data_3TQ4
#
_model_server_result.job_id            Ye18I2WkmegVH0l-RFtSng 
_model_server_result.datetime_utc      '2024-11-13 04:30:42' 
_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          3tq4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":777}' 
#
_entry.id    3TQ4 
#
_exptl.entry_id    3TQ4 
_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            3TQ4 
_cell.length_a            60.564 
_cell.length_b            60.564 
_cell.length_c            64.018 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TQ4 
_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,D,E,F 
_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 60.564 104.899925 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 -60.564 104.899925 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
metalc ? metalc1 C MG MG . A MG 153 1_555 D O1A DUP . A DUP 154 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.952 ? 
metalc ? metalc2 C MG MG . A MG 153 1_555 D O1B DUP . A DUP 154 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc3 C MG MG . A MG 153 1_555 D O2G DUP . A DUP 154 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.25 ? 
metalc ? metalc4 C MG MG . A MG 153 1_555 F O HOH . A HOH 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? 
metalc ? metalc5 C MG MG . A MG 153 1_555 B OP1 UMP . A UMP 777 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.385 ? 
#
_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 422 n n 
N1 C6 UMP sing 423 n n 
N1 C1' UMP sing 424 n n 
C2 N3 UMP sing 425 n n 
C2 O2 UMP doub 426 n n 
N3 C4 UMP sing 427 n n 
N3 HN3 UMP sing 428 n n 
C4 C5 UMP sing 429 n n 
C4 O4 UMP doub 430 n n 
C5 C6 UMP doub 431 n n 
C5 H5 UMP sing 432 n n 
C6 H6 UMP sing 433 n n 
C1' C2' UMP sing 434 n n 
C1' O4' UMP sing 435 n n 
C1' H1' UMP sing 436 n n 
C2' C3' UMP sing 437 n n 
C2' H2' UMP sing 438 n n 
C2' "H2''" UMP sing 439 n n 
C3' C4' UMP sing 440 n n 
C3' O3' UMP sing 441 n n 
C3' H3' UMP sing 442 n n 
C4' O4' UMP sing 443 n n 
C4' C5' UMP sing 444 n n 
C4' H4' UMP sing 445 n n 
O3' HO3' UMP sing 446 n n 
C5' O5' UMP sing 447 n n 
C5' H5' UMP sing 448 n n 
C5' "H5''" UMP sing 449 n n 
O5' P UMP sing 450 n n 
P OP1 UMP doub 451 n n 
P OP2 UMP sing 452 n n 
P OP3 UMP sing 453 n n 
OP2 HOP2 UMP sing 454 n n 
OP3 HOP3 UMP sing 455 n n 
#
_atom_sites.entry_id                     3TQ4 
_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]    0.019066 
_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]    0.015621 
_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 MG A 1 153 1 MG MG . 
D 4 DUP A 1 154 777 DUP DUP . 
E 5 TRS A 1 155 1 TRS TRS . 
F 6 HOH A 1 156 1 HOH HOH . 
F 6 HOH A 2 157 2 HOH HOH . 
F 6 HOH A 3 158 3 HOH HOH . 
F 6 HOH A 4 159 4 HOH HOH . 
F 6 HOH A 5 160 5 HOH HOH . 
F 6 HOH A 6 161 6 HOH HOH . 
F 6 HOH A 7 162 7 HOH HOH . 
F 6 HOH A 8 163 8 HOH HOH . 
F 6 HOH A 9 164 9 HOH HOH . 
F 6 HOH A 10 165 10 HOH HOH . 
F 6 HOH A 11 166 11 HOH HOH . 
F 6 HOH A 12 167 12 HOH HOH . 
F 6 HOH A 13 168 13 HOH HOH . 
F 6 HOH A 14 169 14 HOH HOH . 
F 6 HOH A 15 170 15 HOH HOH . 
F 6 HOH A 16 171 16 HOH HOH . 
F 6 HOH A 17 172 17 HOH HOH . 
F 6 HOH A 18 173 18 HOH HOH . 
