data_5DQW # _model_server_result.job_id K-EKd8NXThVqecUEkaOS9Q _model_server_result.datetime_utc '2025-03-01 19:23:42' _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 5dqw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5DQW # _exptl.entry_id 5DQW _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.33 _cell.angle_gamma 90 _cell.entry_id 5DQW _cell.length_a 46.865 _cell.length_b 52.499 _cell.length_c 82.322 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DQW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 35 A HIS 29 1_555 D NI NI . A NI 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc2 A NE2 HIS 64 A HIS 58 1_555 D NI NI . A NI 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc3 A OD1 ASP 130 A ASP 124 1_555 D NI NI . A NI 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc4 D NI NI . A NI 302 1_555 G O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc5 B NE2 HIS 35 B HIS 29 1_555 F NI NI . B NI 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc6 B OD1 ASP 130 B ASP 124 1_555 F NI NI . B NI 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc7 F NI NI . B NI 302 1_555 H O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? # _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 5DQW _atom_sites.fract_transf_matrix[1][1] 0.021338 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001241 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019048 _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] 0.012168 _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 C 2 ADP A 1 301 301 ADP ADP . D 3 NI A 1 302 1 NI NI . E 2 ADP B 1 301 301 ADP ADP . F 3 NI B 1 302 2 NI NI . G 4 HOH A 1 401 1 HOH HOH . G 4 HOH A 2 402 146 HOH HOH . G 4 HOH A 3 403 23 HOH HOH . G 4 HOH A 4 404 156 HOH HOH . G 4 HOH A 5 405 83 HOH HOH . G 4 HOH A 6 406 24 HOH HOH . G 4 HOH A 7 407 14 HOH HOH . G 4 HOH A 8 408 133 HOH HOH . G 4 HOH A 9 409 75 HOH HOH . G 4 HOH A 10 410 8 HOH HOH . G 4 HOH A 11 411 40 HOH HOH . G 4 HOH A 12 412 10 HOH HOH . G 4 HOH A 13 413 89 HOH HOH . G 4 HOH A 14 414 49 HOH HOH . G 4 HOH A 15 415 12 HOH HOH . G 4 HOH A 16 416 161 HOH HOH . G 4 HOH A 17 417 19 HOH HOH . G 4 HOH A 18 418 150 HOH HOH . G 4 HOH A 19 419 84 HOH HOH . G 4 HOH A 20 420 3 HOH HOH . G 4 HOH A 21 421 160 HOH HOH . G 4 HOH A 22 422 7 HOH HOH . G 4 HOH A 23 423 96 HOH HOH . G 4 HOH A 24 424 71 HOH HOH . G 4 HOH A 25 425 22 HOH HOH . G 4 HOH A 26 426 18 HOH HOH . G 4 HOH A 27 427 30 HOH HOH . G 4 HOH A 28 428 90 HOH HOH . G 4 HOH A 29 429 87 HOH HOH . G 4 HOH A 30 430 42 HOH HOH . G 4 HOH A 31 431 158 HOH HOH . G 4 HOH A 32 432 4 HOH HOH . G 4 HOH A 33 433 44 HOH HOH . G 4 HOH A 34 434 67 HOH HOH . G 4 HOH A 35 435 140 HOH HOH . G 4 HOH A 36 436 43 HOH HOH . G 4 HOH A 37 437 129 HOH HOH . H 4 HOH B 1 401 78 HOH HOH . H 4 HOH B 2 402 2 HOH HOH . H 4 HOH B 3 403 53 HOH HOH . H 4 HOH B 4 404 5 HOH HOH . H 4 HOH B 5 405 57 HOH HOH . H 4 HOH B 6 406 46 HOH HOH . H 4 HOH B 7 407 68 HOH HOH . H 4 HOH B 8 408 101 HOH HOH . H 4 HOH B 9 409 132 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 . . . C 2 9.094 -13.818 8.156 1 84.4 ? PB ADP 301 A 1 HETATM 2 O O1B ADP . . . C 2 9.714 -12.651 7.426 1 83.91 ? O1B ADP 301 A 1 HETATM 3 O O2B ADP . . . C 2 7.759 -14.231 7.554 1 84.6 ? O2B ADP 301 A 1 HETATM 4 O O3B ADP . . . C 2 9.035 -13.662 9.66 1 83.3 ? O3B ADP 301 A 1 HETATM 5 P PA ADP . . . C 2 10.436 -16.192 8.91 1 80.42 ? PA ADP 301 A 1 HETATM 6 O O1A ADP . . . C 2 11.374 -17.238 8.336 1 80.07 ? O1A ADP 301 A 1 HETATM 7 O O2A ADP . . . C 2 9.11 -16.687 9.419 1 81.01 ? O2A ADP 301 A 1 HETATM 8 O O3A ADP . . . C 2 10.145 -15.011 7.85 1 81.86 ? O3A ADP 301 A 1 HETATM 9 O O5' ADP . . . C 2 11.141 -15.349 10.1 1 74.09 ? O5' ADP 301 A 1 HETATM 10 C C5' ADP . . . C 2 10.677 -15.382 11.458 1 67.23 ? C5' ADP 301 A 1 HETATM 11 C C4' ADP . . . C 2 11.797 -14.858 12.341 1 63.31 ? C4' ADP 301 A 1 HETATM 12 O O4' ADP . . . C 2 12.779 -15.876 12.368 1 60.63 ? O4' ADP 301 A 1 HETATM 13 C C3' ADP . . . C 2 12.489 -13.584 11.819 1 61.84 ? C3' ADP 301 A 1 HETATM 14 O O3' ADP . . . C 2 12.986 -12.765 12.884 1 59.7 ? O3' ADP 301 A 1 HETATM 15 C C2' ADP . . . C 2 13.683 -14.082 11.053 1 60.81 ? C2' ADP 301 A 1 HETATM 16 O O2' ADP . . . C 2 14.798 -13.198 11.099 1 61.94 ? O2' ADP 301 A 1 HETATM 17 C C1' ADP . . . C 2 13.998 -15.358 11.824 1 60.15 ? C1' ADP 301 A 1 HETATM 18 N N9 ADP . . . C 2 14.67 -16.313 10.939 1 57.15 ? N9 ADP 301 A 1 HETATM 19 C C8 ADP . . . C 2 14.33 -16.624 9.672 1 56.67 ? C8 ADP 301 A 1 HETATM 20 N N7 ADP . . . C 2 15.194 -17.533 9.153 1 54.76 ? N7 ADP 301 A 1 HETATM 21 C C5 ADP . . . C 2 16.098 -17.806 10.103 1 54.78 ? C5 ADP 301 A 1 HETATM 22 C C6 ADP . . . C 2 17.273 -18.678 10.212 1 54.41 ? C6 ADP 301 A 1 HETATM 23 N N6 ADP . . . C 2 17.634 -19.448 9.157 1 54.44 ? N6 ADP 301 A 1 HETATM 24 N N1 ADP . . . C 2 17.959 -18.663 11.386 1 53.23 ? N1 ADP 301 A 1 HETATM 25 C C2 ADP . . . C 2 17.601 -17.895 12.425 1 53.12 ? C2 ADP 301 A 1 HETATM 26 N N3 ADP . . . C 2 16.529 -17.071 12.387 1 54.13 ? N3 ADP 301 A 1 HETATM 27 C C4 ADP . . . C 2 15.755 -16.993 11.281 1 56.09 ? C4 ADP 301 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #