data_5DQW # _model_server_result.job_id 4mAZT18Ds05iKe-71C07ew _model_server_result.datetime_utc '2025-03-01 19:36:52' _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":"E","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 . . . E 2 21.977 -26.205 33.648 1 83.59 ? PB ADP 301 B 1 HETATM 2 O O1B ADP . . . E 2 21.992 -26.717 32.225 1 84.13 ? O1B ADP 301 B 1 HETATM 3 O O2B ADP . . . E 2 23.114 -25.245 33.94 1 82.99 ? O2B ADP 301 B 1 HETATM 4 O O3B ADP . . . E 2 21.725 -27.265 34.702 1 82.31 ? O3B ADP 301 B 1 HETATM 5 P PA ADP . . . E 2 19.456 -25.338 32.666 1 79.16 ? PA ADP 301 B 1 HETATM 6 O O1A ADP . . . E 2 19.336 -26.709 32.007 1 77.68 ? O1A ADP 301 B 1 HETATM 7 O O2A ADP . . . E 2 18.288 -24.751 33.436 1 78.37 ? O2A ADP 301 B 1 HETATM 8 O O3A ADP . . . E 2 20.659 -25.291 33.738 1 80.93 ? O3A ADP 301 B 1 HETATM 9 O O5' ADP . . . E 2 19.937 -24.249 31.552 1 72.9 ? O5' ADP 301 B 1 HETATM 10 C C5' ADP . . . E 2 20.52 -24.563 30.283 1 65.8 ? C5' ADP 301 B 1 HETATM 11 C C4' ADP . . . E 2 20.42 -23.351 29.369 1 62.18 ? C4' ADP 301 B 1 HETATM 12 O O4' ADP . . . E 2 19.043 -23.076 29.135 1 60.09 ? O4' ADP 301 B 1 HETATM 13 C C3' ADP . . . E 2 21.025 -22.064 29.94 1 60.81 ? C3' ADP 301 B 1 HETATM 14 O O3' ADP . . . E 2 21.591 -21.251 28.888 1 58.41 ? O3' ADP 301 B 1 HETATM 15 C C2' ADP . . . E 2 19.852 -21.342 30.564 1 60.01 ? C2' ADP 301 B 1 HETATM 16 O O2' ADP . . . E 2 19.969 -19.909 30.656 1 60.09 ? O2' ADP 301 B 1 HETATM 17 C C1' ADP . . . E 2 18.735 -21.751 29.622 1 59.32 ? C1' ADP 301 B 1 HETATM 18 N N9 ADP . . . E 2 17.458 -21.637 30.362 1 58.88 ? N9 ADP 301 B 1 HETATM 19 C C8 ADP . . . E 2 17.093 -22.335 31.467 1 58.74 ? C8 ADP 301 B 1 HETATM 20 N N7 ADP . . . E 2 15.861 -21.953 31.882 1 57.84 ? N7 ADP 301 B 1 HETATM 21 C C5 ADP . . . E 2 15.433 -20.991 31.045 1 57.04 ? C5 ADP 301 B 1 HETATM 22 C C6 ADP . . . E 2 14.226 -20.152 30.897 1 57.13 ? C6 ADP 301 B 1 HETATM 23 N N6 ADP . . . E 2 13.198 -20.271 31.769 1 57.54 ? N6 ADP 301 B 1 HETATM 24 N N1 ADP . . . E 2 14.18 -19.267 29.865 1 54.92 ? N1 ADP 301 B 1 HETATM 25 C C2 ADP . . . E 2 15.188 -19.132 28.992 1 54.67 ? C2 ADP 301 B 1 HETATM 26 N N3 ADP . . . E 2 16.316 -19.862 29.071 1 55.77 ? N3 ADP 301 B 1 HETATM 27 C C4 ADP . . . E 2 16.493 -20.781 30.05 1 57.07 ? C4 ADP 301 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #