data_6C4T # _model_server_result.job_id eBeCc9Xy4KlJOtqQyamARg _model_server_result.datetime_utc '2024-10-10 11:24:24' _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 6c4t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6C4T # _exptl.entry_id 6C4T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 623.296 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE' _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 6C4T _cell.length_a 186.096 _cell.length_b 49.258 _cell.length_c 59.106 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C4T _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 186.096 0 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 'C15 H24 N5 O16 P3' _chem_comp.formula_weight 623.296 _chem_comp.id NA7 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE' _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 PA O5B NA7 sing 250 n n PA O2A NA7 doub 251 n n PA O1A NA7 sing 252 n n PA O3 NA7 sing 253 n n O1A HAO1 NA7 sing 254 n n O5B C5B NA7 sing 255 n n C5B C4B NA7 sing 256 n n C5B "H5'1" NA7 sing 257 n n C5B "H5'2" NA7 sing 258 n n C4B C3B NA7 sing 259 n n C4B O4B NA7 sing 260 n n C4B HC4' NA7 sing 261 n n O4B C1B NA7 sing 262 n n C3B O3B NA7 sing 263 n n C3B C2B NA7 sing 264 n n C3B HC3' NA7 sing 265 n n O3B HO3' NA7 sing 266 n n C2B O2B NA7 sing 267 n n C2B C1B NA7 sing 268 n n C2B HC2' NA7 sing 269 n n O2B P2B NA7 sing 270 n n C1B N9A NA7 sing 271 n n C1B HC1' NA7 sing 272 n n N9A C4A NA7 sing 273 n y N9A C8A NA7 sing 274 n y C8A N7A NA7 doub 275 n y C8A HC8 NA7 sing 276 n n N7A C5A NA7 sing 277 n y C5A C4A NA7 doub 278 n y C5A C6A NA7 sing 279 n y C6A N1A NA7 doub 280 n y C6A N6A NA7 sing 281 n n N6A HN61 NA7 sing 282 n n N6A HN62 NA7 sing 283 n n N1A C2A NA7 sing 284 n y C2A N3A NA7 doub 285 n y C2A HC2 NA7 sing 286 n n N3A C4A NA7 sing 287 n y O3 PN NA7 sing 288 n n PN O5D NA7 sing 289 n n PN O1N NA7 doub 290 n n PN O2N NA7 sing 291 n n O2N HNO2 NA7 sing 292 n n O5D C5D NA7 sing 293 n n C5D C4D NA7 sing 294 n n C5D H51' NA7 sing 295 n n C5D H52' NA7 sing 296 n n C4D O4D NA7 sing 297 n n C4D C3D NA7 sing 298 n n C4D HN4' NA7 sing 299 n n O4D C1D NA7 sing 300 n n C3D C2D NA7 sing 301 n n C3D O3D NA7 sing 302 n n C3D HN3' NA7 sing 303 n n O3D HN5' NA7 sing 304 n n C2D O2D NA7 sing 305 n n C2D C1D NA7 sing 306 n n C2D HN6' NA7 sing 307 n n O2D HN7' NA7 sing 308 n n C1D "H1'1" NA7 sing 309 n n C1D "H1'2" NA7 sing 310 n n P2B O3X NA7 doub 311 n n P2B O2X NA7 sing 312 n n P2B O1X NA7 sing 313 n n O1X HOP1 NA7 sing 314 n n O2X HOP2 NA7 sing 315 n n # _atom_sites.entry_id 6C4T _atom_sites.fract_transf_matrix[1][1] 0.005374 _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] 0.020301 _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] 0.016919 _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 NA7 A 1 501 1 NA7 NAP . C 3 GOL A 1 502 1 GOL GOL . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 4 HOH HOH . D 4 HOH A 3 603 9 HOH HOH . D 4 HOH A 4 604 7 HOH HOH . D 4 HOH A 5 605 3 HOH HOH . D 4 HOH A 6 606 6 HOH HOH . D 4 HOH A 7 607 2 HOH HOH . D 4 HOH A 8 608 5 HOH HOH . D 4 HOH A 9 609 10 HOH HOH . D 4 HOH A 10 610 8 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 PA NA7 . . . B 2 62.387 10.554 5.88 1 76.04 ? PA NA7 501 A 1 HETATM 2 O O1A NA7 . . . B 2 63.346 11.669 5.872 1 76.37 ? O1A NA7 501 A 1 HETATM 3 O O2A NA7 . . . B 2 61.826 10.414 4.425 1 75.88 ? O2A NA7 501 A 1 HETATM 4 O O5B NA7 . . . B 2 61.257 10.955 7.034 1 76.32 ? O5B NA7 501 A 1 HETATM 5 C C5B NA7 . . . B 2 59.958 10.364 7.102 1 76.19 ? C5B NA7 501 A 1 HETATM 6 C C4B NA7 . . . B 2 58.841 11.394 6.842 1 76.43 ? C4B NA7 501 A 1 HETATM 7 O O4B NA7 . . . B 2 58.738 12.342 8.07 1 76.99 ? O4B NA7 501 A 1 HETATM 8 C C3B NA7 . . . B 2 59.098 12.128 5.831 1 76.48 ? C3B NA7 501 A 1 HETATM 9 O O3B NA7 . . . B 2 57.996 12.098 4.893 1 76.37 ? O3B NA7 501 A 1 HETATM 10 C C2B NA7 . . . B 2 59.292 13.655 6.412 1 77.11 ? C2B NA7 501 A 1 HETATM 11 O O2B NA7 . . . B 2 58.959 14.608 5.338 1 77.35 ? O2B NA7 501 A 1 HETATM 12 C C1B NA7 . . . B 2 58.499 13.729 7.425 1 77.34 ? C1B NA7 501 A 1 HETATM 13 N N9A NA7 . . . B 2 58.904 14.83 8.393 1 78.03 ? N9A NA7 501 A 1 HETATM 14 C C8A NA7 . . . B 2 60.022 15.239 9.029 1 78.36 ? C8A NA7 501 A 1 HETATM 15 N N7A NA7 . . . B 2 59.662 16.326 9.755 1 79.12 ? N7A NA7 501 A 1 HETATM 16 C C5A NA7 . . . B 2 58.33 16.585 9.573 1 79.23 ? C5A NA7 501 A 1 HETATM 17 C C6A NA7 . . . B 2 57.497 17.586 10.098 1 79.98 ? C6A NA7 501 A 1 HETATM 18 N N6A NA7 . . . B 2 57.619 18.736 11.011 1 81 ? N6A NA7 501 A 1 HETATM 19 N N1A NA7 . . . B 2 56.183 17.609 9.747 1 79.93 ? N1A NA7 501 A 1 HETATM 20 C C2A NA7 . . . B 2 55.687 16.658 8.886 1 79.15 ? C2A NA7 501 A 1 HETATM 21 N N3A NA7 . . . B 2 56.509 15.693 8.382 1 78.49 ? N3A NA7 501 A 1 HETATM 22 C C4A NA7 . . . B 2 57.842 15.655 8.733 1 78.53 ? C4A NA7 501 A 1 HETATM 23 O O3 NA7 . . . B 2 63.202 9.148 6.306 1 75.79 ? O3 NA7 501 A 1 HETATM 24 P PN NA7 . . . B 2 62.59 7.736 6.814 1 75.64 ? PN NA7 501 A 1 HETATM 25 O O1N NA7 . . . B 2 61.436 7.356 5.978 1 75.48 ? O1N NA7 501 A 1 HETATM 26 O O2N NA7 . . . B 2 63.673 6.653 6.683 1 75.51 ? O2N NA7 501 A 1 HETATM 27 O O5D NA7 . . . B 2 62.163 7.971 8.425 1 75.99 ? O5D NA7 501 A 1 HETATM 28 C C5D NA7 . . . B 2 62.064 6.854 9.377 1 76.11 ? C5D NA7 501 A 1 HETATM 29 C C4D NA7 . . . B 2 62.802 7.098 10.706 1 76.52 ? C4D NA7 501 A 1 HETATM 30 O O4D NA7 . . . B 2 64.16 6.241 10.859 1 76.46 ? O4D NA7 501 A 1 HETATM 31 C C3D NA7 . . . B 2 63.209 8.343 10.678 1 76.66 ? C3D NA7 501 A 1 HETATM 32 O O3D NA7 . . . B 2 62.036 9.202 11.078 1 76.98 ? O3D NA7 501 A 1 HETATM 33 C C2D NA7 . . . B 2 64.454 8.412 11.609 1 76.96 ? C2D NA7 501 A 1 HETATM 34 O O2D NA7 . . . B 2 64.25 9.038 12.81 1 77.55 ? O2D NA7 501 A 1 HETATM 35 C C1D NA7 . . . B 2 64.849 6.916 11.768 1 76.81 ? C1D NA7 501 A 1 HETATM 36 P P2B NA7 . . . B 2 59.959 14.858 3.968 1 77.35 ? P2B NA7 501 A 1 HETATM 37 O O1X NA7 . . . B 2 60.095 13.598 3.103 1 76.81 ? O1X NA7 501 A 1 HETATM 38 O O2X NA7 . . . B 2 59.261 15.917 3.195 1 77.81 ? O2X NA7 501 A 1 HETATM 39 O O3X NA7 . . . B 2 61.349 15.297 4.417 1 77.61 ? O3X NA7 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #