data_3N3Y # _model_server_result.job_id HqJJiMuwkdCeqZDBrOgKEA _model_server_result.datetime_utc '2025-03-06 08:53:38' _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 3n3y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":304}' # _entry.id 3N3Y # _exptl.entry_id 3N3Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.14 _cell.angle_gamma 90 _cell.entry_id 3N3Y _cell.length_a 65.525 _cell.length_b 79.956 _cell.length_c 96.405 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N3Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L,M,N,O,P,Q _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 ? 2 E N N ? 2 G N N ? 2 H N N ? 2 J N N ? 2 L N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 449 n n N1 C6 UMP sing 450 n n N1 C1' UMP sing 451 n n C2 N3 UMP sing 452 n n C2 O2 UMP doub 453 n n N3 C4 UMP sing 454 n n N3 HN3 UMP sing 455 n n C4 C5 UMP sing 456 n n C4 O4 UMP doub 457 n n C5 C6 UMP doub 458 n n C5 H5 UMP sing 459 n n C6 H6 UMP sing 460 n n C1' C2' UMP sing 461 n n C1' O4' UMP sing 462 n n C1' H1' UMP sing 463 n n C2' C3' UMP sing 464 n n C2' H2' UMP sing 465 n n C2' "H2''" UMP sing 466 n n C3' C4' UMP sing 467 n n C3' O3' UMP sing 468 n n C3' H3' UMP sing 469 n n C4' O4' UMP sing 470 n n C4' C5' UMP sing 471 n n C4' H4' UMP sing 472 n n O3' HO3' UMP sing 473 n n C5' O5' UMP sing 474 n n C5' H5' UMP sing 475 n n C5' "H5''" UMP sing 476 n n O5' P UMP sing 477 n n P OP1 UMP doub 478 n n P OP2 UMP sing 479 n n P OP3 UMP sing 480 n n OP2 HOP2 UMP sing 481 n n OP3 HOP3 UMP sing 482 n n # _atom_sites.entry_id 3N3Y _atom_sites.fract_transf_matrix[1][1] 0.015261 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003562 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012507 _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] 0.010652 _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 E 2 UMP A 1 305 305 UMP UMP . F 3 FAD A 1 304 304 FAD FAD . G 2 UMP B 1 301 301 UMP UMP . H 2 UMP B 1 304 304 UMP UMP . I 3 FAD B 1 209 301 FAD FAD . J 2 UMP C 1 303 303 UMP UMP . K 3 FAD C 1 302 302 FAD FAD . L 2 UMP D 1 302 302 UMP UMP . M 3 FAD D 1 303 303 FAD FAD . N 4 HOH A 1 209 14 HOH HOH . N 4 HOH A 2 210 18 HOH HOH . N 4 HOH A 3 211 25 HOH HOH . N 4 HOH A 4 212 27 HOH HOH . N 4 HOH A 5 213 28 HOH HOH . N 4 HOH A 6 214 34 HOH HOH . N 4 HOH A 7 215 35 HOH HOH . N 4 HOH A 8 216 37 HOH HOH . N 4 HOH A 9 217 38 HOH HOH . N 4 HOH A 10 218 44 HOH HOH . N 4 HOH A 11 219 45 HOH HOH . N 4 HOH A 12 220 49 HOH HOH . N 4 HOH A 13 221 50 HOH HOH . N 4 HOH A 14 222 52 HOH HOH . N 4 HOH A 15 223 54 HOH HOH . N 4 HOH A 16 224 57 HOH HOH . N 4 HOH A 17 225 60 HOH HOH . N 4 HOH A 18 226 61 HOH HOH . N 4 HOH A 19 227 63 HOH HOH . N 4 HOH A 20 228 69 HOH HOH . N 4 HOH A 21 229 71 HOH HOH . N 4 HOH A 22 230 79 HOH HOH . N 4 HOH A 23 231 80 HOH HOH . N 4 HOH A 24 232 81 HOH HOH . N 4 HOH A 25 233 82 HOH HOH . N 4 HOH A 26 234 85 HOH HOH . N 4 HOH A 27 235 86 HOH HOH . N 4 HOH A 28 236 92 HOH HOH . N 4 HOH A 29 237 94 HOH HOH . N 4 HOH A 30 238 98 HOH HOH . N 4 HOH A 31 239 103 HOH HOH . N 4 HOH A 32 240 107 HOH HOH . N 4 HOH A 33 241 108 HOH HOH . N 4 HOH A 34 242 111 HOH HOH . N 4 HOH A 35 243 118 HOH HOH . N 4 HOH A 36 244 124 HOH HOH . N 4 HOH A 37 245 129 HOH HOH . N 4 HOH A 38 246 138 HOH HOH . N 4 HOH A 39 247 144 HOH HOH . N 4 HOH A 40 248 146 HOH HOH . N 4 HOH A 41 249 147 HOH HOH . O 4 HOH B 1 210 1 HOH HOH . O 4 HOH B 2 211 2 HOH HOH . O 4 HOH B 3 212 8 HOH HOH . O 4 HOH B 4 213 9 HOH HOH . O 4 HOH B 5 214 10 HOH HOH . O 4 HOH B 6 215 11 HOH HOH . O 4 HOH B 7 216 13 HOH HOH . O 4 HOH B 8 217 19 HOH HOH . O 4 HOH B 9 218 20 HOH HOH . O 4 HOH B 10 219 21 HOH HOH . O 4 HOH B 11 220 29 HOH HOH . O 4 HOH B 12 221 30 HOH HOH . O 4 HOH B 13 222 33 HOH HOH . O 4 HOH B 14 223 55 HOH HOH . O 4 HOH B 15 224 58 HOH HOH . O 4 HOH B 16 225 59 HOH HOH . O 4 HOH B 17 226 66 HOH HOH . O 4 HOH B 18 227 70 HOH HOH . O 4 HOH B 19 228 84 HOH HOH . O 4 HOH B 20 229 87 HOH HOH . O 4 HOH B 21 230 88 HOH HOH . O 4 HOH B 22 231 90 HOH HOH . O 4 HOH B 23 232 91 HOH HOH . O 4 HOH B 24 233 93 HOH HOH . O 4 HOH B 25 234 96 HOH HOH . O 4 HOH B 26 235 104 HOH HOH . O 4 HOH B 27 236 105 HOH HOH . O 4 HOH B 28 237 106 HOH HOH . O 4 HOH B 29 238 113 HOH HOH . O 4 HOH B 30 239 116 HOH HOH . O 4 HOH B 31 240 117 HOH HOH . O 4 HOH B 32 241 120 HOH HOH . O 4 HOH B 33 242 123 HOH HOH . O 4 HOH B 34 243 125 HOH HOH . O 4 HOH B 35 244 128 HOH HOH . O 4 HOH B 36 245 130 HOH HOH . O 4 HOH B 37 246 132 HOH HOH . O 4 HOH B 38 247 136 HOH HOH . O 4 HOH B 39 248 137 HOH HOH . O 4 HOH B 40 249 142 HOH HOH . O 4 HOH B 41 250 145 HOH HOH . P 4 HOH C 1 209 3 HOH HOH . P 4 HOH C 2 210 6 HOH HOH . P 4 HOH C 3 211 15 HOH HOH . P 4 HOH C 4 212 24 HOH HOH . P 4 HOH C 5 213 26 HOH HOH . P 4 HOH C 6 214 40 HOH HOH . P 4 HOH C 7 215 46 HOH HOH . P 4 HOH C 8 216 53 HOH HOH . P 4 HOH C 9 217 64 HOH HOH . P 4 HOH C 10 218 65 HOH HOH . P 4 HOH C 11 219 67 HOH HOH . P 4 HOH C 12 220 72 HOH HOH . P 4 HOH C 13 221 83 HOH HOH . P 4 HOH C 14 222 89 HOH HOH . P 4 HOH C 15 223 97 HOH HOH . P 4 HOH C 16 224 112 HOH HOH . P 4 HOH C 17 225 114 HOH HOH . P 4 HOH C 18 226 115 HOH HOH . P 4 HOH C 19 227 126 HOH HOH . P 4 HOH C 20 228 131 HOH HOH . P 4 HOH C 21 229 135 HOH HOH . P 4 HOH C 22 230 139 HOH HOH . P 4 HOH C 23 231 140 HOH HOH . P 4 HOH C 24 232 141 HOH HOH . Q 4 HOH D 1 209 4 HOH HOH . Q 4 HOH D 2 210 5 HOH HOH . Q 4 HOH D 3 211 7 HOH HOH . Q 4 HOH D 4 212 12 HOH HOH . Q 4 HOH D 5 213 16 HOH HOH . Q 4 HOH D 6 214 17 HOH HOH . Q 4 HOH D 7 215 22 HOH HOH . Q 4 HOH D 8 216 23 HOH HOH . Q 4 HOH D 9 217 31 HOH HOH . Q 4 HOH D 10 218 32 HOH HOH . Q 4 HOH D 11 219 36 HOH HOH . Q 4 HOH D 12 220 39 HOH HOH . Q 4 HOH D 13 221 41 HOH HOH . Q 4 HOH D 14 222 42 HOH HOH . Q 4 HOH D 15 223 43 HOH HOH . Q 4 HOH D 16 224 47 HOH HOH . Q 4 HOH D 17 225 48 HOH HOH . Q 4 HOH D 18 226 51 HOH HOH . Q 4 HOH D 19 227 56 HOH HOH . Q 4 HOH D 20 228 62 HOH HOH . Q 4 HOH D 21 229 68 HOH HOH . Q 4 HOH D 22 230 73 HOH HOH . Q 4 HOH D 23 231 74 HOH HOH . Q 4 HOH D 24 232 75 HOH HOH . Q 4 HOH D 25 233 76 HOH HOH . Q 4 HOH D 26 234 77 HOH HOH . Q 4 HOH D 27 235 78 HOH HOH . Q 4 HOH D 28 236 95 HOH HOH . Q 4 HOH D 29 237 99 HOH HOH . Q 4 HOH D 30 238 100 HOH HOH . Q 4 HOH D 31 239 101 HOH HOH . Q 4 HOH D 32 240 102 HOH HOH . Q 4 HOH D 33 241 109 HOH HOH . Q 4 HOH D 34 242 110 HOH HOH . Q 4 HOH D 35 243 119 HOH HOH . Q 4 HOH D 36 244 121 HOH HOH . Q 4 HOH D 37 245 122 HOH HOH . Q 4 HOH D 38 246 127 HOH HOH . Q 4 HOH D 39 247 133 HOH HOH . Q 4 HOH D 40 248 134 HOH HOH . Q 4 HOH D 41 249 143 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 N N1 UMP . . . H 2 14.814 -4.783 46.884 1 38.04 ? N1 UMP 304 B 1 HETATM 2 C C2 UMP . . . H 2 13.821 -3.839 47.044 1 37.28 ? C2 UMP 304 B 1 HETATM 3 N N3 UMP . . . H 2 14.042 -2.538 46.653 1 38.61 ? N3 UMP 304 B 1 HETATM 4 C C4 UMP . . . H 2 15.255 -2.18 46.097 1 37.68 ? C4 UMP 304 B 1 HETATM 5 C C5 UMP . . . H 2 16.255 -3.138 45.938 1 36.37 ? C5 UMP 304 B 1 HETATM 6 C C6 UMP . . . H 2 16.022 -4.449 46.33 1 33.16 ? C6 UMP 304 B 1 HETATM 7 O O2 UMP . . . H 2 12.743 -4.173 47.536 1 33.07 ? O2 UMP 304 B 1 HETATM 8 O O4 UMP . . . H 2 15.438 -1.017 45.746 1 33.33 ? O4 UMP 304 B 1 HETATM 9 C C1' UMP . . . H 2 14.522 -6.162 47.295 1 32.78 ? C1' UMP 304 B 1 HETATM 10 C C2' UMP . . . H 2 13.576 -6.772 46.254 1 31.77 ? C2' UMP 304 B 1 HETATM 11 C C3' UMP . . . H 2 14.195 -8.111 45.909 1 30.68 ? C3' UMP 304 B 1 HETATM 12 C C4' UMP . . . H 2 15.652 -7.944 46.308 1 34.22 ? C4' UMP 304 B 1 HETATM 13 O O3' UMP . . . H 2 13.606 -9.143 46.672 1 28.53 ? O3' UMP 304 B 1 HETATM 14 O O4' UMP . . . H 2 15.715 -6.912 47.28 1 34.66 ? O4' UMP 304 B 1 HETATM 15 C C5' UMP . . . H 2 16.517 -7.586 45.102 1 35.94 ? C5' UMP 304 B 1 HETATM 16 O O5' UMP . . . H 2 15.863 -6.591 44.337 1 37.53 ? O5' UMP 304 B 1 HETATM 17 P P UMP . . . H 2 16.557 -5.92 43.031 1 38.83 ? P UMP 304 B 1 HETATM 18 O OP1 UMP . . . H 2 16.949 -7.04 42.108 1 37.01 ? OP1 UMP 304 B 1 HETATM 19 O OP2 UMP . . . H 2 17.755 -5.079 43.419 1 36.77 ? OP2 UMP 304 B 1 HETATM 20 O OP3 UMP . . . H 2 15.568 -5.006 42.395 1 39.99 ? OP3 UMP 304 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #