data_3D5W # _model_server_result.job_id U1iwUo57xMaxoL9C12CJ0w _model_server_result.datetime_utc '2024-10-10 01:18:27' _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 3d5w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":313}' # _entry.id 3D5W # _exptl.entry_id 3D5W _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 90 _cell.entry_id 3D5W _cell.length_a 133.99 _cell.length_b 133.99 _cell.length_c 133.99 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D5W _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _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 LYS 200 A LYS 195 1_555 A N TPO 201 A TPO 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C TPO 201 A TPO 196 1_555 A N LEU 202 A LEU 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _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 3D5W _atom_sites.fract_transf_matrix[1][1] 0.007463 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007463 _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] 0.007463 _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 1 313 1 ADP ADP . C 3 HOH A 1 314 1 HOH HOH . C 3 HOH A 2 315 2 HOH HOH . C 3 HOH A 3 316 3 HOH HOH . C 3 HOH A 4 317 5 HOH HOH . C 3 HOH A 5 318 6 HOH HOH . C 3 HOH A 6 319 7 HOH HOH . C 3 HOH A 7 320 8 HOH HOH . C 3 HOH A 8 321 9 HOH HOH . C 3 HOH A 9 322 10 HOH HOH . C 3 HOH A 10 323 11 HOH HOH . C 3 HOH A 11 324 13 HOH HOH . C 3 HOH A 12 325 14 HOH HOH . C 3 HOH A 13 326 15 HOH HOH . C 3 HOH A 14 327 16 HOH HOH . C 3 HOH A 15 328 17 HOH HOH . C 3 HOH A 16 329 18 HOH HOH . C 3 HOH A 17 330 19 HOH HOH . C 3 HOH A 18 331 20 HOH HOH . C 3 HOH A 19 332 21 HOH HOH . C 3 HOH A 20 333 22 HOH HOH . C 3 HOH A 21 334 23 HOH HOH . C 3 HOH A 22 335 24 HOH HOH . C 3 HOH A 23 336 25 HOH HOH . C 3 HOH A 24 337 26 HOH HOH . C 3 HOH A 25 338 27 HOH HOH . C 3 HOH A 26 339 28 HOH HOH . C 3 HOH A 27 340 29 HOH HOH . C 3 HOH A 28 341 30 HOH HOH . C 3 HOH A 29 342 31 HOH HOH . C 3 HOH A 30 343 32 HOH HOH . C 3 HOH A 31 344 33 HOH HOH . C 3 HOH A 32 345 34 HOH HOH . C 3 HOH A 33 346 35 HOH HOH . C 3 HOH A 34 347 36 HOH HOH . C 3 HOH A 35 348 37 HOH HOH . C 3 HOH A 36 349 38 HOH HOH . C 3 HOH A 37 350 39 HOH HOH . C 3 HOH A 38 351 41 HOH HOH . C 3 HOH A 39 352 44 HOH HOH . C 3 HOH A 40 353 45 HOH HOH . C 3 HOH A 41 354 49 HOH HOH . C 3 HOH A 42 355 50 HOH HOH . C 3 HOH A 43 356 51 HOH HOH . C 3 HOH A 44 357 52 HOH HOH . C 3 HOH A 45 358 54 HOH HOH . C 3 HOH A 46 359 59 HOH HOH . C 3 HOH A 47 360 61 HOH HOH . C 3 HOH A 48 361 62 HOH HOH . C 3 HOH A 49 362 67 HOH HOH . C 3 HOH A 50 363 68 HOH HOH . C 3 HOH A 51 364 69 HOH HOH . C 3 HOH A 52 365 71 HOH HOH . C 3 HOH A 53 366 72 HOH HOH . C 3 HOH A 54 367 73 HOH HOH . C 3 HOH A 55 368 75 HOH HOH . C 3 HOH A 56 369 77 HOH HOH . C 3 HOH A 57 370 79 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 49.332 22.823 74.151 1 97.97 ? PB ADP 313 A 1 HETATM 2 O O1B ADP . . . B 2 48.651 23.659 75.21 1 97.9 ? O1B ADP 313 A 1 HETATM 3 O O2B ADP . . . B 2 50.841 22.811 74.235 1 98.04 ? O2B ADP 313 A 1 HETATM 4 O O3B ADP . . . B 2 48.802 23.037 72.751 1 97.72 ? O3B ADP 313 A 1 HETATM 5 P PA ADP . . . B 2 47.565 20.636 73.963 1 95.73 ? PA ADP 313 A 1 HETATM 6 O O1A ADP . . . B 2 46.463 21.67 73.985 1 95.92 ? O1A ADP 313 A 1 HETATM 7 O O2A ADP . . . B 2 47.907 19.927 72.673 1 95.78 ? O2A ADP 313 A 1 HETATM 8 O O3A ADP . . . B 2 48.912 21.314 74.536 1 96.66 ? O3A ADP 313 A 1 HETATM 9 O O5' ADP . . . B 2 47.215 19.521 75.071 1 92.98 ? O5' ADP 313 A 1 HETATM 10 C C5' ADP . . . B 2 48.131 18.471 75.375 1 89.46 ? C5' ADP 313 A 1 HETATM 11 C C4' ADP . . . B 2 47.714 17.778 76.666 1 86.19 ? C4' ADP 313 A 1 HETATM 12 O O4' ADP . . . B 2 47.349 18.748 77.653 1 84.32 ? O4' ADP 313 A 1 HETATM 13 C C3' ADP . . . B 2 46.514 16.869 76.443 1 85 ? C3' ADP 313 A 1 HETATM 14 O O3' ADP . . . B 2 46.914 15.495 76.468 1 85.52 ? O3' ADP 313 A 1 HETATM 15 C C2' ADP . . . B 2 45.542 17.191 77.564 1 83.77 ? C2' ADP 313 A 1 HETATM 16 O O2' ADP . . . B 2 45.438 16.106 78.491 1 83.8 ? O2' ADP 313 A 1 HETATM 17 C C1' ADP . . . B 2 46.1 18.42 78.272 1 82.11 ? C1' ADP 313 A 1 HETATM 18 N N9 ADP . . . B 2 45.134 19.546 78.155 1 81.18 ? N9 ADP 313 A 1 HETATM 19 C C8 ADP . . . B 2 45.223 20.588 77.306 1 80.86 ? C8 ADP 313 A 1 HETATM 20 N N7 ADP . . . B 2 44.174 21.438 77.453 1 80.55 ? N7 ADP 313 A 1 HETATM 21 C C5 ADP . . . B 2 43.385 20.938 78.42 1 80.47 ? C5 ADP 313 A 1 HETATM 22 C C6 ADP . . . B 2 42.113 21.331 79.078 1 81.03 ? C6 ADP 313 A 1 HETATM 23 N N6 ADP . . . B 2 41.459 22.462 78.719 1 81 ? N6 ADP 313 A 1 HETATM 24 N N1 ADP . . . B 2 41.626 20.521 80.049 1 81.18 ? N1 ADP 313 A 1 HETATM 25 C C2 ADP . . . B 2 42.264 19.392 80.421 1 80.84 ? C2 ADP 313 A 1 HETATM 26 N N3 ADP . . . B 2 43.419 18.976 79.867 1 80.36 ? N3 ADP 313 A 1 HETATM 27 C C4 ADP . . . B 2 44.02 19.691 78.88 1 80.53 ? C4 ADP 313 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #