data_3TPY
#
_model_server_result.job_id            r_ZX2Yqz_vhXsLKhDglTYQ 
_model_server_result.datetime_utc      '2024-11-23 00:02:49' 
_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          3tpy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":154}' 
#
_entry.id    3TPY 
#
_exptl.entry_id    3TPY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          5 
_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            3TPY 
_cell.length_a            60.559 
_cell.length_b            60.559 
_cell.length_c            63.635 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TPY 
_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 60.559 104.891265 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 -60.559 104.891265 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 
#
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 E OP1 UMP . A UMP 154 1_555 B MG MG . A MG 999 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.509 ? 
metalc ? metalc2 F O HOH . A HOH 223 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc3 F O HOH . A HOH 225 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc4 F O HOH . A HOH 245 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? 
metalc ? metalc5 D O2G DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc6 D O1A DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc7 D O1B DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.303 ? 
#
_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                     3TPY 
_atom_sites.fract_transf_matrix[1][1]    0.016513 
_atom_sites.fract_transf_matrix[1][2]    0.009534 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019067 
_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]    0.015715 
_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 MG A 1 999 999 MG MG . 
C 3 TRS A 1 153 1 TRS TRS . 
D 4 DUP A 1 777 777 DUP DUP . 
E 5 UMP A 1 154 777 UMP UMP . 
F 6 HOH A 1 155 1 HOH HOH . 
F 6 HOH A 2 156 2 HOH HOH . 
F 6 HOH A 3 157 3 HOH HOH . 
F 6 HOH A 4 158 4 HOH HOH . 
F 6 HOH A 5 159 5 HOH HOH . 
F 6 HOH A 6 160 6 HOH HOH . 
F 6 HOH A 7 161 7 HOH HOH . 
F 6 HOH A 8 162 8 HOH HOH . 
F 6 HOH A 9 163 9 HOH HOH . 
F 6 HOH A 10 164 10 HOH HOH . 
F 6 HOH A 11 165 11 HOH HOH . 
F 6 HOH A 12 166 12 HOH HOH . 
F 6 HOH A 13 167 13 HOH HOH . 
F 6 HOH A 14 168 14 HOH HOH . 
F 6 HOH A 15 169 15 HOH HOH . 
F 6 HOH A 16 170 16 HOH HOH . 
F 6 HOH A 17 171 17 HOH HOH . 
F 6 HOH A 18 172 18 HOH HOH . 
F 6 HOH A 19 173 19 HOH HOH . 
F 6 HOH A 20 174 20 HOH HOH . 
F 6 HOH A 21 175 21 HOH HOH . 
F 6 HOH A 22 176 22 HOH HOH . 
F 6 HOH A 23 177 23 HOH HOH . 
F 6 HOH A 24 178 24 HOH HOH . 
F 6 HOH A 25 179 25 HOH HOH . 
F 6 HOH A 26 180 26 HOH HOH . 
F 6 HOH A 27 181 27 HOH HOH . 
F 6 HOH A 28 182 28 HOH HOH . 
F 6 HOH A 29 183 29 HOH HOH . 
F 6 HOH A 30 184 30 HOH HOH . 
F 6 HOH A 31 185 31 HOH HOH . 
F 6 HOH A 32 186 32 HOH HOH . 
F 6 HOH A 33 187 33 HOH HOH . 
F 6 HOH A 34 188 34 HOH HOH . 
F 6 HOH A 35 189 35 HOH HOH . 
F 6 HOH A 36 190 36 HOH HOH . 
F 6 HOH A 37 191 37 HOH HOH . 
F 6 HOH A 38 192 38 HOH HOH . 
F 6 HOH A 39 193 39 HOH HOH . 
F 6 HOH A 40 194 40 HOH HOH . 
F 6 HOH A 41 195 41 HOH HOH . 
F 6 HOH A 42 196 42 HOH HOH . 
F 6 HOH A 43 197 43 HOH HOH . 
F 6 HOH A 44 198 44 HOH HOH . 
F 6 HOH A 45 199 45 HOH HOH . 
F 6 HOH A 46 200 46 HOH HOH . 
F 6 HOH A 47 201 47 HOH HOH . 
F 6 HOH A 48 202 48 HOH HOH . 
F 6 HOH A 49 203 49 HOH HOH . 
F 6 HOH A 50 204 50 HOH HOH . 
F 6 HOH A 51 205 52 HOH HOH . 
F 6 HOH A 52 206 53 HOH HOH . 
F 6 HOH A 53 207 54 HOH HOH . 
F 6 HOH A 54 208 55 HOH HOH . 
F 6 HOH A 55 209 56 HOH HOH . 
F 6 HOH A 56 210 57 HOH HOH . 
F 6 HOH A 57 211 58 HOH HOH . 
F 6 HOH A 58 212 59 HOH HOH . 
F 6 HOH A 59 213 61 HOH HOH . 
F 6 HOH A 60 214 62 HOH HOH . 
F 6 HOH A 61 215 64 HOH HOH . 
F 6 HOH A 62 216 65 HOH HOH . 
F 6 HOH A 63 217 66 HOH HOH . 
F 6 HOH A 64 218 67 HOH HOH . 
F 6 HOH A 65 219 70 HOH HOH . 
F 6 HOH A 66 220 72 HOH HOH . 
F 6 HOH A 67 221 73 HOH HOH . 
F 6 HOH A 68 222 74 HOH HOH . 
F 6 HOH A 69 223 75 HOH HOH . 
F 6 HOH A 70 224 76 HOH HOH . 
F 6 HOH A 71 225 77 HOH HOH . 
F 6 HOH A 72 226 78 HOH HOH . 
F 6 HOH A 73 227 79 HOH HOH . 
F 6 HOH A 74 228 80 HOH HOH . 
F 6 HOH A 75 229 81 HOH HOH . 
F 6 HOH A 76 230 82 HOH HOH . 
F 6 HOH A 77 231 83 HOH HOH . 
F 6 HOH A 78 232 84 HOH HOH . 
F 6 HOH A 79 233 85 HOH HOH . 
F 6 HOH A 80 234 86 HOH HOH . 
F 6 HOH A 81 235 87 HOH HOH . 
F 6 HOH A 82 236 89 HOH HOH . 
F 6 HOH A 83 237 90 HOH HOH . 
F 6 HOH A 84 238 91 HOH HOH . 
F 6 HOH A 85 239 92 HOH HOH . 
F 6 HOH A 86 240 93 HOH HOH . 
F 6 HOH A 87 241 94 HOH HOH . 
F 6 HOH A 88 242 95 HOH HOH . 
F 6 HOH A 89 243 96 HOH HOH . 
F 6 HOH A 90 244 97 HOH HOH . 
F 6 HOH A 91 245 98 HOH HOH . 
F 6 HOH A 92 246 99 HOH HOH . 
F 6 HOH A 93 247 100 HOH HOH . 
F 6 HOH A 94 248 101 HOH HOH . 
F 6 HOH A 95 249 102 HOH HOH . 
F 6 HOH A 96 250 103 HOH HOH . 
F 6 HOH A 97 251 104 HOH HOH . 
F 6 HOH A 98 252 105 HOH HOH . 
F 6 HOH A 99 253 106 HOH HOH . 
F 6 HOH A 100 254 107 HOH HOH . 
F 6 HOH A 101 255 108 HOH HOH . 
F 6 HOH A 102 256 109 HOH HOH . 
F 6 HOH A 103 257 110 HOH HOH . 
F 6 HOH A 104 258 111 HOH HOH . 
F 6 HOH A 105 259 112 HOH HOH . 
F 6 HOH A 106 260 113 HOH HOH . 
F 6 HOH A 107 261 114 HOH HOH . 
F 6 HOH A 108 262 115 HOH HOH . 
F 6 HOH A 109 263 116 HOH HOH . 
F 6 HOH A 110 264 117 HOH HOH . 
F 6 HOH A 111 265 118 HOH HOH . 
F 6 HOH A 112 266 119 HOH HOH . 
