data_5UBV # _model_server_result.job_id NLUjhw7IFyYAUuucb7QT2w _model_server_result.datetime_utc '2025-03-01 07:13:06' _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 5ubv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 5UBV # _exptl.entry_id 5UBV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 5UBV _cell.length_a 45.916 _cell.length_b 86.624 _cell.length_c 155.025 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5UBV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 3 D N N ? 3 F N N # _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 5UBV _atom_sites.fract_transf_matrix[1][1] 0.021779 _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] 0.011544 _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] 0.006451 _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 CIT A 1 301 2 CIT CIT . D 3 ADP A 1 302 1 ADP ADP . E 4 GOL B 1 301 3 GOL GOL . F 3 ADP B 1 302 2 ADP ADP . G 5 HOH A 1 401 46 HOH HOH . G 5 HOH A 2 402 54 HOH HOH . G 5 HOH A 3 403 48 HOH HOH . G 5 HOH A 4 404 60 HOH HOH . G 5 HOH A 5 405 18 HOH HOH . G 5 HOH A 6 406 28 HOH HOH . G 5 HOH A 7 407 56 HOH HOH . G 5 HOH A 8 408 67 HOH HOH . G 5 HOH A 9 409 5 HOH HOH . G 5 HOH A 10 410 59 HOH HOH . G 5 HOH A 11 411 43 HOH HOH . G 5 HOH A 12 412 68 HOH HOH . G 5 HOH A 13 413 63 HOH HOH . G 5 HOH A 14 414 45 HOH HOH . G 5 HOH A 15 415 17 HOH HOH . G 5 HOH A 16 416 57 HOH HOH . G 5 HOH A 17 417 47 HOH HOH . G 5 HOH A 18 418 3 HOH HOH . G 5 HOH A 19 419 1 HOH HOH . G 5 HOH A 20 420 51 HOH HOH . G 5 HOH A 21 421 16 HOH HOH . G 5 HOH A 22 422 7 HOH HOH . G 5 HOH A 23 423 64 HOH HOH . G 5 HOH A 24 424 31 HOH HOH . G 5 HOH A 25 425 26 HOH HOH . G 5 HOH A 26 426 2 HOH HOH . G 5 HOH A 27 427 39 HOH HOH . G 5 HOH A 28 428 49 HOH HOH . G 5 HOH A 29 429 35 HOH HOH . G 5 HOH A 30 430 52 HOH HOH . G 5 HOH A 31 431 38 HOH HOH . G 5 HOH A 32 432 65 HOH HOH . G 5 HOH A 33 433 25 HOH HOH . G 5 HOH A 34 434 27 HOH HOH . H 5 HOH B 1 401 33 HOH HOH . H 5 HOH B 2 402 29 HOH HOH . H 5 HOH B 3 403 66 HOH HOH . H 5 HOH B 4 404 32 HOH HOH . H 5 HOH B 5 405 12 HOH HOH . H 5 HOH B 6 406 41 HOH HOH . H 5 HOH B 7 407 6 HOH HOH . H 5 HOH B 8 408 55 HOH HOH . H 5 HOH B 9 409 15 HOH HOH . H 5 HOH B 10 410 13 HOH HOH . H 5 HOH B 11 411 4 HOH HOH . H 5 HOH B 12 412 34 HOH HOH . H 5 HOH B 13 413 40 HOH HOH . H 5 HOH B 14 414 50 HOH HOH . H 5 HOH B 15 415 58 HOH HOH . H 5 HOH B 16 416 10 HOH HOH . H 5 HOH B 17 417 36 HOH HOH . H 5 HOH B 18 418 19 HOH HOH . H 5 HOH B 19 419 62 HOH HOH . H 5 HOH B 20 420 69 HOH HOH . H 5 HOH B 21 421 44 HOH HOH . H 5 HOH B 22 422 42 HOH HOH . H 5 HOH B 23 423 37 HOH HOH . H 5 HOH B 24 424 21 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 . . . D 3 31.039 23.173 92.711 1 47.17 ? PB ADP 302 A 1 HETATM 2 O O1B ADP . . . D 3 31.34 24.606 92.258 1 41.68 ? O1B ADP 302 A 1 HETATM 3 O O2B ADP . . . D 3 32.163 22.722 93.646 1 46 ? O2B ADP 302 A 1 HETATM 4 O O3B ADP . . . D 3 29.686 23.032 93.319 1 30.57 ? O3B ADP 302 A 1 HETATM 5 P PA ADP . . . D 3 30.096 21.612 90.426 1 48.52 ? PA ADP 302 A 1 HETATM 6 O O1A ADP . . . D 3 28.993 22.638 90.189 1 55.16 ? O1A ADP 302 A 1 HETATM 7 O O2A ADP . . . D 3 29.517 20.399 91.045 1 52.56 ? O2A ADP 302 A 1 HETATM 8 O O3A ADP . . . D 3 31.168 22.262 91.41 1 54.41 ? O3A ADP 302 A 1 HETATM 9 O O5' ADP . . . D 3 30.833 21.335 89.032 1 53.31 ? O5' ADP 302 A 1 HETATM 10 C C5' ADP . . . D 3 30.345 21.754 87.74 1 49.84 ? C5' ADP 302 A 1 HETATM 11 C C4' ADP . . . D 3 30.598 20.657 86.736 1 57.97 ? C4' ADP 302 A 1 HETATM 12 O O4' ADP . . . D 3 32.019 20.441 86.603 1 59.58 ? O4' ADP 302 A 1 HETATM 13 C C3' ADP . . . D 3 30.024 19.296 87.104 1 58.9 ? C3' ADP 302 A 1 HETATM 14 O O3' ADP . . . D 3 28.674 19.182 86.671 1 65.08 ? O3' ADP 302 A 1 HETATM 15 C C2' ADP . . . D 3 30.949 18.34 86.349 1 57.37 ? C2' ADP 302 A 1 HETATM 16 O O2' ADP . . . D 3 30.567 18.2 84.986 1 63.35 ? O2' ADP 302 A 1 HETATM 17 C C1' ADP . . . D 3 32.297 19.058 86.465 1 52.53 ? C1' ADP 302 A 1 HETATM 18 N N9 ADP . . . D 3 33.099 18.636 87.611 1 48.17 ? N9 ADP 302 A 1 HETATM 19 C C8 ADP . . . D 3 33.418 19.382 88.712 1 52.86 ? C8 ADP 302 A 1 HETATM 20 N N7 ADP . . . D 3 34.131 18.738 89.607 1 46.67 ? N7 ADP 302 A 1 HETATM 21 C C5 ADP . . . D 3 34.29 17.48 89.052 1 45.25 ? C5 ADP 302 A 1 HETATM 22 C C6 ADP . . . D 3 34.944 16.316 89.508 1 52.27 ? C6 ADP 302 A 1 HETATM 23 N N6 ADP . . . D 3 35.575 16.23 90.682 1 50.37 ? N6 ADP 302 A 1 HETATM 24 N N1 ADP . . . D 3 34.917 15.227 88.709 1 54.2 ? N1 ADP 302 A 1 HETATM 25 C C2 ADP . . . D 3 34.277 15.303 87.539 1 52.62 ? C2 ADP 302 A 1 HETATM 26 N N3 ADP . . . D 3 33.623 16.339 87.006 1 50.5 ? N3 ADP 302 A 1 HETATM 27 C C4 ADP . . . D 3 33.665 17.4 87.818 1 48.59 ? C4 ADP 302 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #