data_7V7X # _model_server_result.job_id eaHcS9GuI6MJIXcR7SOhog _model_server_result.datetime_utc '2024-10-11 04:28:26' _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 7v7x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7V7X # _exptl.entry_id 7V7X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 7V7X _cell.length_a 140.311 _cell.length_b 140.311 _cell.length_c 48.322 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7V7X _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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' _chem_comp.formula_weight 331.222 _chem_comp.id D5M _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 O5' C5' D5M sing 83 n n O5' P D5M sing 84 n n C5' C4' D5M sing 85 n n C5' "H5'1" D5M sing 86 n n C5' "H5'2" D5M sing 87 n n C4' O4' D5M sing 88 n n C4' C3' D5M sing 89 n n C4' H4' D5M sing 90 n n O4' C1' D5M sing 91 n n C3' O3' D5M sing 92 n n C3' C2' D5M sing 93 n n C3' H1 D5M sing 94 n n O3' H3' D5M sing 95 n n C2' C1' D5M sing 96 n n C2' "H2'1" D5M sing 97 n n C2' "H2'2" D5M sing 98 n n C1' N9 D5M sing 99 n n C1' H1' D5M sing 100 n n N9 C8 D5M sing 101 n y N9 C4 D5M sing 102 n y C8 N7 D5M doub 103 n y C8 H8 D5M sing 104 n n N7 C5 D5M sing 105 n y C5 C6 D5M sing 106 n y C5 C4 D5M doub 107 n y C6 N6 D5M sing 108 n n C6 N1 D5M doub 109 n y N6 HN61 D5M sing 110 n n N6 HN62 D5M sing 111 n n N1 C2 D5M sing 112 n y C2 N3 D5M doub 113 n y C2 H2 D5M sing 114 n n N3 C4 D5M sing 115 n y P O1P D5M doub 116 n n P O3P D5M sing 117 n n P O2P D5M sing 118 n n O3P H3P D5M sing 119 n n O2P H2P D5M sing 120 n n # _atom_sites.entry_id 7V7X _atom_sites.fract_transf_matrix[1][1] 0.007127 _atom_sites.fract_transf_matrix[1][2] 0.004115 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00823 _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] 0.020695 _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 D5M A 1 401 302 D5M D5M . C 3 HOH A 1 501 318 HOH HOH . C 3 HOH A 2 502 335 HOH HOH . C 3 HOH A 3 503 315 HOH HOH . C 3 HOH A 4 504 332 HOH HOH . C 3 HOH A 5 505 305 HOH HOH . C 3 HOH A 6 506 314 HOH HOH . C 3 HOH A 7 507 342 HOH HOH . C 3 HOH A 8 508 303 HOH HOH . C 3 HOH A 9 509 317 HOH HOH . C 3 HOH A 10 510 320 HOH HOH . C 3 HOH A 11 511 306 HOH HOH . C 3 HOH A 12 512 341 HOH HOH . C 3 HOH A 13 513 324 HOH HOH . C 3 HOH A 14 514 329 HOH HOH . C 3 HOH A 15 515 326 HOH HOH . C 3 HOH A 16 516 330 HOH HOH . C 3 HOH A 17 517 338 HOH HOH . C 3 HOH A 18 518 312 HOH HOH . C 3 HOH A 19 519 313 HOH HOH . C 3 HOH A 20 520 307 HOH HOH . C 3 HOH A 21 521 336 HOH HOH . C 3 HOH A 22 522 325 HOH HOH . C 3 HOH A 23 523 337 HOH HOH . C 3 HOH A 24 524 334 HOH HOH . C 3 HOH A 25 525 311 HOH HOH . C 3 HOH A 26 526 309 HOH HOH . C 3 HOH A 27 527 321 HOH HOH . C 3 HOH A 28 528 323 HOH HOH . C 3 HOH A 29 529 322 HOH HOH . C 3 HOH A 30 530 327 HOH HOH . C 3 HOH A 31 531 316 HOH HOH . C 3 HOH A 32 532 308 HOH HOH . C 3 HOH A 33 533 304 HOH HOH . C 3 HOH A 34 534 340 HOH HOH . C 3 HOH A 35 535 339 HOH HOH . C 3 HOH A 36 536 328 HOH HOH . C 3 HOH A 37 537 319 HOH HOH . C 3 HOH A 38 538 333 HOH HOH . C 3 HOH A 39 539 331 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 O5' D5M . . . B 2 44.252 45.787 -1.761 1 201.04 ? O5' D5M 401 A 1 HETATM 2 C C5' D5M . . . B 2 43.786 47.123 -1.415 1 191.18 ? C5' D5M 401 A 1 HETATM 3 C C4' D5M . . . B 2 44.289 47.649 -0.103 1 183.02 ? C4' D5M 401 A 1 HETATM 4 O O4' D5M . . . B 2 45.661 48.065 -0.225 1 190.67 ? O4' D5M 401 A 1 HETATM 5 C C3' D5M . . . B 2 43.573 48.687 0.754 1 183.07 ? C3' D5M 401 A 1 HETATM 6 O O3' D5M . . . B 2 43.216 47.619 1.667 1 192.91 ? O3' D5M 401 A 1 HETATM 7 C C2' D5M . . . B 2 44.492 49.906 0.784 1 172.79 ? C2' D5M 401 A 1 HETATM 8 C C1' D5M . . . B 2 45.779 49.43 0.149 1 172.76 ? C1' D5M 401 A 1 HETATM 9 N N9 D5M . . . B 2 46.514 50.185 -0.839 1 157.76 ? N9 D5M 401 A 1 HETATM 10 C C8 D5M . . . B 2 46.596 51.559 -0.969 1 140.34 ? C8 D5M 401 A 1 HETATM 11 N N7 D5M . . . B 2 47.44 51.911 -1.912 1 135.3 ? N7 D5M 401 A 1 HETATM 12 C C5 D5M . . . B 2 47.928 50.711 -2.428 1 133.46 ? C5 D5M 401 A 1 HETATM 13 C C6 D5M . . . B 2 48.845 50.405 -3.458 1 124.35 ? C6 D5M 401 A 1 HETATM 14 N N6 D5M . . . B 2 49.441 51.311 -4.226 1 122.14 ? N6 D5M 401 A 1 HETATM 15 N N1 D5M . . . B 2 49.125 49.099 -3.697 1 115.99 ? N1 D5M 401 A 1 HETATM 16 C C2 D5M . . . B 2 48.472 48.174 -2.988 1 114.89 ? C2 D5M 401 A 1 HETATM 17 N N3 D5M . . . B 2 47.589 48.336 -2.009 1 128.06 ? N3 D5M 401 A 1 HETATM 18 C C4 D5M . . . B 2 47.35 49.642 -1.777 1 139.29 ? C4 D5M 401 A 1 HETATM 19 P P D5M . . . B 2 44.847 45.496 -3.249 1 196.9 ? P D5M 401 A 1 HETATM 20 O O1P D5M . . . B 2 43.706 44.873 -4.027 1 167.31 -1 O1P D5M 401 A 1 HETATM 21 O O3P D5M . . . B 2 45.27 46.846 -3.795 1 202.92 ? O3P D5M 401 A 1 HETATM 22 O O2P D5M . . . B 2 46.015 44.549 -3.051 1 192.69 ? O2P D5M 401 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #