data_2YA3 # _model_server_result.job_id fZozDFKSV53MP3wz3T39uw _model_server_result.datetime_utc '2024-11-05 14:46:39' _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 2ya3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1325}' # _entry.id 2YA3 # _exptl.entry_id 2YA3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 669.474 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-(7-diethylaminocoumarin-3-carbonylamino)-3'-deoxy-ADP" _entity.pdbx_number_of_molecules 2 _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 2YA3 _cell.length_a 48.943 _cell.length_b 124.06 _cell.length_c 125.315 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YA3 _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N # _chem_comp.formula 'C24 H29 N7 O12 P2' _chem_comp.formula_weight 669.474 _chem_comp.id J7V _chem_comp.mon_nstd_flag . _chem_comp.name "3'-(7-diethylaminocoumarin-3-carbonylamino)-3'-deoxy-ADP" _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 N1 C2 J7V doub 212 n y N1 C6 J7V sing 213 n y C2 N3 J7V sing 214 n y N3 C4 J7V doub 215 n y C4 C5 J7V sing 216 n y C4 N9 J7V sing 217 n y C5 C6 J7V doub 218 n y C5 N7 J7V sing 219 n y C6 N6 J7V sing 220 n n N7 C8 J7V doub 221 n y C8 N9 J7V sing 222 n y N9 CBO J7V sing 223 n n CAA CAR J7V sing 224 n n CAB CAS J7V sing 225 n n OAD CBC J7V doub 226 n n OAE CBG J7V doub 227 n n OAF PBR J7V sing 228 n n OAG PBS J7V sing 229 n n OAH CBL J7V sing 230 n n OAI PBR J7V doub 231 n n OAJ PBR J7V sing 232 n n OAK PBS J7V doub 233 n n CAM CAN J7V doub 234 n y CAM CBE J7V sing 235 n y CAN CBH J7V sing 236 n y CAP CBE J7V doub 237 n y CAP CBI J7V sing 238 n y CAQ CBF J7V doub 239 n n CAQ CBH J7V sing 240 n n CAR NBP J7V sing 241 n n CAS NBP J7V sing 242 n n CAT OAY J7V sing 243 n n CAT CBM J7V sing 244 n n NAX CBC J7V sing 245 n n NAX CBN J7V sing 246 n n OAY PBS J7V sing 247 n n OAZ CBM J7V sing 248 n n OAZ CBO J7V sing 249 n n OBA PBR J7V sing 250 n n OBA PBS J7V sing 251 n n OBB CBG J7V sing 252 n n OBB CBI J7V sing 253 n n CBC CBF J7V sing 254 n n CBE NBP J7V sing 255 n n CBF CBG J7V sing 256 n n CBH CBI J7V doub 257 n y CBL CBN J7V sing 258 n n CBL CBO J7V sing 259 n n CBM CBN J7V sing 260 n n C2 H2 J7V sing 261 n n N6 HN6 J7V sing 262 n n N6 HN6A J7V sing 263 n n C8 H8 J7V sing 264 n n CAA HAA J7V sing 265 n n CAA HAAA J7V sing 266 n n CAA HAAB J7V sing 267 n n CAB HAB J7V sing 268 n n CAB HABA J7V sing 269 n n CAB HABB J7V sing 270 n n OAH HOAH J7V sing 271 n n CAM HAM J7V sing 272 n n CAN HAN J7V sing 273 n n CAP HAP J7V sing 274 n n CAQ HAQ J7V sing 275 n n CAR HAR J7V sing 276 n n CAR HARA J7V sing 277 n n CAS HAS J7V sing 278 n n CAS HASA J7V sing 279 n n CAT HAT J7V sing 280 n n CAT HATA J7V sing 281 n n NAX HNAX J7V sing 282 n n CBL HBL J7V sing 283 n n CBM HBM J7V sing 284 n n CBN HBN J7V sing 285 n n CBO HBO J7V sing 286 n n OAG HAG J7V sing 287 n n OAJ HAJ J7V sing 288 n n OAF HAF J7V sing 289 n n # _atom_sites.entry_id 2YA3 _atom_sites.fract_transf_matrix[1][1] 0.020432 _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] 0.008061 _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] 0.00798 _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 D 4 J7V E 1 1325 1325 J7V J7V . E 4 J7V E 1 1326 1326 J7V J7V . F 5 AMP E 1 1327 1327 AMP AMP . G 6 HOH A 1 2001 2001 HOH HOH . G 6 HOH A 2 2002 2002 HOH HOH . G 6 HOH A 3 2003 2003 HOH HOH . G 6 HOH A 4 2004 2004 HOH HOH . G 6 HOH A 5 2005 2005 HOH HOH . G 6 HOH A 6 2006 2006 HOH HOH . G 6 HOH A 7 2007 2007 HOH HOH . G 6 HOH A 8 2008 2008 HOH HOH . G 6 HOH A 9 2009 2009 HOH HOH . G 6 HOH A 10 2010 2010 HOH HOH . G 6 HOH A 11 2011 2011 HOH HOH . G 6 HOH A 12 2012 2012 HOH HOH . G 6 HOH A 13 2013 2013 HOH HOH . G 6 HOH A 14 2014 2014 HOH HOH . G 6 HOH A 15 2015 2015 HOH HOH . G 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH A 17 2017 2017 HOH HOH . G 6 HOH A 18 2018 2018 HOH HOH . G 6 HOH A 19 2019 2019 HOH HOH . G 6 HOH A 20 2020 2020 HOH HOH . G 6 HOH A 21 2021 2021 HOH HOH . G 6 HOH A 22 2022 2022 HOH HOH . G 6 HOH A 23 2023 2023 HOH HOH . G 6 HOH A 24 2024 2024 HOH HOH . G 6 HOH A 25 2025 2025 HOH HOH . G 6 HOH A 26 2026 2026 HOH HOH . G 6 HOH A 27 2027 2027 HOH HOH . G 6 HOH A 28 2028 2028 HOH HOH . G 6 HOH A 29 2029 2029 HOH HOH . G 6 HOH A 30 2030 2030 HOH HOH . G 6 HOH A 31 2031 2031 HOH HOH . G 6 HOH A 32 2032 2032 HOH HOH . H 6 HOH B 1 2001 2001 HOH HOH . H 6 HOH B 2 2002 2002 HOH HOH . H 6 HOH B 3 2003 2003 HOH HOH . H 6 HOH B 4 2004 2004 HOH HOH . H 6 HOH B 5 2005 2005 HOH HOH . H 6 HOH B 6 2006 2006 HOH HOH . H 6 HOH B 7 2007 2007 HOH HOH . H 6 HOH B 8 2008 2008 HOH HOH . H 6 HOH B 9 2009 2009 HOH HOH . H 6 HOH B 10 2010 2010 HOH HOH . H 6 HOH B 11 2011 2011 HOH HOH . H 6 HOH B 12 2012 2012 HOH HOH . H 6 HOH B 13 2013 2013 HOH HOH . H 6 HOH B 14 2014 2014 HOH HOH . H 6 HOH B 15 2015 2015 HOH HOH . H 6 HOH B 16 2016 2016 HOH HOH . H 6 HOH B 17 2017 2017 HOH HOH . H 6 HOH B 18 2018 2018 HOH HOH . H 6 HOH B 19 2019 2019 HOH HOH . H 6 HOH B 20 2020 2020 HOH HOH . I 6 HOH E 1 2001 2001 HOH HOH . I 6 HOH E 2 2002 2002 HOH HOH . I 6 HOH E 3 2003 2003 HOH HOH . I 6 HOH E 4 2004 2004 HOH HOH . I 6 HOH E 5 2005 2005 HOH HOH . I 6 HOH E 6 2006 2006 HOH HOH . I 6 HOH E 7 2007 2007 HOH HOH . I 6 HOH E 8 2008 2008 HOH HOH . I 6 HOH E 9 2009 2009 HOH HOH . I 6 HOH E 10 2010 2010 HOH HOH . I 6 HOH E 11 2011 2011 HOH HOH . I 6 HOH E 12 2012 2012 HOH HOH . I 6 HOH E 13 2013 2013 HOH HOH . I 6 HOH E 14 2014 2014 HOH HOH . I 6 HOH E 15 2015 2015 HOH HOH . I 6 HOH E 16 2016 2016 HOH HOH . I 6 HOH E 17 2017 2017 HOH HOH . I 6 HOH E 18 2018 2018 HOH HOH . I 6 HOH E 19 2019 2019 HOH HOH . I 6 HOH E 20 2020 2020 HOH HOH . I 6 HOH E 21 2021 2021 HOH HOH . I 6 HOH E 22 2022 2022 HOH HOH . I 6 HOH E 23 2023 2023 HOH