F 6 HOH A 19 174 19 HOH HOH . 
F 6 HOH A 20 175 20 HOH HOH . 
F 6 HOH A 21 176 21 HOH HOH . 
F 6 HOH A 22 177 22 HOH HOH . 
F 6 HOH A 23 178 23 HOH HOH . 
F 6 HOH A 24 179 24 HOH HOH . 
F 6 HOH A 25 180 25 HOH HOH . 
F 6 HOH A 26 181 26 HOH HOH . 
F 6 HOH A 27 182 27 HOH HOH . 
F 6 HOH A 28 183 28 HOH HOH . 
F 6 HOH A 29 184 29 HOH HOH . 
F 6 HOH A 30 185 30 HOH HOH . 
F 6 HOH A 31 186 31 HOH HOH . 
F 6 HOH A 32 187 32 HOH HOH . 
F 6 HOH A 33 188 33 HOH HOH . 
F 6 HOH A 34 189 34 HOH HOH . 
F 6 HOH A 35 190 35 HOH HOH . 
F 6 HOH A 36 191 36 HOH HOH . 
F 6 HOH A 37 192 37 HOH HOH . 
F 6 HOH A 38 193 38 HOH HOH . 
F 6 HOH A 39 194 39 HOH HOH . 
F 6 HOH A 40 195 40 HOH HOH . 
F 6 HOH A 41 196 41 HOH HOH . 
F 6 HOH A 42 197 42 HOH HOH . 
F 6 HOH A 43 198 43 HOH HOH . 
F 6 HOH A 44 199 44 HOH HOH . 
F 6 HOH A 45 200 45 HOH HOH . 
F 6 HOH A 46 201 46 HOH HOH . 
F 6 HOH A 47 202 47 HOH HOH . 
F 6 HOH A 48 203 48 HOH HOH . 
F 6 HOH A 49 204 49 HOH HOH . 
F 6 HOH A 50 205 50 HOH HOH . 
F 6 HOH A 51 206 54 HOH HOH . 
F 6 HOH A 52 207 55 HOH HOH . 
F 6 HOH A 53 208 56 HOH HOH . 
F 6 HOH A 54 209 57 HOH HOH . 
F 6 HOH A 55 210 58 HOH HOH . 
F 6 HOH A 56 211 59 HOH HOH . 
F 6 HOH A 57 212 60 HOH HOH . 
F 6 HOH A 58 213 61 HOH HOH . 
F 6 HOH A 59 214 62 HOH HOH . 
F 6 HOH A 60 215 63 HOH HOH . 
F 6 HOH A 61 216 64 HOH HOH . 
F 6 HOH A 62 217 65 HOH HOH . 
F 6 HOH A 63 218 66 HOH HOH . 
F 6 HOH A 64 219 67 HOH HOH . 
F 6 HOH A 65 220 68 HOH HOH . 
F 6 HOH A 66 221 69 HOH HOH . 
F 6 HOH A 67 222 70 HOH HOH . 
F 6 HOH A 68 223 71 HOH HOH . 
F 6 HOH A 69 224 72 HOH HOH . 
F 6 HOH A 70 225 73 HOH HOH . 
F 6 HOH A 71 226 74 HOH HOH . 
F 6 HOH A 72 227 75 HOH HOH . 
F 6 HOH A 73 228 76 HOH HOH . 
F 6 HOH A 74 229 77 HOH HOH . 
F 6 HOH A 75 230 78 HOH HOH . 
F 6 HOH A 76 231 79 HOH HOH . 
F 6 HOH A 77 232 80 HOH HOH . 
F 6 HOH A 78 233 81 HOH HOH . 
F 6 HOH A 79 234 82 HOH HOH . 
F 6 HOH A 80 235 83 HOH HOH . 
F 6 HOH A 81 236 84 HOH HOH . 
F 6 HOH A 82 237 87 HOH HOH . 
F 6 HOH A 83 238 88 HOH HOH . 
F 6 HOH A 84 239 89 HOH HOH . 
F 6 HOH A 85 240 90 HOH HOH . 
F 6 HOH A 86 241 91 HOH HOH . 
F 6 HOH A 87 242 92 HOH HOH . 
F 6 HOH A 88 243 93 HOH HOH . 
F 6 HOH A 89 244 95 HOH HOH . 
F 6 HOH A 90 245 96 HOH HOH . 
F 6 HOH A 91 246 98 HOH HOH . 
F 6 HOH A 92 247 99 HOH HOH . 
F 6 HOH A 93 248 100 HOH HOH . 
F 6 HOH A 94 249 101 HOH HOH . 
F 6 HOH A 95 250 102 HOH HOH . 
F 6 HOH A 96 251 103 HOH HOH . 
F 6 HOH A 97 252 104 HOH HOH . 
F 6 HOH A 98 253 105 HOH HOH . 
F 6 HOH A 99 254 106 HOH HOH . 
F 6 HOH A 100 255 107 HOH HOH . 
F 6 HOH A 101 256 108 HOH HOH . 
F 6 HOH A 102 257 109 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 . A . B 2 -4.917 57.263 30.798 0.8 13.11 ? N1 UMP 777 A 1 
HETATM 2 C C2 UMP . A . B 2 -3.698 56.792 30.387 0.8 15.28 ? C2 UMP 777 A 1 
HETATM 3 N N3 UMP . A . B 2 -2.805 57.609 29.778 0.8 12.11 ? N3 UMP 777 A 1 
HETATM 4 C C4 UMP . A . B 2 -3.063 58.922 29.553 0.8 13.44 ? C4 UMP 777 A 1 
HETATM 5 C C5 UMP . A . B 2 -4.285 59.407 30.012 0.8 10.5 ? C5 UMP 777 A 1 
HETATM 6 C C6 UMP . A . B 2 -5.238 58.583 30.624 0.8 13.61 ? C6 UMP 777 A 1 
HETATM 7 O O2 UMP . A . B 2 -3.359 55.594 30.496 0.8 17.56 ? O2 UMP 777 A 1 
HETATM 8 O O4 UMP . A . B 2 -2.186 59.642 29.014 0.8 13.92 ? O4 UMP 777 A 1 
HETATM 9 C C1' UMP . A . B 2 -5.825 56.317 31.467 0.8 12.82 ? C1' UMP 777 A 1 
HETATM 10 C C2' UMP . A . B 2 -5.716 56.619 32.994 0.8 16.68 ? C2' UMP 777 A 1 
HETATM 11 C C3' UMP . A . B 2 -6.929 57.472 33.266 0.8 18.88 ? C3' UMP 777 A 1 
HETATM 12 C C4' UMP . A . B 2 -7.939 56.872 32.278 0.8 14.27 ? C4' UMP 777 A 1 
HETATM 13 O O3' UMP . A . B 2 -7.363 57.336 34.607 0.8 19.49 ? O3' UMP 777 A 1 
HETATM 14 O O4' UMP . A . B 2 -7.182 56.523 31.125 0.8 18.06 ? O4' UMP 777 A 1 
HETATM 15 C C5' UMP . A . B 2 -9.132 57.71 31.855 0.8 17.6 ? C5' UMP 777 A 1 
HETATM 16 O O5' UMP . A . B 2 -8.555 58.832 31.204 0.8 16.74 ? O5' UMP 777 A 1 
HETATM 17 P P UMP . A . B 2 -9.067 60.347 31.517 0.8 15.41 ? P UMP 777 A 1 
HETATM 18 O OP1 UMP . A . B 2 -10.547 60.258 31.389 0.8 19.35 ? OP1 UMP 777 A 1 
HETATM 19 O OP2 UMP . A . B 2 -8.294 61.255 30.627 0.8 19.79 ? OP2 UMP 777 A 1 
HETATM 20 O OP3 UMP . A . B 2 -8.644 60.67 32.955 0.8 20.16 ? OP3 UMP 777 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           377 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#