data_7SP7
#
_model_server_result.job_id            2rrbqmWYQ6lpbbuwDe_xuw 
_model_server_result.datetime_utc      '2024-10-15 11:27:59' 
_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          7sp7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":603}' 
#
_entry.id    7SP7 
#
_exptl.entry_id    7SP7 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          6 
_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            7SP7 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7SP7 
_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_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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    ? 
_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                      6 
_struct_asym.id                             F 
_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 22 B CYS 22 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 C SG CYS 22 C CYS 22 1_555 C SG CYS 96 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 F O2A UDP . A UDP 603 1_555 H MN MN . A MN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? 
#
_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     ? 
#
_atom_sites.entry_id                     7SP7 
_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 3PE A 1 601 605 3PE 3PE . 
E 5 Y01 A 1 602 606 Y01 CHO . 
F 6 UDP A 1 603 607 UDP UDP . 
G 7 MN A 1 604 1 MN MN . 
H 7 MN A 1 605 2 MN MN . 
#
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 . . . F 6 122.811 146.752 157.429 1 82.58 ? N1 UDP 603 A 1 
HETATM 2 C C2 UDP . . . F 6 122.245 147.508 158.573 1 82.58 ? C2 UDP 603 A 1 
HETATM 3 N N3 UDP . . . F 6 120.96 148.297 158.405 1 82.58 ? N3 UDP 603 A 1 
HETATM 4 C C4 UDP . . . F 6 120.292 148.317 157.15 1 82.58 ? C4 UDP 603 A 1 
HETATM 5 C C5 UDP . . . F 6 120.863 147.552 155.987 1 82.58 ? C5 UDP 603 A 1 
HETATM 6 C C6 UDP . . . F 6 122.143 146.767 156.159 1 82.58 ? C6 UDP 603 A 1 
HETATM 7 O O2 UDP . . . F 6 122.78 147.495 159.587 1 82.58 ? O2 UDP 603 A 1 
HETATM 8 O O4 UDP . . . F 6 119.295 148.93 157.021 1 82.58 ? O4 UDP 603 A 1 
HETATM 9 C C1' UDP . . . F 6 124.029 146.006 157.593 1 82.58 ? C1' UDP 603 A 1 
HETATM 10 C C2' UDP . . . F 6 123.731 144.427 157.53 1 82.58 ? C2' UDP 603 A 1 
HETATM 11 O O2' UDP . . . F 6 123.306 143.94 158.85 1 82.58 ? O2' UDP 603 A 1 
HETATM 12 C C3' UDP . . . F 6 124.854 143.866 157.194 1 82.58 ? C3' UDP 603 A 1 
HETATM 13 C C4' UDP . . . F 6 125.67 144.962 156.454 1 82.58 ? C4' UDP 603 A 1 
HETATM 14 O O4' UDP . . . F 6 124.858 146.245 156.603 1 82.58 ? O4' UDP 603 A 1 
HETATM 15 O O3' UDP . . . F 6 125.571 143.431 158.389 1 82.58 ? O3' UDP 603 A 1 
HETATM 16 C C5' UDP . . . F 6 125.832 144.628 155.107 1 82.58 ? C5' UDP 603 A 1 
HETATM 17 O O5' UDP . . . F 6 124.667 144.841 154.444 1 82.58 ? O5' UDP 603 A 1 
HETATM 18 P PA UDP . . . F 6 124.314 143.916 153.139 1 82.58 ? PA UDP 603 A 1 
HETATM 19 O O1A UDP . . . F 6 122.797 143.898 152.928 1 82.58 ? O1A UDP 603 A 1 
HETATM 20 O O2A UDP . . . F 6 124.79 142.529 153.37 1 82.58 ? O2A UDP 603 A 1 
HETATM 21 O O3A UDP . . . F 6 125.078 144.567 151.732 1 82.58 ? O3A UDP 603 A 1 
HETATM 22 P PB UDP . . . F 6 126.681 144.986 151.642 1 82.58 ? PB UDP 603 A 1 
HETATM 23 O O1B UDP . . . F 6 127.109 145.02 150.2 1 82.58 ? O1B UDP 603 A 1 
HETATM 24 O O2B UDP . . . F 6 127.505 143.979 152.379 1 82.58 ? O2B UDP 603 A 1 
HETATM 25 O O3B UDP . . . F 6 126.878 146.351 152.259 1 82.58 ? O3B UDP 603 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#