data_3ZBZ # _model_server_result.job_id R9_5V_75ATvGg0OFd1Z7dQ _model_server_result.datetime_utc '2024-11-28 21:27:07' _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 3zbz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1380}' # _entry.id 3ZBZ # _exptl.entry_id 3ZBZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.287 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 3ZBZ _cell.length_a 41.25 _cell.length_b 46.99 _cell.length_c 107.38 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZBZ _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,D _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 3 _struct_asym.id C _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 244 n n P S2P OVE sing 245 n n P O3P OVE doub 246 n n P O2' OVE sing 247 n n O2' C2' OVE sing 248 n n C2' C3' OVE sing 249 n n C2' C1' OVE sing 250 n n C3' O3' OVE sing 251 n n C3' C4' OVE sing 252 n n C1' O4' OVE sing 253 n n C1' N9 OVE sing 254 n n O4' C4' OVE sing 255 n n C4' C5' OVE sing 256 n n C5' O5' OVE sing 257 n n N9 C8 OVE sing 258 n y N9 C4 OVE sing 259 n y C8 N7 OVE doub 260 n y N7 C5 OVE sing 261 n y C5 C6 OVE doub 262 n y C5 C4 OVE sing 263 n y C6 N6 OVE sing 264 n n C6 N1 OVE sing 265 n y C4 N3 OVE doub 266 n y N3 C2 OVE sing 267 n y H2 C2 OVE sing 268 n n N1 C2 OVE doub 269 n y O1P H1P OVE sing 270 n n S2P H2P OVE sing 271 n n C2' H2' OVE sing 272 n n C3' H3' OVE sing 273 n n C1' H1' OVE sing 274 n n O3' HA OVE sing 275 n n C4' H4' OVE sing 276 n n C5' "H5'1" OVE sing 277 n n C5' "H5'2" OVE sing 278 n n O5' H5' OVE sing 279 n n C8 H8 OVE sing 280 n n N6 H61N OVE sing 281 n n N6 H62N OVE sing 282 n n # _atom_sites.entry_id 3ZBZ _atom_sites.fract_transf_matrix[1][1] 0.024242 _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] 0.021281 _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] 0.009313 _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 ACY A 1 1379 1379 ACY ACY . C 3 OVE A 1 1380 1380 OVE OVE . D 4 HOH A 1 2001 2001 HOH HOH . D 4 HOH A 2 2002 2002 HOH HOH . D 4 HOH A 3 2003 2003 HOH HOH . D 4 HOH A 4 2004 2004 HOH HOH . D 4 HOH A 5 2005 2005 HOH HOH . D 4 HOH A 6 2006 2006 HOH HOH . D 4 HOH A 7 2007 2007 HOH HOH . D 4 HOH A 8 2008 2008 HOH HOH . D 4 HOH A 9 2009 2009 HOH HOH . D 4 HOH A 10 2010 2010 HOH HOH . D 4 HOH A 11 2011 2011 HOH HOH . D 4 HOH A 12 2012 2012 HOH HOH . D 4 HOH A 13 2013 2013 HOH HOH . D 4 HOH A 14 2014 2014 HOH HOH . D 4 HOH A 15 2015 2015 HOH HOH . D 4 HOH A 16 2016 2016 HOH HOH . D 4 HOH A 17 2017 2017 HOH HOH . D 4 HOH A 18 2018 2018 HOH HOH . D 4 HOH A 19 2019 2019 HOH HOH . D 4 HOH A 20 2020 2020 HOH HOH . D 4 HOH A 21 2021 2021 HOH HOH . D 4 HOH A 22 2022 2022 HOH HOH . D 4 HOH A 23 2023 2023 HOH HOH . D 4 HOH A 24 2024 2024 HOH HOH . D 4 HOH A 25 2025 2025 HOH HOH . D 4 HOH A 26 2026 2026 HOH HOH . D 4 HOH A 27 2027 2027 HOH HOH . D 4 HOH A 28 2028 2028 HOH HOH . D 4 HOH A 29 2029 2029 HOH HOH . D 4 HOH A 30 2030 2030 HOH HOH . D 4 HOH A 31 2031 2031 HOH HOH . D 4 HOH A 32 2032 2032 HOH HOH . D 4 HOH A 33 2033 2033 HOH HOH . D 4 HOH A 34 2034 2034 HOH HOH . D 4 HOH A 35 2035 2035 HOH HOH . D 4 HOH A 36 2036 2036 HOH HOH . D 4 HOH A 37 2037 2037 HOH HOH . D 4 HOH A 38 2038 2038 HOH HOH . D 4 HOH A 39 2039 2039 HOH HOH . D 4 HOH A 40 2040 2040 HOH HOH . D 4 HOH A 41 2041 2041 HOH HOH . D 4 HOH A 42 2042 2042 HOH HOH . D 4 HOH A 43 2043 2043 HOH HOH . D 4 HOH A 44 2044 2044 HOH HOH . D 4 HOH A 45 2045 2045 HOH HOH . D 4 HOH A 46 2046 2046 HOH HOH . D 4 HOH A 47 2047 2047 HOH HOH . D 4 HOH A 48 2048 2048 HOH HOH . D 4 HOH A 49 2049 2049 HOH HOH . D 4 HOH A 50 2050 2050 HOH HOH . D 4 HOH A 51 2051 2051 HOH HOH . D 4 HOH A 52 2052 2052 HOH HOH . D 4 HOH A 53 2053 2053 HOH HOH . D 4 HOH A 54 2054 2054 HOH HOH . D 4 HOH A 55 2055 2055 HOH HOH . D 4 HOH A 56 2056 2056 HOH HOH . D 4 HOH A 57 2057 2057 HOH HOH . D 4 HOH A 58 2058 2058 HOH HOH . D 4 HOH A 59 2059 2059 HOH HOH . D 4 HOH A 60 2060 2060 HOH HOH . D 4 HOH A 61 2061 2061 HOH HOH . D 4 HOH A 62 2062 2062 HOH HOH . D 4 HOH A 63 2063 2063 HOH HOH . D 4 HOH A 64 2064 2064 HOH HOH . D 4 HOH A 65 2065 2065 HOH HOH . D 4 HOH A 66 2066 2066 HOH HOH . D 4 HOH A 67 2067 2067 HOH HOH . D 4 HOH A 68 2068 2068 HOH HOH . D 4 HOH A 69 2069 2069 HOH HOH . D 4 HOH A 70 2070 2070 HOH HOH . D 4 HOH A 71 2071 2071 HOH HOH . D 4 HOH A 72 2072 2072 HOH HOH . D 4 HOH A 73 2073 2073 HOH HOH . D 4 HOH A 74 2074 2074 HOH HOH . D 4 HOH A 75 2075 2075 HOH HOH . D 4 HOH A 76 2076 2076 HOH HOH . D 4 HOH A 77 2077 2077 HOH HOH . D 4 HOH A 78 2078 2078 HOH HOH . D 4 HOH A 79 2079 2079 HOH HOH . D 4 HOH A 80 2080 2080 HOH HOH . D 4 HOH A 81 2081 2081 HOH HOH . D 4 HOH A 82 2082 2082 HOH HOH . D 4 HOH A 83 2083 2083 HOH HOH . D 4 HOH A 84 2084 2084 HOH HOH . D 4 HOH A 85 2085 2085 HOH HOH . D 4 HOH A 86 2086 2086 HOH HOH . D 4 HOH A 87 2087 2087 HOH HOH . D 4 HOH A 88 2088 2088 HOH HOH . D 4 HOH A 89 2089 2089 HOH HOH . D 4 HOH A 90 2090 2090 HOH HOH . D 4 HOH A 91 2091 2091 HOH HOH . D 4 HOH A 92 2092 2092 HOH HOH . D 4 HOH A 93 2093 2093 HOH HOH . D 4 HOH A 94 2094 2094 HOH HOH . D 4 HOH A 95 2095 2095 HOH HOH . D 4 HOH A 96 2096 2096 HOH HOH . D 4 HOH A 97 2097 2097 HOH HOH . D 4 HOH A 98 2098 2098 HOH HOH . D 4 HOH A 99 2099 2099 HOH HOH . D 4 HOH A 100 2100 2100 HOH HOH . D 4 HOH A 101 2101 2101 HOH HOH . D 4 HOH A 102 2102 2102 HOH HOH . D 4 HOH A 103 2103 2103 HOH HOH . D 4 HOH A 104 2104 2104 HOH HOH . D 4 HOH A 105 2105 2105 HOH HOH . D 4 HOH A 106 2106 2106 HOH HOH . D 4 HOH A 107 2107 2107 HOH HOH . D 4 HOH A 108 2108 2108 HOH HOH . D 4 HOH A 109 2109 2109 HOH HOH . D 4 HOH A 110 2110 2110 HOH HOH . D 4 HOH A 111 2111 2111 HOH HOH . D 4 HOH A 112 2112 2112 HOH HOH . D 4 HOH A 113 2113 2113 HOH HOH . D 4 HOH A 114 2114 2114 HOH HOH . D 4 HOH A 115 2115 2115 HOH HOH . D 4 HOH A 116 2116 2116 HOH HOH . D 4 HOH A 117 2117 2117 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 . . . C 3 -4.665 5.361 -20.964 1 47.24 ? O1P OVE 1380 A 1 HETATM 2 P P OVE . . . C 3 -5.606 4.285 -21.379 1 40.16 ? P OVE 1380 A 1 HETATM 3 S S2P OVE . . . C 3 -4.646 2.962 -22.487 1 52.64 ? S2P OVE 1380 A 1 HETATM 4 O O3P OVE . . . C 3 -6.202 3.609 -20.153 1 34.39 ? O3P OVE 1380 A 1 HETATM 5 O O2' OVE . . . C 3 -6.753 4.915 -22.203 1 34.73 ? O2' OVE 1380 A 1 HETATM 6 C C2' OVE . . . C 3 -6.956 4.84 -23.551 1 27.45 ? C2' OVE 1380 A 1 HETATM 7 C C3' OVE . . . C 3 -6.114 5.845 -24.249 1 30.06 ? C3' OVE 1380 A 1 HETATM 8 O O3' OVE . . . C 3 -5.739 6.878 -23.389 1 30.31 ? O3' OVE 1380 A 1 HETATM 9 C C1' OVE . . . C 3 -8.277 5.5 -23.644 1 26.9 ? C1' OVE 1380 A 1 HETATM 10 O O4' OVE . . . C 3 -8.303 6.141 -24.875 1 29.6 ? O4' OVE 1380 A 1 HETATM 11 C C4' OVE . . . C 3 -7.001 6.391 -25.287 1 26.71 ? C4' OVE 1380 A 1 HETATM 12 C C5' OVE . . . C 3 -6.736 5.75 -26.602 1 25.62 ? C5' OVE 1380 A 1 HETATM 13 O O5' OVE . . . C 3 -6.935 4.393 -26.453 1 27.22 ? O5' OVE 1380 A 1 HETATM 14 N N9 OVE . . . C 3 -9.468 4.691 -23.489 1 29.54 ? N9 OVE 1380 A 1 HETATM 15 C C8 OVE . . . C 3 -10.484 4.812 -22.519 1 29.57 ? C8 OVE 1380 A 1 HETATM 16 N N7 OVE . . . C 3 -11.423 3.824 -22.773 1 31.55 ? N7 OVE 1380 A 1 HETATM 17 C C5 OVE . . . C 3 -10.972 3.1 -23.906 1 29.86 ? C5 OVE 1380 A 1 HETATM 18 C C6 OVE . . . C 3 -11.54 2.046 -24.535 1 30.78 ? C6 OVE 1380 A 1 HETATM 19 N N6 OVE . . . C 3 -12.789 1.519 -24.048 1 36.74 ? N6 OVE 1380 A 1 HETATM 20 C C4 OVE . . . C 3 -9.784 3.603 -24.365 1 25.24 ? C4 OVE 1380 A 1 HETATM 21 N N3 OVE . . . C 3 -9.136 3.112 -25.42 1 25.91 ? N3 OVE 1380 A 1 HETATM 22 C C2 OVE . . . C 3 -9.698 2.038 -26.075 1 26.47 ? C2 OVE 1380 A 1 HETATM 23 N N1 OVE . . . C 3 -10.902 1.52 -25.615 1 36.68 ? N1 OVE 1380 A 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 1329 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 23 #