data_1F7R
#
_model_server_result.job_id            -_h-GwAIJWDtOEjpOPQFeA 
_model_server_result.datetime_utc      '2025-02-17 01:18:40' 
_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          1f7r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":138}' 
#
_entry.id    1F7R 
#
_exptl.entry_id    1F7R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_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         90 
_cell.entry_id            1F7R 
_cell.length_a            72.44 
_cell.length_b            72.44 
_cell.length_c            72.44 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1F7R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 3' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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 
_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' 8_645 -z+1,x-1/2,-y+1/2 0 0 -1 1 0 0 0 -1 0 72.44 -36.22 36.22 
3 'crystal symmetry operation' 11_556 y+1/2,-z+1/2,-x+1 0 1 0 0 0 -1 -1 0 0 36.22 36.22 72.44 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 A OD1 ASP 64 A ASP 64 1_555 B MG MG . A MG 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc2 A OD1 ASP 64 A ASP 64 8_645 B MG MG . A MG 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc3 A OD2 ASP 64 A ASP 64 8_645 B MG MG . A MG 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
#
_chem_comp.formula           'C9 H14 N2 O12 P2' 
_chem_comp.formula_weight    404.161 
_chem_comp.id                UDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
N1 C2 UDP sing 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     1F7R 
_atom_sites.fract_transf_matrix[1][1]    0.013805 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013805 
_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]    0.013805 
_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 1 137 135 MG MG . 
C 3 UDP A 1 138 134 UDP UDP . 
D 4 HOH A 1 201 201 HOH TIP . 
D 4 HOH A 2 202 202 HOH TIP . 
D 4 HOH A 3 203 203 HOH TIP . 
D 4 HOH A 4 204 204 HOH TIP . 
D 4 HOH A 5 205 205 HOH TIP . 
D 4 HOH A 6 206 206 HOH TIP . 
D 4 HOH A 7 207 207 HOH TIP . 
D 4 HOH A 8 208 208 HOH TIP . 
D 4 HOH A 9 209 209 HOH TIP . 
D 4 HOH A 10 210 210 HOH TIP . 
D 4 HOH A 11 211 211 HOH TIP . 
D 4 HOH A 12 213 213 HOH TIP . 
D 4 HOH A 13 214 214 HOH TIP . 
D 4 HOH A 14 215 215 HOH TIP . 
D 4 HOH A 15 216 216 HOH TIP . 
D 4 HOH A 16 217 217 HOH TIP . 
D 4 HOH A 17 218 218 HOH TIP . 
D 4 HOH A 18 219 219 HOH TIP . 
D 4 HOH A 19 220 220 HOH TIP . 
D 4 HOH A 20 221 221 HOH TIP . 
D 4 HOH A 21 222 222 HOH TIP . 
D 4 HOH A 22 223 223 HOH TIP . 
D 4 HOH A 23 224 224 HOH TIP . 
D 4 HOH A 24 225 225 HOH TIP . 
D 4 HOH A 25 226 226 HOH TIP . 
D 4 HOH A 26 227 227 HOH TIP . 
D 4 HOH A 27 228 228 HOH TIP . 
D 4 HOH A 28 229 229 HOH TIP . 
D 4 HOH A 29 230 230 HOH TIP . 
D 4 HOH A 30 231 231 HOH TIP . 
D 4 HOH A 31 232 232 HOH TIP . 
D 4 HOH A 32 233 233 HOH TIP . 
D 4 HOH A 33 234 234 HOH TIP . 
D 4 HOH A 34 235 235 HOH TIP . 
D 4 HOH A 35 236 236 HOH TIP . 
D 4 HOH A 36 237 237 HOH TIP . 
D 4 HOH A 37 238 238 HOH TIP . 
D 4 HOH A 38 239 239 HOH TIP . 
D 4 HOH A 39 240 240 HOH TIP . 
D 4 HOH A 40 241 241 HOH TIP . 
D 4 HOH A 41 242 242 HOH TIP . 
D 4 HOH A 42 243 243 HOH TIP . 
D 4 HOH A 43 244 244 HOH TIP . 
D 4 HOH A 44 245 245 HOH TIP . 
D 4 HOH A 45 246 246 HOH TIP . 
D 4 HOH A 46 247 247 HOH TIP . 
D 4 HOH A 47 248 248 HOH TIP . 
D 4 HOH A 48 249 249 HOH TIP . 
D 4 HOH A 49 250 250 HOH TIP . 
D 4 HOH A 50 251 251 HOH TIP . 
D 4 HOH A 51 252 252 HOH TIP . 
D 4 HOH A 52 253 253 HOH TIP . 
D 4 HOH A 53 254 254 HOH TIP . 
D 4 HOH A 54 255 255 HOH TIP . 
#
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 UDP . . . C 3 43 23.514 30.08 1 20.36 ? N1 UDP 138 A 1 
HETATM 2 C C2 UDP . . . C 3 43.792 23.183 31.21 1 19.86 ? C2 UDP 138 A 1 
HETATM 3 N N3 UDP . . . C 3 44.12 21.827 31.322 1 18.87 ? N3 UDP 138 A 1 
HETATM 4 C C4 UDP . . . C 3 43.724 20.8 30.446 1 20.09 ? C4 UDP 138 A 1 
HETATM 5 C C5 UDP . . . C 3 42.896 21.205 29.294 1 20.43 ? C5 UDP 138 A 1 
HETATM 6 C C6 UDP . . . C 3 42.565 22.521 29.157 1 20.36 ? C6 UDP 138 A 1 
HETATM 7 O O2 UDP . . . C 3 44.187 24.002 32.025 1 21.35 ? O2 UDP 138 A 1 
HETATM 8 O O4 UDP . . . C 3 44.088 19.67 30.686 1 21.48 ? O4 UDP 138 A 1 
HETATM 9 C C1' UDP . . . C 3 42.607 24.943 29.884 1 17.78 ? C1' UDP 138 A 1 
HETATM 10 C C2' UDP . . . C 3 43.612 25.707 29.013 1 17.64 ? C2' UDP 138 A 1 
HETATM 11 C C3' UDP . . . C 3 42.888 25.863 27.702 1 18.64 ? C3' UDP 138 A 1 
HETATM 12 C C4' UDP . . . C 3 41.433 25.885 28.084 1 19.93 ? C4' UDP 138 A 1 
HETATM 13 O O4' UDP . . . C 3 41.324 25.079 29.29 1 20.78 ? O4' UDP 138 A 1 
HETATM 14 O O3' UDP . . . C 3 43.194 27.083 27.066 1 18.87 ? O3' UDP 138 A 1 
HETATM 15 C C5' UDP . . . C 3 40.553 25.28 27.012 1 23.94 ? C5' UDP 138 A 1 
HETATM 16 O O5' UDP . . . C 3 39.259 25.323 27.43 1 28.99 ? O5' UDP 138 A 1 
HETATM 17 P PA UDP . . . C 3 38.009 25.588 26.435 1 30.42 ? PA UDP 138 A 1 
HETATM 18 O O1A UDP . . . C 3 36.767 25.75 27.206 1 29.81 ? O1A UDP 138 A 1 
HETATM 19 O O2A UDP . . . C 3 38.291 26.716 25.574 1 34.25 ? O2A UDP 138 A 1 
HETATM 20 O O3A UDP . . . C 3 37.873 24.366 25.517 1 36.54 ? O3A UDP 138 A 1 
HETATM 21 P PB UDP . . . C 3 38.017 22.829 25.775 1 40.77 ? PB UDP 138 A 1 
HETATM 22 O O1B UDP . . . C 3 36.806 22.394 26.587 1 34.72 ? O1B UDP 138 A 1 
HETATM 23 O O2B UDP . . . C 3 39.4 22.439 26.46 1 36.08 ? O2B UDP 138 A 1 
HETATM 24 O O3B UDP . . . C 3 38.04 22.258 24.379 1 40.25 ? O3B UDP 138 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           24 
#