data_4YLR # _model_server_result.job_id nScEmW8cnPHzn6vSR7vCtQ _model_server_result.datetime_utc '2024-12-26 12:58:50' _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 4ylr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 4YLR # _exptl.entry_id 4YLR _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 4YLR _cell.length_a 78.548 _cell.length_b 121.762 _cell.length_c 129.858 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YLR _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 # _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 4YLR _atom_sites.fract_transf_matrix[1][1] 0.012731 _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] 0.008213 _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] 0.007701 _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 1 601 1 ADP ADP . C 3 HOH A 1 701 4 HOH HOH . C 3 HOH A 2 702 5 HOH HOH . C 3 HOH A 3 703 1 HOH HOH . C 3 HOH A 4 704 7 HOH HOH . C 3 HOH A 5 705 2 HOH HOH . C 3 HOH A 6 706 3 HOH HOH . C 3 HOH A 7 707 6 HOH HOH . C 3 HOH A 8 708 8 HOH HOH . C 3 HOH A 9 709 9 HOH HOH . C 3 HOH A 10 710 10 HOH HOH . C 3 HOH A 11 711 11 HOH HOH . C 3 HOH A 12 712 12 HOH HOH . C 3 HOH A 13 713 13 HOH HOH . C 3 HOH A 14 714 14 HOH HOH . C 3 HOH A 15 715 15 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 -29.539 -23.727 -14.283 1 143.32 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . B 2 -29.368 -24.124 -15.705 1 144.18 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . B 2 -30.061 -22.358 -14.216 1 141.88 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . B 2 -30.485 -24.641 -13.626 1 142.96 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . B 2 -27.961 -24.435 -12.117 1 176.62 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . B 2 -28.342 -25.951 -12.164 1 129.11 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . B 2 -26.498 -24.283 -11.689 1 175.12 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . B 2 -28.164 -23.781 -13.554 1 215.35 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . B 2 -28.943 -23.658 -11.028 1 99.71 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . B 2 -28.588 -22.336 -10.621 1 93.04 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . B 2 -29.358 -21.965 -9.497 1 85.51 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . B 2 -28.642 -22.355 -8.207 1 78.17 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . B 2 -29.492 -20.382 -9.45 1 99.66 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . B 2 -30.86 -19.989 -8.965 1 102.16 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . B 2 -28.61 -20.019 -8.623 1 95.08 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . B 2 -29.017 -18.799 -7.961 1 93.16 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . B 2 -28.511 -21.238 -7.529 1 73.07 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . B 2 -27.303 -21.159 -6.782 1 77.81 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . B 2 -26.583 -21.92 -7.666 1 80.68 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . B 2 -25.317 -22.022 -7.182 1 74.16 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . B 2 -25.253 -21.319 -6.002 1 72.78 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . B 2 -24.201 -21.092 -5.095 1 74.07 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . B 2 -22.827 -21.511 -5.078 1 73.3 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . B 2 -24.414 -20.352 -3.992 1 77.08 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . B 2 -25.667 -19.81 -3.747 1 77.44 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . B 2 -26.693 -20.028 -4.627 1 76.77 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . B 2 -26.481 -20.786 -5.757 1 74.2 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #