data_2YOZ # _model_server_result.job_id k710929_EEZRptxN8G3X9Q _model_server_result.datetime_utc '2024-11-28 21:59:02' _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 2yoz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1379}' # _entry.id 2YOZ # _exptl.entry_id 2YOZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.287 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-O-(sulfidophosphinato)adenosine" _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 94.45 _cell.angle_gamma 90 _cell.entry_id 2YOZ _cell.length_a 38.4 _cell.length_b 47.88 _cell.length_c 51.15 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YOZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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,D,E,F,G,H,I,J _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 O6 P S' _chem_comp.formula_weight 363.287 _chem_comp.id OVE _chem_comp.mon_nstd_flag . _chem_comp.name "2'-O-(sulfidophosphinato)adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-2'-MONOPHOSPHOROTHIOATE" # 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 O1P P OVE sing 293 n n P S2P OVE sing 294 n n P O3P OVE doub 295 n n P O2' OVE sing 296 n n O2' C2' OVE sing 297 n n C2' C3' OVE sing 298 n n C2' C1' OVE sing 299 n n C3' O3' OVE sing 300 n n C3' C4' OVE sing 301 n n C1' O4' OVE sing 302 n n C1' N9 OVE sing 303 n n O4' C4' OVE sing 304 n n C4' C5' OVE sing 305 n n C5' O5' OVE sing 306 n n N9 C8 OVE sing 307 n y N9 C4 OVE sing 308 n y C8 N7 OVE doub 309 n y N7 C5 OVE sing 310 n y C5 C6 OVE doub 311 n y C5 C4 OVE sing 312 n y C6 N6 OVE sing 313 n n C6 N1 OVE sing 314 n y C4 N3 OVE doub 315 n y N3 C2 OVE sing 316 n y H2 C2 OVE sing 317 n n N1 C2 OVE doub 318 n y O1P H1P OVE sing 319 n n S2P H2P OVE sing 320 n n C2' H2' OVE sing 321 n n C3' H3' OVE sing 322 n n C1' H1' OVE sing 323 n n O3' HA OVE sing 324 n n C4' H4' OVE sing 325 n n C5' "H5'1" OVE sing 326 n n C5' "H5'2" OVE sing 327 n n O5' H5' OVE sing 328 n n C8 H8 OVE sing 329 n n N6 H61N OVE sing 330 n n N6 H62N OVE sing 331 n n # _atom_sites.entry_id 2YOZ _atom_sites.fract_transf_matrix[1][1] 0.026042 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002027 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020886 _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] 0.019609 _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 OVE A 1 1379 1379 OVE OVE . C 3 GOL A 1 1380 1380 GOL GOL . D 4 1PE A 1 1381 1381 1PE 1PE . E 5 ACT A 1 1382 1382 ACT ACT . F 5 ACT A 1 1383 1383 ACT ACT . G 5 ACT A 1 1384 1384 ACT ACT . H 6 CL A 1 1385 1385 CL CL . I 5 ACT A 1 1386 1386 ACT ACT . J 7 HOH A 1 2001 2001 HOH HOH . J 7 HOH A 2 2002 2002 HOH HOH . J 7 HOH A 3 2003 2003 HOH HOH . J 7 HOH A 4 2004 2004 HOH HOH . J 7 HOH A 5 2005 2005 HOH HOH . J 7 HOH A 6 2006 2006 HOH HOH . J 7 HOH A 7 2007 2007 HOH HOH . J 7 HOH A 8 2008 2008 HOH HOH . J 7 HOH A 9 2009 2009 HOH HOH . J 7 HOH A 10 2010 2010 HOH HOH . J 7 HOH A 11 2011 2011 HOH HOH . J 7 HOH A 12 2012 2012 HOH HOH . J 7 HOH A 13 2013 2013 HOH HOH . J 7 HOH A 14 2014 2014 HOH HOH . J 7 HOH A 15 2015 2015 HOH HOH . J 7 HOH A 16 2016 2016 HOH HOH . J 7 HOH A 17 2017 2017 HOH HOH . J 7 HOH A 18 2018 2018 HOH HOH . J 7 HOH A 19 2019 2019 HOH HOH . J 7 HOH A 20 2020 2020 HOH HOH . J 7 HOH A 21 2021 2021 HOH HOH . J 7 HOH A 22 2022 2022 HOH HOH . J 7 HOH A 23 2023 2023 HOH HOH . J 7 HOH A 24 2024 2024 HOH HOH . J 7 HOH A 25 2025 2025 HOH HOH . J 7 HOH A 26 2026 2026 HOH HOH . J 7 HOH A 27 2027 2027 HOH HOH . J 7 HOH A 28 2028 2028 HOH HOH . J 7 HOH A 29 2029 2029 HOH HOH . J 7 HOH A 30 2030 2030 HOH HOH . J 7 HOH A 31 2031 2031 HOH HOH . J 7 HOH A 32 2032 2032 HOH HOH . J 7 HOH A 33 2033 2033 HOH HOH . J 7 HOH A 34 2034 2034 HOH HOH . J 7 HOH A 35 2035 2035 HOH HOH . J 7 HOH A 36 2036 2036 HOH HOH . J 7 HOH A 37 2037 2037 HOH HOH . J 7 HOH A 38 2038 2038 HOH HOH . J 7 HOH A 39 2039 2039 HOH HOH . J 7 HOH A 40 2040 2040 HOH HOH . J 7 HOH A 41 2041 2041 HOH HOH . J 7 HOH A 42 2042 2042 HOH HOH . J 7 HOH A 43 2043 2043 HOH HOH . J 7 HOH A 44 2044 2044 HOH HOH . J 7 HOH A 45 2045 2045 HOH HOH . J 7 HOH A 46 2046 2046 HOH HOH . J 7 HOH A 47 2047 2047 HOH HOH . J 7 HOH A 48 2048 2048 HOH HOH . J 7 HOH A 49 2049 2049 HOH HOH . J 7 HOH A 50 2050 2050 HOH HOH . J 7 HOH A 51 2051 2051 HOH HOH . J 7 HOH A 52 2052 2052 HOH HOH . J 7 HOH A 53 2053 2053 HOH HOH . J 7 HOH A 54 2054 2054 HOH HOH . J 7 HOH A 55 2055 2055 HOH HOH . J 7 HOH A 56 2056 2056 HOH HOH . J 7 HOH A 57 2057 2057 HOH HOH . J 7 HOH A 58 2058 2058 HOH HOH . J 7 HOH A 59 2059 2059 HOH HOH . J 7 HOH A 60 2060 2060 HOH HOH . J 7 HOH A 61 2061 2061 HOH HOH . J 7 HOH A 62 2062 2062 HOH HOH . J 7 HOH A 63 2063 2063 HOH HOH . J 7 HOH A 64 2064 2064 HOH HOH . J 7 HOH A 65 2065 2065 HOH HOH . J 7 HOH A 66 2066 2066 HOH HOH . J 7 HOH A 67 2067 2067 HOH HOH . J 7 HOH A 68 2068 2068 HOH HOH . J 7 HOH A 69 2069 2069 HOH HOH . J 7 HOH A 70 2070 2070 HOH HOH . J 7 HOH A 71 2071 2071 HOH HOH . J 7 HOH A 72 2072 2072 HOH HOH . J 7 HOH A 73 2073 2073 HOH HOH . J 7 HOH A 74 2074 2074 HOH HOH . J 7 HOH A 75 2075 2075 HOH HOH . J 7 HOH A 76 2076 2076 HOH HOH . J 7 HOH A 77 2077 2077 HOH HOH . J 7 HOH A 78 2078 2078 HOH HOH . J 7 HOH A 79 2079 2079 HOH HOH . J 7 HOH A 80 2080 2080 HOH HOH . J 7 HOH A 81 2081 2081 HOH HOH . J 7 HOH A 82 2082 2082 HOH HOH . J 7 HOH A 83 2083 2083 HOH HOH . J 7 HOH A 84 2084 2084 HOH HOH . J 7 HOH A 85 2085 2085 HOH HOH . J 7 HOH A 86 2086 2086 HOH HOH . J 7 HOH A 87 2087 2087 HOH HOH . J 7 HOH A 88 2088 2088 HOH HOH . J 7 HOH A 89 2089 2089 HOH HOH . J 7 HOH A 90 2090 2090 HOH HOH . J 7 HOH A 91 2091 2091 HOH HOH . J 7 HOH A 92 2092 2092 HOH HOH . J 7 HOH A 93 2093 2093 HOH HOH . J 7 HOH A 94 2094 2094 HOH HOH . J 7 HOH A 95 2095 2095 HOH HOH . J 7 HOH A 96 2096 2096 HOH HOH . J 7 HOH A 97 2097 2097 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 O O1P OVE . . . B 2 36.673 5.01 71.023 1 46.42 ? O1P OVE 1379 A 1 HETATM 2 P P OVE . . . B 2 37.755 3.954 70.901 1 48.69 ? P OVE 1379 A 1 HETATM 3 S S2P OVE . . . B 2 37.011 2.344 71.764 1 86.53 ? S2P OVE 1379 A 1 HETATM 4 O O3P OVE . . . B 2 37.805 3.599 69.464 1 42.4 ? O3P OVE 1379 A 1 HETATM 5 O O2' OVE . . . B 2 39.156 4.398 71.497 1 43.35 ? O2' OVE 1379 A 1 HETATM 6 C C2' OVE . . . B 2 39.344 4.484 72.867 1 42.48 ? C2' OVE 1379 A 1 HETATM 7 C C3' OVE . . . B 2 38.332 5.259 73.532 1 38.36 ? C3' OVE 1379 A 1 HETATM 8 O O3' OVE . . . B 2 37.763 6.263 72.718 1 34.15 ? O3' OVE 1379 A 1 HETATM 9 C C1' OVE . . . B 2 40.6 5.262 73.146 1 41.94 ? C1' OVE 1379 A 1 HETATM 10 O O4' OVE . . . B 2 40.413 5.853 74.389 1 43.43 ? O4' OVE 1379 A 1 HETATM 11 C C4' OVE . . . B 2 39.054 5.963 74.595 1 40.1 ? C4' OVE 1379 A 1 HETATM 12 C C5' OVE . . . B 2 38.668 5.344 75.91 1 39.79 ? C5' OVE 1379 A 1 HETATM 13 O O5' OVE . . . B 2 39.264 4.082 76.029 1 39.76 ? O5' OVE 1379 A 1 HETATM 14 N N9 OVE . . . B 2 41.811 4.455 73.112 1 35.62 ? N9 OVE 1379 A 1 HETATM 15 C C8 OVE . . . B 2 42.854 4.527 72.199 1 31.87 ? C8 OVE 1379 A 1 HETATM 16 N N7 OVE . . . B 2 43.789 3.605 72.546 1 31.17 ? N7 OVE 1379 A 1 HETATM 17 C C5 OVE . . . B 2 43.352 2.955 73.675 1 31.8 ? C5 OVE 1379 A 1 HETATM 18 C C6 OVE . . . B 2 43.917 1.945 74.435 1 33.71 ? C6 OVE 1379 A 1 HETATM 19 N N6 OVE . . . B 2 45.2 1.396 74.065 1 33.06 ? N6 OVE 1379 A 1 HETATM 20 C C4 OVE . . . B 2 42.116 3.481 74.04 1 31.75 ? C4 OVE 1379 A 1 HETATM 21 N N3 OVE . . . B 2 41.481 3.016 75.109 1 31.56 ? N3 OVE 1379 A 1 HETATM 22 C C2 OVE . . . B 2 42.033 2.01 75.866 1 33.89 ? C2 OVE 1379 A 1 HETATM 23 N N1 OVE . . . B 2 43.27 1.473 75.516 1 35.47 ? N1 OVE 1379 A 1 HETATM 24 H H2' OVE . . . B 2 39.397 3.598 73.283 1 50.98 ? H2' OVE 1379 A 1 HETATM 25 H H3' OVE . . . B 2 37.646 4.645 73.893 1 46.04 ? H3' OVE 1379 A 1 HETATM 26 H H1' OVE . . . B 2 40.691 5.986 72.474 1 50.33 ? H1' OVE 1379 A 1 HETATM 27 H HA OVE . . . B 2 36.918 6.095 72.597 1 40.97 ? HA OVE 1379 A 1 HETATM 28 H H4' OVE . . . B 2 38.8 6.862 74.598 1 48.12 ? H4' OVE 1379 A 1 HETATM 29 H "H5'1" OVE . . . B 2 37.719 5.252 75.953 1 47.75 ? "H5'1" OVE 1379 A 1 HETATM 30 H "H5'2" OVE . . . B 2 38.971 5.915 76.638 1 47.75 ? "H5'2" OVE 1379 A 1 HETATM 31 H H5' OVE . . . B 2 38.741 3.456 75.608 1 47.71 ? H5' OVE 1379 A 1 HETATM 32 H H2 OVE . . . B 2 41.554 1.67 76.66 1 40.66 ? H2 OVE 1379 A 1 HETATM 33 H H8 OVE . . . B 2 42.903 5.115 71.457 1 38.25 ? H8 OVE 1379 A 1 HETATM 34 H H61N OVE . . . B 2 45.338 1.087 73.21 1 39.67 ? H61N OVE 1379 A 1 HETATM 35 H H62N OVE . . . B 2 45.874 1.356 74.678 1 39.67 ? H62N OVE 1379 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #