data_1RY2 # _model_server_result.job_id GbXcy9XcvagfbtA9ka4L5A _model_server_result.datetime_utc '2024-12-06 07:31:43' _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 1ry2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":720}' # _entry.id 1RY2 # _exptl.entry_id 1RY2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 1RY2 _cell.length_a 107.13 _cell.length_b 107.13 _cell.length_c 54.79 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RY2 _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 107.13 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 53.565 92.777302 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 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 1RY2 _atom_sites.fract_transf_matrix[1][1] 0.009334 _atom_sites.fract_transf_matrix[1][2] 0.005389 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010778 _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] 0.018252 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id AMP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 720 _pdbx_nonpoly_scheme.auth_seq_num 720 _pdbx_nonpoly_scheme.pdb_mon_id AMP _pdbx_nonpoly_scheme.auth_mon_id AMP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 P AMP . . . B 2 93.176 31.895 -5.081 1 32.03 ? P AMP 720 A 1 HETATM 2 O O1P AMP . . . B 2 92.406 31.235 -3.903 1 32.21 ? O1P AMP 720 A 1 HETATM 3 O O2P AMP . . . B 2 92.512 31.562 -6.364 1 31.52 ? O2P AMP 720 A 1 HETATM 4 O O3P AMP . . . B 2 94.639 31.381 -5.092 1 31.05 ? O3P AMP 720 A 1 HETATM 5 O O5' AMP . . . B 2 93.21 33.478 -4.873 1 30.59 ? O5' AMP 720 A 1 HETATM 6 C C5' AMP . . . B 2 93.785 34.032 -3.718 1 33.35 ? C5' AMP 720 A 1 HETATM 7 C C4' AMP . . . B 2 93.757 35.535 -3.801 1 34.94 ? C4' AMP 720 A 1 HETATM 8 O O4' AMP . . . B 2 92.478 36.065 -3.452 1 37.58 ? O4' AMP 720 A 1 HETATM 9 C C3' AMP . . . B 2 94.791 36.193 -2.909 1 36.35 ? C3' AMP 720 A 1 HETATM 10 O O3' AMP . . . B 2 95.828 36.795 -3.655 1 37.77 ? O3' AMP 720 A 1 HETATM 11 C C2' AMP . . . B 2 94.016 37.169 -2.044 1 37.38 ? C2' AMP 720 A 1 HETATM 12 O O2' AMP . . . B 2 94.444 38.491 -2.208 1 39.22 ? O2' AMP 720 A 1 HETATM 13 C C1' AMP . . . B 2 92.553 37.043 -2.42 1 37.78 ? C1' AMP 720 A 1 HETATM 14 N N9 AMP . . . B 2 91.699 36.653 -1.252 1 38.32 ? N9 AMP 720 A 1 HETATM 15 C C8 AMP . . . B 2 91.365 35.381 -0.845 1 38.96 ? C8 AMP 720 A 1 HETATM 16 N N7 AMP . . . B 2 90.582 35.441 0.266 1 37.74 ? N7 AMP 720 A 1 HETATM 17 C C5 AMP . . . B 2 90.411 36.742 0.572 1 38.45 ? C5 AMP 720 A 1 HETATM 18 C C6 AMP . . . B 2 89.698 37.348 1.616 1 36.48 ? C6 AMP 720 A 1 HETATM 19 N N6 AMP . . . B 2 89.046 36.605 2.504 1 34.93 ? N6 AMP 720 A 1 HETATM 20 N N1 AMP . . . B 2 89.703 38.76 1.682 1 35.36 ? N1 AMP 720 A 1 HETATM 21 C C2 AMP . . . B 2 90.386 39.539 0.754 1 35.36 ? C2 AMP 720 A 1 HETATM 22 N N3 AMP . . . B 2 91.1 38.928 -0.289 1 39.23 ? N3 AMP 720 A 1 HETATM 23 C C4 AMP . . . B 2 91.103 37.533 -0.367 1 38.84 ? C4 AMP 720 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #