data_1UBE # _model_server_result.job_id ADLjeG6jk-8gsbWV-2dwIA _model_server_result.datetime_utc '2025-03-25 15:16:26' _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 1ube # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":503}' # _entry.id 1UBE # _exptl.entry_id 1UBE _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 1UBE _cell.length_a 103.32 _cell.length_b 103.32 _cell.length_c 73.663 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1UBE _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 1UBE _atom_sites.fract_transf_matrix[1][1] 0.009679 _atom_sites.fract_transf_matrix[1][2] 0.005588 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011176 _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] 0.013575 _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 1 503 503 ADP ADP . C 3 HOH A 1 504 504 HOH HOH . C 3 HOH A 2 505 505 HOH HOH . C 3 HOH A 3 506 506 HOH HOH . C 3 HOH A 4 507 507 HOH HOH . C 3 HOH A 5 509 509 HOH HOH . C 3 HOH A 6 512 512 HOH HOH . C 3 HOH A 7 514 514 HOH HOH . C 3 HOH A 8 518 518 HOH HOH . C 3 HOH A 9 521 521 HOH HOH . C 3 HOH A 10 522 522 HOH HOH . C 3 HOH A 11 526 526 HOH HOH . C 3 HOH A 12 528 528 HOH HOH . C 3 HOH A 13 532 532 HOH HOH . C 3 HOH A 14 538 538 HOH HOH . C 3 HOH A 15 540 540 HOH HOH . C 3 HOH A 16 541 541 HOH HOH . C 3 HOH A 17 542 542 HOH HOH . C 3 HOH A 18 545 545 HOH HOH . C 3 HOH A 19 546 546 HOH HOH . C 3 HOH A 20 548 548 HOH HOH . C 3 HOH A 21 552 552 HOH HOH . C 3 HOH A 22 554 554 HOH HOH . C 3 HOH A 23 555 555 HOH HOH . C 3 HOH A 24 563 563 HOH HOH . C 3 HOH A 25 577 577 HOH HOH . C 3 HOH A 26 578 578 HOH HOH . C 3 HOH A 27 586 586 HOH HOH . C 3 HOH A 28 589 589 HOH HOH . C 3 HOH A 29 604 604 HOH HOH . C 3 HOH A 30 607 607 HOH HOH . C 3 HOH A 31 609 609 HOH HOH . C 3 HOH A 32 624 624 HOH HOH . C 3 HOH A 33 631 631 HOH HOH . C 3 HOH A 34 639 639 HOH HOH . C 3 HOH A 35 713 713 HOH HOH . C 3 HOH A 36 718 718 HOH HOH . C 3 HOH A 37 764 764 HOH HOH . C 3 HOH A 38 765 765 HOH HOH . C 3 HOH A 39 768 768 HOH HOH . C 3 HOH A 40 769 769 HOH HOH . C 3 HOH A 41 770 770 HOH HOH . C 3 HOH A 42 771 771 HOH HOH . C 3 HOH A 43 772 772 HOH HOH . C 3 HOH A 44 778 778 HOH HOH . C 3 HOH A 45 781 781 HOH HOH . C 3 HOH A 46 783 783 HOH HOH . C 3 HOH A 47 784 784 HOH HOH . C 3 HOH A 48 787 787 HOH HOH . C 3 HOH A 49 790 790 HOH HOH . C 3 HOH A 50 791 791 HOH HOH . C 3 HOH A 51 793 793 HOH HOH . C 3 HOH A 52 794 794 HOH HOH . C 3 HOH A 53 796 796 HOH HOH . C 3 HOH A 54 797 797 HOH HOH . C 3 HOH A 55 798 798 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 78.602 8.629 6.375 1 62.86 ? PB ADP 503 A 1 HETATM 2 O O1B ADP . . . B 2 77.349 8.208 5.647 1 62.86 ? O1B ADP 503 A 1 HETATM 3 O O2B ADP . . . B 2 78.695 9.867 7.118 1 62.86 ? O2B ADP 503 A 1 HETATM 4 O O3B ADP . . . B 2 79.548 7.446 6.767 1 62.86 ? O3B ADP 503 A 1 HETATM 5 P PA ADP . . . B 2 76.391 8.108 8.365 1 62.86 ? PA ADP 503 A 1 HETATM 6 O O1A ADP . . . B 2 75.588 9.197 7.731 1 62.86 ? O1A ADP 503 A 1 HETATM 7 O O2A ADP . . . B 2 76.329 7.415 9.635 1 62.86 ? O2A ADP 503 A 1 HETATM 8 O O3A ADP . . . B 2 77.934 8.085 7.726 1 62.86 ? O3A ADP 503 A 1 HETATM 9 O O5' ADP . . . B 2 76.805 9.421 9.261 1 62.86 ? O5' ADP 503 A 1 HETATM 10 C C5' ADP . . . B 2 77.731 9.382 10.399 1 62.86 ? C5' ADP 503 A 1 HETATM 11 C C4' ADP . . . B 2 77.115 9.834 11.721 1 62.86 ? C4' ADP 503 A 1 HETATM 12 O O4' ADP . . . B 2 75.649 9.552 11.696 1 62.86 ? O4' ADP 503 A 1 HETATM 13 C C3' ADP . . . B 2 77.578 9.083 12.966 1 62.86 ? C3' ADP 503 A 1 HETATM 14 O O3' ADP . . . B 2 78.751 9.711 13.55 1 62.86 ? O3' ADP 503 A 1 HETATM 15 C C2' ADP . . . B 2 76.353 9.143 13.953 1 62.86 ? C2' ADP 503 A 1 HETATM 16 O O2' ADP . . . B 2 76.381 10.373 14.755 1 62.86 ? O2' ADP 503 A 1 HETATM 17 C C1' ADP . . . B 2 75.162 9.155 12.998 1 62.86 ? C1' ADP 503 A 1 HETATM 18 N N9 ADP . . . B 2 74.456 7.783 12.872 1 62.86 ? N9 ADP 503 A 1 HETATM 19 C C8 ADP . . . B 2 74.317 7.073 11.767 1 62.86 ? C8 ADP 503 A 1 HETATM 20 N N7 ADP . . . B 2 73.686 5.977 11.934 1 62.86 ? N7 ADP 503 A 1 HETATM 21 C C5 ADP . . . B 2 73.357 5.953 13.281 1 62.86 ? C5 ADP 503 A 1 HETATM 22 C C6 ADP . . . B 2 72.635 5.02 14.14 1 62.86 ? C6 ADP 503 A 1 HETATM 23 N N6 ADP . . . B 2 72.088 3.844 13.676 1 62.86 ? N6 ADP 503 A 1 HETATM 24 N N1 ADP . . . B 2 72.51 5.332 15.465 1 62.86 ? N1 ADP 503 A 1 HETATM 25 C C2 ADP . . . B 2 73.04 6.463 15.927 1 62.86 ? C2 ADP 503 A 1 HETATM 26 N N3 ADP . . . B 2 73.709 7.397 15.199 1 62.86 ? N3 ADP 503 A 1 HETATM 27 C C4 ADP . . . B 2 73.846 7.076 13.884 1 62.86 ? C4 ADP 503 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #