.199 1 71.02 ? C5 ADP 801 A 1 HETATM 22 C C6 ADP . . . B 2 -64.606 -45.671 -3.853 1 77.67 ? C6 ADP 801 A 1 HETATM 23 N N6 ADP . . . B 2 -64.154 -44.431 -4.159 1 93.57 ? N6 ADP 801 A 1 HETATM 24 N N1 ADP . . . B 2 -63.82 -46.572 -3.223 1 81.21 ? N1 ADP 801 A 1 HETATM 25 C C2 ADP . . . B 2 -64.262 -47.806 -2.915 1 79.11 ? C2 ADP 801 A 1 HETATM 26 N N3 ADP . . . B 2 -65.499 -48.25 -3.2 1 64.56 ? N3 ADP 801 A 1 HETATM 27 C C4 ADP . . . B 2 -66.392 -47.449 -3.83 1 64.74 ? C4 ADP 801 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #