data_2YPH # _model_server_result.job_id Ymw3JJ5jMsXC5ltAzRmdpQ _model_server_result.datetime_utc '2024-11-24 09:42:38' _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 2yph # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1381}' # _entry.id 2YPH # _exptl.entry_id 2YPH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 345.272 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanylidene-2-sulfanyl-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol' _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 2YPH _cell.length_a 40.63 _cell.length_b 47.53 _cell.length_c 107.55 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YPH _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 software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H12 N5 O5 P S' _chem_comp.formula_weight 345.272 _chem_comp.id QQY _chem_comp.mon_nstd_flag . _chem_comp.name '[(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanylidene-2-sulfanyl-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol' _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 OP3 P QQY doub 283 n n S1P P QQY sing 284 n n O5' C5' QQY sing 285 n n C5' C4' QQY sing 286 n n C4' O4' QQY sing 287 n n C4' C3' QQY sing 288 n n O4' C1' QQY sing 289 n n C3' O3' QQY sing 290 n n C3' C2' QQY sing 291 n n O3' P QQY sing 292 n n C2' O2' QQY sing 293 n n C2' C1' QQY sing 294 n n O2' P QQY sing 295 n n C1' N9 QQY sing 296 n n N9 C8 QQY sing 297 n y N9 C4 QQY sing 298 n y C8 N7 QQY doub 299 n y N7 C5 QQY sing 300 n y C5 C6 QQY doub 301 n y C5 C4 QQY sing 302 n y N3 C4 QQY doub 303 n y C6 N6 QQY sing 304 n n C6 N1 QQY sing 305 n y N1 C2 QQY doub 306 n y C2 N3 QQY sing 307 n y S1P H1P QQY sing 308 n n O5' H5' QQY sing 309 n n C5' "H5'1" QQY sing 310 n n C5' "H5'2" QQY sing 311 n n C4' H4' QQY sing 312 n n C3' H3' QQY sing 313 n n C1' H1' QQY sing 314 n n C2' H2' QQY sing 315 n n C8 H8 QQY sing 316 n n N6 H61N QQY sing 317 n n N6 H62N QQY sing 318 n n C2 H2 QQY sing 319 n n # _atom_sites.entry_id 2YPH _atom_sites.fract_transf_matrix[1][1] 0.024612 _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] 0.021039 _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] 0.009298 _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 ACT A 1 1379 1379 ACT ACT . C 3 CL A 1 1380 1380 CL CL . D 4 QQY A 1 1381 1381 QQY QQY . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 HOH HOH . E 5 HOH A 74 2074 2074 HOH HOH . E 5 HOH A 75 2075 2075 HOH HOH . E 5 HOH A 76 2076 2076 HOH HOH . E 5 HOH A 77 2077 2077 HOH HOH . E 5 HOH A 78 2078 2078 HOH HOH . E 5 HOH A 79 2079 2079 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 OP3 QQY . . . D 4 -4.989 5.08 -20.729 0.81 55.86 ? OP3 QQY 1381 A 1 HETATM 2 S S1P QQY . . . D 4 -7.83 5.655 -20.865 0.81 60.05 ? S1P QQY 1381 A 1 HETATM 3 O O5' QQY . . . D 4 -6.464 4.777 -27.073 0.81 86.27 ? O5' QQY 1381 A 1 HETATM 4 C C5' QQY . . . D 4 -6.061 6.039 -26.635 0.81 86.66 ? C5' QQY 1381 A 1 HETATM 5 C C4' QQY . . . D 4 -6.696 6.388 -25.291 0.81 87.2 ? C4' QQY 1381 A 1 HETATM 6 O O4' QQY . . . D 4 -8.052 5.975 -25.279 0.81 87.46 ? O4' QQY 1381 A 1 HETATM 7 C C3' QQY . . . D 4 -5.956 5.724 -24.136 0.81 87.55 ? C3' QQY 1381 A 1 HETATM 8 O O3' QQY . . . D 4 -6.11 6.493 -22.968 0.81 87.45 ? O3' QQY 1381 A 1 HETATM 9 C C2' QQY . . . D 4 -6.753 4.442 -24.024 0.81 87.85 ? C2' QQY 1381 A 1 HETATM 10 O O2' QQY . . . D 4 -6.664 3.884 -22.738 0.81 88.06 ? O2' QQY 1381 A 1 HETATM 11 C C1' QQY . . . D 4 -8.149 4.939 -24.327 0.81 87.75 ? C1' QQY 1381 A 1 HETATM 12 N N9 QQY . . . D 4 -8.997 3.852 -24.797 0.81 87.67 ? N9 QQY 1381 A 1 HETATM 13 C C8 QQY . . . D 4 -8.746 2.967 -25.796 0.81 87.37 ? C8 QQY 1381 A 1 HETATM 14 N N7 QQY . . . D 4 -9.776 2.086 -25.949 0.81 87.29 ? N7 QQY 1381 A 1 HETATM 15 C C5 QQY . . . D 4 -10.67 2.456 -25.011 0.81 87.53 ? C5 QQY 1381 A 1 HETATM 16 C C6 QQY . . . D 4 -11.91 1.921 -24.7 0.81 87.58 ? C6 QQY 1381 A 1 HETATM 17 N N6 QQY . . . D 4 -12.429 0.815 -25.401 0.81 87.61 ? N6 QQY 1381 A 1 HETATM 18 N N1 QQY . . . D 4 -12.621 2.5 -23.686 0.81 87.47 ? N1 QQY 1381 A 1 HETATM 19 C C2 QQY . . . D 4 -12.121 3.58 -22.997 0.81 87.58 ? C2 QQY 1381 A 1 HETATM 20 C C4 QQY . . . D 4 -10.201 3.514 -24.322 0.81 87.71 ? C4 QQY 1381 A 1 HETATM 21 N N3 QQY . . . D 4 -10.893 4.098 -23.317 0.81 87.7 ? N3 QQY 1381 A 1 HETATM 22 P P QQY . . . D 4 -6.361 5.279 -21.774 0.81 74.02 ? P QQY 1381 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 22 #