data_8SMP
#
_model_server_result.job_id            -C6dXkAjlvgBIocVaI51bA 
_model_server_result.datetime_utc      '2024-10-25 20:33:59' 
_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          8smp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":601}' 
#
_entry.id    8SMP 
#
_exptl.entry_id    8SMP 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          4 
_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            8SMP 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8SMP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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
disulf ? disulf1 B SG CYS 25 H CYS 25 1_555 B SG CYS 99 H CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 C SG CYS 24 L CYS 24 1_555 C SG CYS 89 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
metalc ? metalc1 A OD2 ASP 255 A ASP 242 1_555 E MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? 
metalc ? metalc2 D O2B UDP . A UDP 601 1_555 E MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
#
_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 356 n n 
N1 C6 UDP sing 357 n n 
N1 C1' UDP sing 358 n n 
C2 N3 UDP sing 359 n n 
C2 O2 UDP doub 360 n n 
N3 C4 UDP sing 361 n n 
N3 HN3 UDP sing 362 n n 
C4 C5 UDP sing 363 n n 
C4 O4 UDP doub 364 n n 
C5 C6 UDP doub 365 n n 
C5 H5 UDP sing 366 n n 
C6 H6 UDP sing 367 n n 
C1' C2' UDP sing 368 n n 
C1' O4' UDP sing 369 n n 
C1' H1' UDP sing 370 n n 
C2' O2' UDP sing 371 n n 
C2' C3' UDP sing 372 n n 
C2' H2' UDP sing 373 n n 
O2' HO2' UDP sing 374 n n 
C3' C4' UDP sing 375 n n 
C3' O3' UDP sing 376 n n 
C3' H3' UDP sing 377 n n 
C4' O4' UDP sing 378 n n 
C4' C5' UDP sing 379 n n 
C4' H4' UDP sing 380 n n 
O3' HO3' UDP sing 381 n n 
C5' O5' UDP sing 382 n n 
C5' "H5'1" UDP sing 383 n n 
C5' "H5'2" UDP sing 384 n n 
O5' PA UDP sing 385 n n 
PA O1A UDP doub 386 n n 
PA O2A UDP sing 387 n n 
PA O3A UDP sing 388 n n 
O2A HOA2 UDP sing 389 n n 
O3A PB UDP sing 390 n n 
PB O1B UDP doub 391 n n 
PB O2B UDP sing 392 n n 
PB O3B UDP sing 393 n n 
O2B HOB2 UDP sing 394 n n 
O3B HOB3 UDP sing 395 n n 
#
_atom_sites.entry_id                     8SMP 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
D 4 UDP A 1 601 601 UDP UDP . 
E 5 MG A 1 602 1 MG MG . 
#
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 . . . D 4 159.304 166.428 186.748 1 58.83 ? N1 UDP 601 A 1 
HETATM 2 C C2 UDP . . . D 4 158.504 167.035 187.696 1 63.26 ? C2 UDP 601 A 1 
HETATM 3 N N3 UDP . . . D 4 157.286 167.471 187.235 1 63.57 ? N3 UDP 601 A 1 
HETATM 4 C C4 UDP . . . D 4 156.802 167.363 185.946 1 63.44 ? C4 UDP 601 A 1 
HETATM 5 C C5 UDP . . . D 4 157.689 166.724 185.024 1 65.04 ? C5 UDP 601 A 1 
HETATM 6 C C6 UDP . . . D 4 158.888 166.285 185.445 1 64.05 ? C6 UDP 601 A 1 
HETATM 7 O O2 UDP . . . D 4 158.844 167.176 188.862 1 69.85 ? O2 UDP 601 A 1 
HETATM 8 O O4 UDP . . . D 4 155.676 167.807 185.675 1 62.58 ? O4 UDP 601 A 1 
HETATM 9 C C1' UDP . . . D 4 160.621 165.937 187.179 1 60.66 ? C1' UDP 601 A 1 
HETATM 10 C C2' UDP . . . D 4 161.01 164.604 186.544 1 63.29 ? C2' UDP 601 A 1 
HETATM 11 O O2' UDP . . . D 4 160.541 163.517 187.334 1 71.91 ? O2' UDP 601 A 1 
HETATM 12 C C3' UDP . . . D 4 162.535 164.701 186.558 1 66 ? C3' UDP 601 A 1 
HETATM 13 C C4' UDP . . . D 4 162.777 166.185 186.29 1 67.26 ? C4' UDP 601 A 1 
HETATM 14 O O4' UDP . . . D 4 161.6 166.873 186.771 1 64.96 ? O4' UDP 601 A 1 
HETATM 15 O O3' UDP . . . D 4 163.082 164.312 187.813 1 65.27 ? O3' UDP 601 A 1 
HETATM 16 C C5' UDP . . . D 4 163.022 166.55 184.847 1 62.52 ? C5' UDP 601 A 1 
HETATM 17 O O5' UDP . . . D 4 162.04 165.895 184.017 1 69.04 ? O5' UDP 601 A 1 
HETATM 18 P PA UDP . . . D 4 162.441 165.237 182.637 1 84.5 ? PA UDP 601 A 1 
HETATM 19 O O1A UDP . . . D 4 161.203 165.143 181.828 1 70.97 ? O1A UDP 601 A 1 
HETATM 20 O O2A UDP . . . D 4 163.23 163.948 182.851 1 69.53 ? O2A UDP 601 A 1 
HETATM 21 O O3A UDP . . . D 4 163.447 166.269 181.982 1 74.78 ? O3A UDP 601 A 1 
HETATM 22 P PB UDP . . . D 4 164.477 165.886 180.841 1 77.61 ? PB UDP 601 A 1 
HETATM 23 O O1B UDP . . . D 4 163.65 164.992 179.915 1 68.76 ? O1B UDP 601 A 1 
HETATM 24 O O2B UDP . . . D 4 165.516 165.044 181.583 1 67.58 ? O2B UDP 601 A 1 
HETATM 25 O O3B UDP . . . D 4 165.044 167.093 180.171 1 64.94 ? O3B UDP 601 A 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#