data_3TRN
#
_model_server_result.job_id            am5pQ77Fww8guYO7yFqxTw 
_model_server_result.datetime_utc      '2024-11-13 05:04:20' 
_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          3trn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":777}' 
#
_entry.id    3TRN 
#
_exptl.entry_id    3TRN 
_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    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            3TRN 
_cell.length_a            60.566 
_cell.length_b            60.566 
_cell.length_c            63.524 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TRN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 60.566 104.903389 0 
3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -60.566 104.903389 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 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale ? covale1 A C LEU 43 A LEU 43 1_555 A N CSO 44 A CSO 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale2 A C CSO 44 A CSO 44 1_555 A N SER 45 A SER 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
#
_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 372 n n 
N1 C6 UMP sing 373 n n 
N1 C1' UMP sing 374 n n 
C2 N3 UMP sing 375 n n 
C2 O2 UMP doub 376 n n 
N3 C4 UMP sing 377 n n 
N3 HN3 UMP sing 378 n n 
C4 C5 UMP sing 379 n n 
C4 O4 UMP doub 380 n n 
C5 C6 UMP doub 381 n n 
C5 H5 UMP sing 382 n n 
C6 H6 UMP sing 383 n n 
C1' C2' UMP sing 384 n n 
C1' O4' UMP sing 385 n n 
C1' H1' UMP sing 386 n n 
C2' C3' UMP sing 387 n n 
C2' H2' UMP sing 388 n n 
C2' "H2''" UMP sing 389 n n 
C3' C4' UMP sing 390 n n 
C3' O3' UMP sing 391 n n 
C3' H3' UMP sing 392 n n 
C4' O4' UMP sing 393 n n 
C4' C5' UMP sing 394 n n 
C4' H4' UMP sing 395 n n 
O3' HO3' UMP sing 396 n n 
C5' O5' UMP sing 397 n n 
C5' H5' UMP sing 398 n n 
C5' "H5''" UMP sing 399 n n 
O5' P UMP sing 400 n n 
P OP1 UMP doub 401 n n 
P OP2 UMP sing 402 n n 
P OP3 UMP sing 403 n n 
OP2 HOP2 UMP sing 404 n n 
OP3 HOP3 UMP sing 405 n n 
#
_atom_sites.entry_id                     3TRN 
_atom_sites.fract_transf_matrix[1][1]    0.016511 
_atom_sites.fract_transf_matrix[1][2]    0.009533 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019065 
_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]    0.015742 
_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 UMP A 1 777 777 UMP UMP . 
C 3 HOH A 1 153 1 HOH HOH . 
C 3 HOH A 2 154 2 HOH HOH . 
C 3 HOH A 3 155 3 HOH HOH . 
C 3 HOH A 4 156 4 HOH HOH . 
C 3 HOH A 5 157 5 HOH HOH . 
C 3 HOH A 6 158 6 HOH HOH . 
C 3 HOH A 7 159 7 HOH HOH . 
C 3 HOH A 8 160 8 HOH HOH . 
C 3 HOH A 9 161 9 HOH HOH . 
C 3 HOH A 10 162 10 HOH HOH . 
C 3 HOH A 11 163 11 HOH HOH . 
C 3 HOH A 12 164 12 HOH HOH . 
C 3 HOH A 13 165 13 HOH HOH . 
C 3 HOH A 14 166 14 HOH HOH . 
C 3 HOH A 15 167 15 HOH HOH . 
C 3 HOH A 16 168 16 HOH HOH . 
C 3 HOH A 17 169 17 HOH HOH . 
C 3 HOH A 18 170 18 HOH HOH . 
C 3 HOH A 19 171 19 HOH HOH . 
C 3 HOH A 20 172 20 HOH HOH . 
C 3 HOH A 21 173 21 HOH HOH . 
C 3 HOH A 22 174 22 HOH HOH . 
C 3 HOH A 23 175 23 HOH HOH . 
C 3 HOH A 24 176 24 HOH HOH . 
C 3 HOH A 25 177 25 HOH HOH . 
C 3 HOH A 26 178 26 HOH HOH . 
C 3 HOH A 27 179 27 HOH HOH . 
C 3 HOH A 28 180 28 HOH HOH . 
C 3 HOH A 29 181 29 HOH HOH . 
C 3 HOH A 30 182 30 HOH HOH . 
C 3 HOH A 31 183 31 HOH HOH . 
C 3 HOH A 32 184 33 HOH HOH . 
C 3 HOH A 33 185 34 HOH HOH . 
C 3 HOH A 34 186 35 HOH HOH . 
C 3 HOH A 35 187 36 HOH HOH . 
C 3 HOH A 36 188 37 HOH HOH . 
C 3 HOH A 37 189 38 HOH HOH . 
C 3 HOH A 38 190 40 HOH HOH . 
C 3 HOH A 39 191 41 HOH HOH . 
C 3 HOH A 40 192 42 HOH HOH . 
C 3 HOH A 41 193 43 HOH HOH . 
C 3 HOH A 42 194 44 HOH HOH . 
C 3 HOH A 43 195 45 HOH HOH . 
C 3 HOH A 44 196 46 HOH HOH . 
C 3 HOH A 45 197 47 HOH HOH . 
C 3 HOH A 46 198 48 HOH HOH . 
C 3 HOH A 47 199 49 HOH HOH . 
C 3 HOH A 48 200 50 HOH HOH . 
C 3 HOH A 49 201 51 HOH HOH . 
C 3 HOH A 50 202 52 HOH HOH . 
C 3 HOH A 51 203 53 HOH HOH . 
C 3 HOH A 52 204 54 HOH HOH . 
C 3 HOH A 53 205 55 HOH HOH . 
C 3 HOH A 54 206 56 HOH HOH . 
C 3 HOH A 55 207 57 HOH HOH . 
C 3 HOH A 56 208 58 HOH HOH . 
C 3 HOH A 57 209 59 HOH HOH . 
C 3 HOH A 58 210 60 HOH HOH . 
C 3 HOH A 59 211 61 HOH HOH . 
C 3 HOH A 60 212 62 HOH HOH . 
C 3 HOH A 61 213 63 HOH HOH . 
C 3 HOH A 62 214 64 HOH HOH . 
C 3 HOH A 63 215 66 HOH HOH . 
C 3 HOH A 64 216 67 HOH HOH . 
C 3 HOH A 65 217 68 HOH HOH . 
C 3 HOH A 66 218 69 HOH HOH . 
C 3 HOH A 67 219 70 HOH HOH . 
C 3 HOH A 68 220 71 HOH HOH . 
C 3 HOH A 69 221 72 HOH HOH . 
C 3 HOH A 70 222 73 HOH HOH . 
C 3 HOH A 71 223 74 HOH HOH . 
C 3 HOH A 72 224 75 HOH HOH . 
C 3 HOH A 73 225 76 HOH HOH . 
C 3 HOH A 74 226 77 HOH HOH . 
C 3 HOH A 75 227 78 HOH HOH . 
C 3 HOH A 76 228 80 HOH HOH . 
C 3 HOH A 77 229 81 HOH HOH . 
C 3 HOH A 78 230 82 HOH HOH . 
C 3 HOH A 79 231 83 HOH HOH . 
C 3 HOH A 80 232 84 HOH HOH . 
C 3 HOH A 81 233 85 HOH HOH . 
C 3 HOH A 82 234 86 HOH HOH . 
C 3 HOH A 83 235 87 HOH HOH . 
C 3 HOH A 84 236 88 HOH HOH . 
C 3 HOH A 85 237 89 HOH HOH . 
C 3 HOH A 86 238 90 HOH HOH . 
C 3 HOH A 87 239 91 HOH HOH . 
C 3 HOH A 88 240 94 HOH HOH . 
C 3 HOH A 89 241 96 HOH HOH . 
C 3 HOH A 90 242 97 HOH HOH . 
C 3 HOH A 91 243 98 HOH HOH . 
C 3 HOH A 92 244 99 HOH HOH . 
C 3 HOH A 93 245 101 HOH HOH . 
C 3 HOH A 94 246 102 HOH HOH . 
C 3 HOH A 95 247 120 HOH HOH . 
C 3 HOH A 96 248 121 HOH HOH . 
C 3 HOH A 97 249 122 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 . . . B 2 -4.923 57.314 30.557 1 20.81 ? N1 UMP 777 A 1 
HETATM 2 C C2 UMP . . . B 2 -3.732 56.812 30.098 1 21.14 ? C2 UMP 777 A 1 
HETATM 3 N N3 UMP . . . B 2 -2.872 57.663 29.451 1 19.24 ? N3 UMP 777 A 1 
HETATM 4 C C4 UMP . . . B 2 -3.178 58.993 29.289 1 18.49 ? C4 UMP 777 A 1 
HETATM 5 C C5 UMP . . . B 2 -4.41 59.515 29.721 1 17.53 ? C5 UMP 777 A 1 
HETATM 6 C C6 UMP . . . B 2 -5.269 58.639 30.386 1 20.17 ? C6 UMP 777 A 1 
HETATM 7 O O2 UMP . . . B 2 -3.42 55.614 30.256 1 22.26 ? O2 UMP 777 A 1 
HETATM 8 O O4 UMP . . . B 2 -2.352 59.667 28.702 1 21.04 ? O4 UMP 777 A 1 
HETATM 9 C C1' UMP . . . B 2 -5.825 56.408 31.248 1 23.38 ? C1' UMP 777 A 1 
HETATM 10 C C2' UMP . . . B 2 -5.731 56.728 32.754 1 23.65 ? C2' UMP 777 A 1 
HETATM 11 C C3' UMP . . . B 2 -6.979 57.556 32.986 1 20.42 ? C3' UMP 777 A 1 
HETATM 12 C C4' UMP . . . B 2 -7.941 56.921 32.012 1 17.38 ? C4' UMP 777 A 1 
HETATM 13 O O3' UMP . . . B 2 -7.436 57.365 34.301 1 22.77 ? O3' UMP 777 A 1 
HETATM 14 O O4' UMP . . . B 2 -7.18 56.65 30.853 1 20.11 ? O4' UMP 777 A 1 
HETATM 15 C C5' UMP . . . B 2 -9.121 57.793 31.616 1 21.51 ? C5' UMP 777 A 1 
HETATM 16 O O5' UMP . . . B 2 -8.506 58.892 30.975 1 24.9 ? O5' UMP 777 A 1 
HETATM 17 P P UMP . . . B 2 -9.011 60.412 31.243 1 22 ? P UMP 777 A 1 
HETATM 18 O OP1 UMP . . . B 2 -10.404 60.407 31.127 1 20.61 ? OP1 UMP 777 A 1 
HETATM 19 O OP2 UMP . . . B 2 -8.55 60.696 32.687 1 33.52 ? OP2 UMP 777 A 1 
HETATM 20 O OP3 UMP . . . B 2 -8.334 61.383 30.374 1 22.05 ? OP3 UMP 777 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#