data_3Q6Z # _model_server_result.job_id YVPG1yFFIcCQKAJ4s0sHqw _model_server_result.datetime_utc '2025-02-27 11:53:04' _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 3q6z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3Q6Z # _exptl.entry_id 3Q6Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _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 3Q6Z _cell.length_a 71.357 _cell.length_b 71.357 _cell.length_c 71.436 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3Q6Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _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 N1 C2 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 3Q6Z _atom_sites.fract_transf_matrix[1][1] 0.014014 _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] 0.014014 _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] 0.013999 _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 APR A 1 1 1 APR APR . C 3 HOH A 1 2 2 HOH HOH . C 3 HOH A 2 3 3 HOH HOH . C 3 HOH A 3 4 4 HOH HOH . C 3 HOH A 4 5 5 HOH HOH . C 3 HOH A 5 6 6 HOH HOH . C 3 HOH A 6 7 7 HOH HOH . C 3 HOH A 7 8 8 HOH HOH . C 3 HOH A 8 9 9 HOH HOH . C 3 HOH A 9 10 10 HOH HOH . C 3 HOH A 10 11 11 HOH HOH . C 3 HOH A 11 12 12 HOH HOH . C 3 HOH A 12 13 13 HOH HOH . C 3 HOH A 13 14 14 HOH HOH . C 3 HOH A 14 15 15 HOH HOH . C 3 HOH A 15 16 16 HOH HOH . C 3 HOH A 16 17 17 HOH HOH . C 3 HOH A 17 18 18 HOH HOH . C 3 HOH A 18 19 19 HOH HOH . C 3 HOH A 19 20 20 HOH HOH . C 3 HOH A 20 21 21 HOH HOH . C 3 HOH A 21 22 22 HOH HOH . C 3 HOH A 22 23 23 HOH HOH . C 3 HOH A 23 24 24 HOH HOH . C 3 HOH A 24 25 25 HOH HOH . C 3 HOH A 25 26 26 HOH HOH . C 3 HOH A 26 27 27 HOH HOH . C 3 HOH A 27 28 28 HOH HOH . C 3 HOH A 28 29 29 HOH HOH . C 3 HOH A 29 30 30 HOH HOH . C 3 HOH A 30 31 31 HOH HOH . C 3 HOH A 31 32 32 HOH HOH . C 3 HOH A 32 33 33 HOH HOH . C 3 HOH A 33 34 34 HOH HOH . C 3 HOH A 34 35 35 HOH HOH . C 3 HOH A 35 36 36 HOH HOH . C 3 HOH A 36 37 37 HOH HOH . C 3 HOH A 37 38 38 HOH HOH . C 3 HOH A 38 39 39 HOH HOH . C 3 HOH A 39 40 40 HOH HOH . C 3 HOH A 40 41 41 HOH HOH . C 3 HOH A 41 42 42 HOH HOH . C 3 HOH A 42 43 43 HOH HOH . C 3 HOH A 43 44 44 HOH HOH . C 3 HOH A 44 45 45 HOH HOH . C 3 HOH A 45 46 46 HOH HOH . C 3 HOH A 46 47 47 HOH HOH . C 3 HOH A 47 48 48 HOH HOH . C 3 HOH A 48 49 49 HOH HOH . C 3 HOH A 49 50 50 HOH HOH . C 3 HOH A 50 51 51 HOH HOH . C 3 HOH A 51 52 52 HOH HOH . C 3 HOH A 52 53 53 HOH HOH . C 3 HOH A 53 54 54 HOH HOH . C 3 HOH A 54 55 55 HOH HOH . C 3 HOH A 55 56 56 HOH HOH . C 3 HOH A 56 57 57 HOH HOH . C 3 HOH A 57 58 58 HOH HOH . C 3 HOH A 58 59 59 HOH HOH . C 3 HOH A 59 60 60 HOH HOH . C 3 HOH A 60 980 1 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 N N1 APR . . . B 2 18.015 25.518 15.654 1 41.14 ? N1 APR 1 A 1 HETATM 2 C C2 APR . . . B 2 17.927 24.472 16.492 1 42.95 ? C2 APR 1 A 1 HETATM 3 N N3 APR . . . B 2 17.089 23.451 16.285 1 41.18 ? N3 APR 1 A 1 HETATM 4 C C4 APR . . . B 2 16.289 23.46 15.209 1 40.87 ? C4 APR 1 A 1 HETATM 5 C C5 APR . . . B 2 16.336 24.523 14.285 1 41.9 ? C5 APR 1 A 1 HETATM 6 C C6 APR . . . B 2 17.251 25.589 14.537 1 41.26 ? C6 APR 1 A 1 HETATM 7 N N6 APR . . . B 2 17.4 26.652 13.726 1 37.13 ? N6 APR 1 A 1 HETATM 8 N N7 APR . . . B 2 15.43 24.22 13.312 1 40.5 ? N7 APR 1 A 1 HETATM 9 C C8 APR . . . B 2 14.854 23.047 13.626 1 38.66 ? C8 APR 1 A 1 HETATM 10 N N9 APR . . . B 2 15.381 22.584 14.777 1 39.64 ? N9 APR 1 A 1 HETATM 11 C C1' APR . . . B 2 15.032 21.333 15.513 1 35.99 ? C1' APR 1 A 1 HETATM 12 C C2' APR . . . B 2 13.688 20.914 14.943 1 36.28 ? C2' APR 1 A 1 HETATM 13 O O2' APR . . . B 2 12.659 21.658 15.606 1 41.35 ? O2' APR 1 A 1 HETATM 14 C C3' APR . . . B 2 13.652 19.445 15.321 1 33.47 ? C3' APR 1 A 1 HETATM 15 O O3' APR . . . B 2 13.264 19.348 16.676 1 28.96 ? O3' APR 1 A 1 HETATM 16 O O4' APR . . . B 2 15.924 20.241 15.266 1 33.1 ? O4' APR 1 A 1 HETATM 17 C C4' APR . . . B 2 15.12 19.008 15.146 1 30.77 ? C4' APR 1 A 1 HETATM 18 C C5' APR . . . B 2 15.402 18.307 13.774 1 26.8 ? C5' APR 1 A 1 HETATM 19 O O5' APR . . . B 2 14.77 19.029 12.687 1 20.84 ? O5' APR 1 A 1 HETATM 20 P PA APR . . . B 2 15.429 19.223 11.256 1 19.81 ? PA APR 1 A 1 HETATM 21 O O1A APR . . . B 2 16.681 19.987 11.484 1 22.4 ? O1A APR 1 A 1 HETATM 22 O O2A APR . . . B 2 14.472 19.825 10.288 1 21.64 ? O2A APR 1 A 1 HETATM 23 O O3A APR . . . B 2 15.868 17.587 10.884 1 16.55 ? O3A APR 1 A 1 HETATM 24 P PB APR . . . B 2 15.142 16.469 9.817 1 19.01 ? PB APR 1 A 1 HETATM 25 O O1B APR . . . B 2 13.766 16.706 10.337 1 19.34 ? O1B APR 1 A 1 HETATM 26 O O2B APR . . . B 2 16.051 15.394 10.362 1 16.2 ? O2B APR 1 A 1 HETATM 27 O O5D APR . . . B 2 15.673 17.399 8.669 1 19.64 ? O5D APR 1 A 1 HETATM 28 C C5D APR . . . B 2 16.815 17.028 7.937 1 24.06 ? C5D APR 1 A 1 HETATM 29 O O4D APR . . . B 2 16.629 19.272 7.378 1 28.99 ? O4D APR 1 A 1 HETATM 30 O O1D APR . . . B 2 17.124 20.725 5.728 1 35.68 ? O1D APR 1 A 1 HETATM 31 C C1D APR . . . B 2 17.691 20.198 6.961 1 32.2 ? C1D APR 1 A 1 HETATM 32 O O2D APR . . . B 2 19.981 19.833 5.995 1 30.91 ? O2D APR 1 A 1 HETATM 33 C C2D APR . . . B 2 18.915 19.279 6.806 1 31.71 ? C2D APR 1 A 1 HETATM 34 O O3D APR . . . B 2 17.978 18.508 4.661 1 31.69 ? O3D APR 1 A 1 HETATM 35 C C3D APR . . . B 2 18.235 18.131 6.05 1 31.18 ? C3D APR 1 A 1 HETATM 36 C C4D APR . . . B 2 16.899 17.998 6.785 1 27.01 ? C4D APR 1 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 36 #