HOH . I 6 HOH E 24 2024 2024 HOH HOH . I 6 HOH E 25 2025 2025 HOH HOH . I 6 HOH E 26 2026 2026 HOH HOH . I 6 HOH E 27 2027 2027 HOH HOH . I 6 HOH E 28 2028 2028 HOH HOH . I 6 HOH E 29 2029 2029 HOH HOH . I 6 HOH E 30 2030 2030 HOH HOH . I 6 HOH E 31 2031 2031 HOH HOH . I 6 HOH E 32 2032 2032 HOH HOH . I 6 HOH E 33 2033 2033 HOH HOH . I 6 HOH E 34 2034 2034 HOH HOH . I 6 HOH E 35 2035 2035 HOH HOH . I 6 HOH E 36 2036 2036 HOH HOH . I 6 HOH E 37 2037 2037 HOH HOH . I 6 HOH E 38 2038 2038 HOH HOH . I 6 HOH E 39 2039 2039 HOH HOH . I 6 HOH E 40 2040 2040 HOH HOH . I 6 HOH E 41 2041 2041 HOH HOH . I 6 HOH E 42 2042 2042 HOH HOH . I 6 HOH E 43 2043 2043 HOH HOH . I 6 HOH E 44 2044 2044 HOH HOH . I 6 HOH E 45 2045 2045 HOH HOH . I 6 HOH E 46 2046 2046 HOH HOH . I 6 HOH E 47 2047 2047 HOH HOH . I 6 HOH E 48 2048 2048 HOH HOH . I 6 HOH E 49 2049 2049 HOH HOH . I 6 HOH E 50 2050 2050 HOH HOH . I 6 HOH E 51 2051 2051 HOH HOH . I 6 HOH E 52 2052 2052 HOH HOH . I 6 HOH E 53 2053 2053 HOH HOH . I 6 HOH E 54 2054 2054 HOH HOH . I 6 HOH E 55 2055 2055 HOH HOH . I 6 HOH E 56 2056 2056 HOH HOH . I 6 HOH E 57 2057 2057 HOH HOH . I 6 HOH E 58 2058 2058 HOH HOH . I 6 HOH E 59 2059 2059 HOH HOH . I 6 HOH E 60 2060 2060 HOH HOH . I 6 HOH E 61 2061 2061 HOH HOH . I 6 HOH E 62 2062 2062 HOH HOH . I 6 HOH E 63 2063 2063 HOH HOH . I 6 HOH E 64 2064 2064 HOH HOH . I 6 HOH E 65 2065 2065 HOH HOH . I 6 HOH E 66 2066 2066 HOH HOH . I 6 HOH E 67 2067 2067 HOH HOH . I 6 HOH E 68 2068 2068 HOH HOH . I 6 HOH E 69 2069 2069 HOH HOH . I 6 HOH E 70 2070 2070 HOH HOH . I 6 HOH E 71 2071 2071 HOH HOH . I 6 HOH E 72 2072 2072 HOH HOH . I 6 HOH E 73 2073 2073 HOH HOH . I 6 HOH E 74 2074 2074 HOH HOH . I 6 HOH E 75 2075 2075 HOH HOH . I 6 HOH E 76 2076 2076 HOH HOH . I 6 HOH E 77 2077 2077 HOH HOH . I 6 HOH E 78 2078 2078 HOH HOH . I 6 HOH E 79 2079 2079 HOH HOH . I 6 HOH E 80 2080 2080 HOH HOH . I 6 HOH E 81 2081 2081 HOH HOH . I 6 HOH E 82 2082 2082 HOH HOH . I 6 HOH E 83 2083 2083 HOH HOH . I 6 HOH E 84 2084 2084 HOH HOH . I 6 HOH E 85 2085 2085 HOH HOH . I 6 HOH E 86 2086 2086 HOH HOH . I 6 HOH E 87 2087 2087 HOH HOH . I 6 HOH E 88 2088 2088 HOH HOH . I 6 HOH E 89 2089 2089 HOH HOH . I 6 HOH E 90 2090 2090 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 PBR J7V . . . D 4 2.452 7.743 25.285 1 35.43 ? PBR J7V 1325 E 1 HETATM 2 O OAI J7V . . . D 4 3.917 7.434 25.399 1 36.12 ? OAI J7V 1325 E 1 HETATM 3 O OAF J7V . . . D 4 1.568 6.528 25.454 1 35.54 ? OAF J7V 1325 E 1 HETATM 4 O OAJ J7V . . . D 4 2.048 8.666 24.162 1 35.54 ? OAJ J7V 1325 E 1 HETATM 5 P PBS J7V . . . D 4 2.529 10.042 27.036 1 35 ? PBS J7V 1325 E 1 HETATM 6 O OAK J7V . . . D 4 1.514 10.423 28.075 1 36.71 ? OAK J7V 1325 E 1 HETATM 7 O OAG J7V . . . D 4 2.737 10.978 25.879 1 36.89 ? OAG J7V 1325 E 1 HETATM 8 O OBA J7V . . . D 4 2.097 8.559 26.614 1 35.67 ? OBA J7V 1325 E 1 HETATM 9 O OAY J7V . . . D 4 3.939 9.836 27.759 1 38.08 ? OAY J7V 1325 E 1 HETATM 10 C CAT J7V . . . D 4 4.766 10.983 27.966 1 39.53 ? CAT J7V 1325 E 1 HETATM 11 C CBM J7V . . . D 4 5.633 10.841 29.213 1 40.81 ? CBM J7V 1325 E 1 HETATM 12 O OAZ J7V . . . D 4 4.939 11.264 30.391 1 40.81 ? OAZ J7V 1325 E 1 HETATM 13 C CBN J7V . . . D 4 6.138 9.421 29.461 1 41.26 ? CBN J7V 1325 E 1 HETATM 14 C CBL J7V . . . D 4 5.456 8.964 30.749 1 40.71 ? CBL J7V 1325 E 1 HETATM 15 O OAH J7V . . . D 4 6.326 8.213 31.61 1 41.18 ? OAH J7V 1325 E 1 HETATM 16 C CBO J7V . . . D 4 4.896 10.236 31.387 1 40.26 ? CBO J7V 1325 E 1 HETATM 17 N N9 J7V . . . D 4 3.472 10.14 31.812 1 39.59 ? N9 J7V 1325 E 1 HETATM 18 C C8 J7V . . . D 4 2.456 9.64 31.091 1 38.86 ? C8 J7V 1325 E 1 HETATM 19 N N7 J7V . . . D 4 1.313 9.747 31.801 1 38.69 ? N7 J7V 1325 E 1 HETATM 20 C C5 J7V . . . D 4 1.62 10.324 32.979 1 39.49 ? C5 J7V 1325 E 1 HETATM 21 C C6 J7V . . . D 4 0.872 10.675 34.101 1 39.72 ? C6 J7V 1325 E 1 HETATM 22 N N6 J7V . . . D 4 -0.46 10.446 34.138 1 38.6 ? N6 J7V 1325 E 1 HETATM 23 N N1 J7V . . . D 4 1.492 11.255 35.158 1 40.48 ? N1 J7V 1325 E 1 HETATM 24 C C2 J7V . . . D 4 2.814 11.493 35.132 1 40.32 ? C2 J7V 1325 E 1 HETATM 25 N N3 J7V . . . D 4 3.555 11.163 34.063 1 40.34 ? N3 J7V 1325 E 1 HETATM 26 C C4 J7V . . . D 4 2.982 10.576 32.977 1 39.75 ? C4 J7V 1325 E 1 HETATM 27 C CAA J7V . . . D 4 17.198 9.551 29.329 1 54.9 ? CAA J7V 1325 E 1 HETATM 28 C CAB J7V . . . D 4 17.127 13.931 29.235 1 57.68 ? CAB J7V 1325 E 1 HETATM 29 O OAD J7V . . . D 4 7.877 11.105 31.229 1 46.25 ? OAD J7V 1325 E 1 HETATM 30 O OAE J7V . . . D 4 9.84 8.622 28.688 1 48.1 ? OAE J7V 1325 E 1 HETATM 31 C CAM J7V . . . D 4 14.105 12.661 30.688 1 53.07 ? CAM J7V 1325 E 1 HETATM 32 C CAN J7V . . . D 4 12.734 12.6 30.971 1 52.04 ? CAN J7V 1325 E 1 HETATM 33 C CAP J7V . . . D 4 13.904 10.716 29.285 1 52.08 ? CAP J7V 1325 E 1 HETATM 34 C CAQ J7V . . . D 4 10.579 11.497 30.661 1 48.78 ? CAQ J7V 1325 E 1 HETATM 35 C CAR J7V . . . D 4 16.643 10.758 28.594 1 54.8 ? CAR J7V 1325 E 1 HETATM 36 C CAS J7V . . . D 4 16.987 12.719 30.134 1 56.46 ? CAS J7V 1325 E 1 HETATM 37 N NAX J7V . . . D 4 7.594 9.627 29.53 1 43.5 ? NAX J7V 1325 E 1 HETATM 38 O OBB J7V . . . D 4 11.798 9.659 29.003 1 49.35 ? OBB J7V 1325 E 1 HETATM 39 C CBC J7V . . . D 4 8.339 10.404 30.341 1 45.75 ? CBC J7V 1325 E 1 HETATM 40 C CBE J7V . . . D 4 14.704 11.716 29.839 1 53.57 ? CBE J7V 1325 E 1 HETATM 41 C CBF J7V . . . D 4 9.825 10.465 30.091 1 47.43 ? CBF J7V 1325 E 1 HETATM 42 C CBG J7V . . . D 4 10.456 9.561 29.24 1 48.21 ? CBG J7V 1325 E 1 HETATM 43 C CBH J7V . . . D 4 11.948 11.589 30.408 1 50.67 ? CBH J7V 1325 E 1 HETATM 44 C CBI J7V . . . D 4 12.545 10.653 29.567 1 50.67 ? CBI J7V 1325 E 1 HETATM 45 N NBP J7V . . . D 4 16.086 11.735 29.531 1 55.05 ? NBP J7V 1325 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 45 #