F 6 HOH A 113 267 120 HOH HOH . 
F 6 HOH A 114 268 121 HOH HOH . 
F 6 HOH A 115 269 122 HOH HOH . 
F 6 HOH A 116 270 123 HOH HOH . 
F 6 HOH A 117 271 124 HOH HOH . 
F 6 HOH A 118 272 125 HOH HOH . 
F 6 HOH A 119 273 126 HOH HOH . 
F 6 HOH A 120 274 127 HOH HOH . 
F 6 HOH A 121 275 128 HOH HOH . 
F 6 HOH A 122 276 129 HOH HOH . 
F 6 HOH A 123 277 130 HOH HOH . 
F 6 HOH A 124 278 131 HOH HOH . 
F 6 HOH A 125 279 132 HOH HOH . 
F 6 HOH A 126 280 133 HOH HOH . 
F 6 HOH A 127 281 134 HOH HOH . 
F 6 HOH A 128 282 135 HOH HOH . 
F 6 HOH A 129 283 136 HOH HOH . 
F 6 HOH A 130 284 138 HOH HOH . 
F 6 HOH A 131 285 139 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 . E 5 -5.104 57.349 30.797 0.3 17.14 ? N1 UMP 154 A 1 
HETATM 2 C C2 UMP . A . E 5 -3.866 56.929 30.359 0.3 13.37 ? C2 UMP 154 A 1 
HETATM 3 N N3 UMP . A . E 5 -3.088 57.775 29.613 0.3 9.76 ? N3 UMP 154 A 1 
HETATM 4 C C4 UMP . A . E 5 -3.504 59.047 29.312 0.3 18.2 ? C4 UMP 154 A 1 
HETATM 5 C C5 UMP . A . E 5 -4.747 59.488 29.746 0.3 15.45 ? C5 UMP 154 A 1 
HETATM 6 C C6 UMP . A . E 5 -5.545 58.62 30.487 0.3 6.87 ? C6 UMP 154 A 1 
HETATM 7 O O2 UMP . A . E 5 -3.445 55.802 30.628 0.3 15 ? O2 UMP 154 A 1 
HETATM 8 O O4 UMP . A . E 5 -2.765 59.764 28.648 0.3 19.91 ? O4 UMP 154 A 1 
HETATM 9 C C1' UMP . A . E 5 -5.918 56.413 31.595 0.3 23.52 ? C1' UMP 154 A 1 
HETATM 10 C C2' UMP . A . E 5 -5.936 56.883 33.047 0.3 22.54 ? C2' UMP 154 A 1 
HETATM 11 C C3' UMP . A . E 5 -7.302 57.52 33.185 0.3 19.78 ? C3' UMP 154 A 1 
HETATM 12 C C4' UMP . A . E 5 -8.148 56.838 32.116 0.3 19.28 ? C4' UMP 154 A 1 
HETATM 13 O O3' UMP . A . E 5 -7.804 57.33 34.493 0.3 14.94 ? O3' UMP 154 A 1 
HETATM 14 O O4' UMP . A . E 5 -7.258 56.383 31.124 0.3 25.82 ? O4' UMP 154 A 1 
HETATM 15 C C5' UMP . A . E 5 -9.163 57.754 31.441 0.3 10.2 ? C5' UMP 154 A 1 
HETATM 16 O O5' UMP . A . E 5 -8.521 58.879 30.879 0.3 15.05 ? O5' UMP 154 A 1 
HETATM 17 P P UMP . A . E 5 -9.01 60.358 31.334 0.3 11.42 ? P UMP 154 A 1 
HETATM 18 O OP1 UMP . A . E 5 -10.518 60.355 31.198 0.3 9.66 ? OP1 UMP 154 A 1 
HETATM 19 O OP2 UMP . A . E 5 -8.565 60.691 32.747 0.3 9.21 ? OP2 UMP 154 A 1 
HETATM 20 O OP3 UMP . A . E 5 -8.384 61.289 30.355 0.3 12.88 ? OP3 UMP 154 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           20 
#