data_2YDD # _model_server_result.job_id UtDQfEJuw8M5TnHOcx5faA _model_server_result.datetime_utc '2024-12-02 21:06:55' _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 2ydd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1379}' # _entry.id 2YDD # _exptl.entry_id 2YDD _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-2'-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 90 _cell.entry_id 2YDD _cell.length_a 41.36 _cell.length_b 46.81 _cell.length_c 106.59 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 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 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id 2AM _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-2'-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 2AM doub 1 n n P O2P 2AM sing 2 n n P O3P 2AM sing 3 n n P O2' 2AM sing 4 n n O2P HOP2 2AM sing 5 n n O3P HOP3 2AM sing 6 n n C5' O5' 2AM sing 7 n n C5' C4' 2AM sing 8 n n C5' "H5'1" 2AM sing 9 n n C5' "H5'2" 2AM sing 10 n n O5' HO5' 2AM sing 11 n n C4' O4' 2AM sing 12 n n C4' C3' 2AM sing 13 n n C4' H4' 2AM sing 14 n n O4' C1' 2AM sing 15 n n C3' O3' 2AM sing 16 n n C3' C2' 2AM sing 17 n n C3' H3' 2AM sing 18 n n O3' HO3' 2AM sing 19 n n C2' O2' 2AM sing 20 n n C2' C1' 2AM sing 21 n n C2' H2' 2AM sing 22 n n C1' N9 2AM sing 23 n n C1' H1' 2AM sing 24 n n N9 C8 2AM sing 25 n y N9 C4 2AM sing 26 n y C8 N7 2AM doub 27 n y C8 H8 2AM sing 28 n n N7 C5 2AM sing 29 n y C5 C6 2AM sing 30 n y C5 C4 2AM doub 31 n y C6 N6 2AM sing 32 n n C6 N1 2AM doub 33 n y N6 HN61 2AM sing 34 n n N6 HN62 2AM sing 35 n n N1 C2 2AM sing 36 n y C2 N3 2AM doub 37 n y C2 H2 2AM sing 38 n n N3 C4 2AM sing 39 n y # _atom_sites.entry_id 2YDD _atom_sites.fract_transf_matrix[1][1] 0.024178 _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] 0.021363 _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] 0.009382 _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 2AM A 1 1379 1379 2AM 2AM . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 HOH HOH . C 3 HOH A 27 2027 2027 HOH HOH . C 3 HOH A 28 2028 2028 HOH HOH . C 3 HOH A 29 2029 2029 HOH HOH . C 3 HOH A 30 2030 2030 HOH HOH . C 3 HOH A 31 2031 2031 HOH HOH . C 3 HOH A 32 2032 2032 HOH HOH . C 3 HOH A 33 2033 2033 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 P 2AM . . . B 2 -6.042 5.774 -21.486 1 70.24 ? P 2AM 1379 A 1 HETATM 2 O O1P 2AM . . . B 2 -4.56 6.043 -21.694 1 66.79 ? O1P 2AM 1379 A 1 HETATM 3 O O2P 2AM . . . B 2 -6.26 4.413 -20.852 1 66.57 ? O2P 2AM 1379 A 1 HETATM 4 O O3P 2AM . . . B 2 -6.694 6.767 -20.547 1 69.71 ? O3P 2AM 1379 A 1 HETATM 5 C C5' 2AM . . . B 2 -5.886 5.093 -27.413 1 69.11 ? C5' 2AM 1379 A 1 HETATM 6 O O5' 2AM . . . B 2 -4.993 5.944 -28.109 1 71.05 ? O5' 2AM 1379 A 1 HETATM 7 C C4' 2AM . . . B 2 -6.348 5.796 -26.141 1 65.28 ? C4' 2AM 1379 A 1 HETATM 8 O O4' 2AM . . . B 2 -7.743 5.661 -25.959 1 66.41 ? O4' 2AM 1379 A 1 HETATM 9 C C3' 2AM . . . B 2 -5.677 5.234 -24.908 1 64.93 ? C3' 2AM 1379 A 1 HETATM 10 O O3' 2AM . . . B 2 -4.736 6.174 -24.449 1 60.13 ? O3' 2AM 1379 A 1 HETATM 11 C C2' 2AM . . . B 2 -6.799 4.994 -23.908 1 65.06 ? C2' 2AM 1379 A 1 HETATM 12 O O2' 2AM . . . B 2 -6.752 5.99 -22.924 1 66.42 ? O2' 2AM 1379 A 1 HETATM 13 C C1' 2AM . . . B 2 -8.101 5.202 -24.661 1 64.68 ? C1' 2AM 1379 A 1 HETATM 14 N N9 2AM . . . B 2 -8.995 4.023 -24.834 1 63.37 ? N9 2AM 1379 A 1 HETATM 15 C C8 2AM . . . B 2 -8.795 2.972 -25.702 1 62.57 ? C8 2AM 1379 A 1 HETATM 16 N N7 2AM . . . B 2 -9.84 2.108 -25.62 1 61.12 ? N7 2AM 1379 A 1 HETATM 17 C C5 2AM . . . B 2 -10.72 2.6 -24.721 1 61.91 ? C5 2AM 1379 A 1 HETATM 18 C C6 2AM . . . B 2 -11.947 2.125 -24.264 1 62.43 ? C6 2AM 1379 A 1 HETATM 19 N N6 2AM . . . B 2 -12.421 0.972 -24.734 1 64.41 ? N6 2AM 1379 A 1 HETATM 20 N N1 2AM . . . B 2 -12.658 2.845 -23.315 1 61.75 ? N1 2AM 1379 A 1 HETATM 21 C C2 2AM . . . B 2 -12.148 4.039 -22.826 1 60.75 ? C2 2AM 1379 A 1 HETATM 22 N N3 2AM . . . B 2 -10.93 4.507 -23.286 1 61.66 ? N3 2AM 1379 A 1 HETATM 23 C C4 2AM . . . B 2 -10.216 3.804 -24.218 1 62.78 ? C4 2AM 1379 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #