data_8PUU # _model_server_result.job_id TEdmXBqX1aYTtpHZ4DLScw _model_server_result.datetime_utc '2024-12-14 07:01:32' _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 8puu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 8PUU # _exptl.entry_id 8PUU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 5 _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 8PUU _cell.length_a 103.13 _cell.length_b 103.13 _cell.length_c 147.109 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PUU _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 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 _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 5 _struct_asym.id E _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 8PUU _atom_sites.fract_transf_matrix[1][1] 0.009696 _atom_sites.fract_transf_matrix[1][2] 0.005598 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011197 _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] 0.006798 _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 DAT A 1 301 301 DAT DAT . E 5 D5M B 1 301 301 D5M LIG . F 6 HOH A 1 401 98 HOH HOH . F 6 HOH A 2 402 85 HOH HOH . F 6 HOH A 3 403 50 HOH HOH . F 6 HOH A 4 404 132 HOH HOH . F 6 HOH A 5 405 19 HOH HOH . F 6 HOH A 6 406 6 HOH HOH . F 6 HOH A 7 407 39 HOH HOH . F 6 HOH A 8 408 13 HOH HOH . F 6 HOH A 9 409 66 HOH HOH . F 6 HOH A 10 410 75 HOH HOH . F 6 HOH A 11 411 15 HOH HOH . F 6 HOH A 12 412 7 HOH HOH . F 6 HOH A 13 413 44 HOH HOH . F 6 HOH A 14 414 10 HOH HOH . F 6 HOH A 15 415 148 HOH HOH . F 6 HOH A 16 416 9 HOH HOH . F 6 HOH A 17 417 16 HOH HOH . F 6 HOH A 18 418 25 HOH HOH . F 6 HOH A 19 419 54 HOH HOH . F 6 HOH A 20 420 23 HOH HOH . F 6 HOH A 21 421 37 HOH HOH . F 6 HOH A 22 422 26 HOH HOH . F 6 HOH A 23 423 11 HOH HOH . F 6 HOH A 24 424 40 HOH HOH . F 6 HOH A 25 425 149 HOH HOH . F 6 HOH A 26 426 92 HOH HOH . F 6 HOH A 27 427 43 HOH HOH . F 6 HOH A 28 428 42 HOH HOH . F 6 HOH A 29 429 122 HOH HOH . F 6 HOH A 30 430 1 HOH HOH . F 6 HOH A 31 431 38 HOH HOH . F 6 HOH A 32 432 114 HOH HOH . F 6 HOH A 33 433 52 HOH HOH . F 6 HOH A 34 434 128 HOH HOH . F 6 HOH A 35 435 27 HOH HOH . F 6 HOH A 36 436 8 HOH HOH . F 6 HOH A 37 437 109 HOH HOH . F 6 HOH A 38 438 147 HOH HOH . F 6 HOH A 39 439 140 HOH HOH . F 6 HOH A 40 440 130 HOH HOH . F 6 HOH A 41 441 127 HOH HOH . F 6 HOH A 42 442 103 HOH HOH . F 6 HOH A 43 443 102 HOH HOH . F 6 HOH A 44 444 150 HOH HOH . F 6 HOH A 45 445 12 HOH HOH . F 6 HOH A 46 446 121 HOH HOH . F 6 HOH A 47 447 80 HOH HOH . F 6 HOH A 48 448 79 HOH HOH . F 6 HOH A 49 449 145 HOH HOH . F 6 HOH A 50 450 123 HOH HOH . F 6 HOH A 51 451 146 HOH HOH . F 6 HOH A 52 452 117 HOH HOH . F 6 HOH A 53 453 142 HOH HOH . F 6 HOH A 54 454 143 HOH HOH . G 6 HOH B 1 401 138 HOH HOH . G 6 HOH B 2 402 46 HOH HOH . G 6 HOH B 3 403 86 HOH HOH . G 6 HOH B 4 404 30 HOH HOH . G 6 HOH B 5 405 49 HOH HOH . G 6 HOH B 6 406 107 HOH HOH . G 6 HOH B 7 407 34 HOH HOH . G 6 HOH B 8 408 84 HOH HOH . G 6 HOH B 9 409 136 HOH HOH . G 6 HOH B 10 410 95 HOH HOH . G 6 HOH B 11 411 2 HOH HOH . G 6 HOH B 12 412 28 HOH HOH . G 6 HOH B 13 413 110 HOH HOH . G 6 HOH B 14 414 113 HOH HOH . G 6 HOH B 15 415 64 HOH HOH . G 6 HOH B 16 416 91 HOH HOH . G 6 HOH B 17 417 17 HOH HOH . G 6 HOH B 18 418 3 HOH HOH . G 6 HOH B 19 419 77 HOH HOH . G 6 HOH B 20 420 21 HOH HOH . G 6 HOH B 21 421 57 HOH HOH . G 6 HOH B 22 422 48 HOH HOH . G 6 HOH B 23 423 14 HOH HOH . G 6 HOH B 24 424 126 HOH HOH . G 6 HOH B 25 425 22 HOH HOH . G 6 HOH B 26 426 33 HOH HOH . G 6 HOH B 27 427 151 HOH HOH . G 6 HOH B 28 428 36 HOH HOH . G 6 HOH B 29 429 112 HOH HOH . G 6 HOH B 30 430 74 HOH HOH . G 6 HOH B 31 431 90 HOH HOH . G 6 HOH B 32 432 35 HOH HOH . G 6 HOH B 33 433 71 HOH HOH . G 6 HOH B 34 434 63 HOH HOH . G 6 HOH B 35 435 94 HOH HOH . G 6 HOH B 36 436 20 HOH HOH . G 6 HOH B 37 437 61 HOH HOH . G 6 HOH B 38 438 32 HOH HOH . G 6 HOH B 39 439 31 HOH HOH . G 6 HOH B 40 440 4 HOH HOH . G 6 HOH B 41 441 53 HOH HOH . G 6 HOH B 42 442 41 HOH HOH . G 6 HOH B 43 443 87 HOH HOH . G 6 HOH B 44 444 5 HOH HOH . G 6 HOH B 45 445 89 HOH HOH . G 6 HOH B 46 446 93 HOH HOH . G 6 HOH B 47 447 29 HOH HOH . G 6 HOH B 48 448 137 HOH HOH . G 6 HOH B 49 449 67 HOH HOH . G 6 HOH B 50 450 83 HOH HOH . G 6 HOH B 51 451 152 HOH HOH . G 6 HOH B 52 452 82 HOH HOH . G 6 HOH B 53 453 115 HOH HOH . G 6 HOH B 54 454 134 HOH HOH . G 6 HOH B 55 455 125 HOH HOH . G 6 HOH B 56 456 45 HOH HOH . G 6 HOH B 57 457 116 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 . . . E 5 36.55 -64.689 -3.478 1 49.74 ? O5' D5M 301 B 1 HETATM 2 C C5' D5M . . . E 5 36.556 -64.45 -4.842 1 49.79 ? C5' D5M 301 B 1 HETATM 3 C C4' D5M . . . E 5 36.92 -65.791 -5.544 1 46.72 ? C4' D5M 301 B 1 HETATM 4 O O4' D5M . . . E 5 36.771 -65.661 -6.824 1 48.18 ? O4' D5M 301 B 1 HETATM 5 C C3' D5M . . . E 5 38.438 -66.124 -5.319 1 47.77 ? C3' D5M 301 B 1 HETATM 6 O O3' D5M . . . E 5 38.687 -67.487 -5.449 1 44.53 ? O3' D5M 301 B 1 HETATM 7 C C2' D5M . . . E 5 39.08 -65.361 -6.43 1 46.63 ? C2' D5M 301 B 1 HETATM 8 C C1' D5M . . . E 5 38.223 -65.581 -7.457 1 45.73 ? C1' D5M 301 B 1 HETATM 9 N N9 D5M . . . E 5 38.186 -64.517 -8.412 1 49.46 ? N9 D5M 301 B 1 HETATM 10 C C8 D5M . . . E 5 37.406 -63.393 -8.37 1 46.81 ? C8 D5M 301 B 1 HETATM 11 N N7 D5M . . . E 5 37.677 -62.661 -9.479 1 46.91 ? N7 D5M 301 B 1 HETATM 12 C C5 D5M . . . E 5 38.605 -63.321 -10.188 1 46.06 ? C5 D5M 301 B 1 HETATM 13 C C6 D5M . . . E 5 39.315 -63.018 -11.507 1 41.04 ? C6 D5M 301 B 1 HETATM 14 N N6 D5M . . . E 5 39.009 -61.788 -12.258 1 43.19 ? N6 D5M 301 B 1 HETATM 15 N N1 D5M . . . E 5 40.256 -63.933 -12.023 1 45.26 ? N1 D5M 301 B 1 HETATM 16 C C2 D5M . . . E 5 40.599 -65.136 -11.304 1 48.13 ? C2 D5M 301 B 1 HETATM 17 N N3 D5M . . . E 5 39.912 -65.425 -10.056 1 43.82 ? N3 D5M 301 B 1 HETATM 18 C C4 D5M . . . E 5 38.904 -64.477 -9.524 1 43.1 ? C4 D5M 301 B 1 HETATM 19 P P D5M . . . E 5 36.616 -63.416 -2.448 1 47.17 ? P D5M 301 B 1 HETATM 20 O O1P D5M . . . E 5 37.652 -62.455 -2.988 1 42.95 ? O1P D5M 301 B 1 HETATM 21 O O3P D5M . . . E 5 37.043 -63.966 -1.105 1 42.83 ? O3P D5M 301 B 1 HETATM 22 O O2P D5M . . . E 5 35.285 -62.739 -2.293 1 51.82 ? O2P D5M 301 B 1 # _model_server_stats.io_time_ms 112 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 22 #