data_7UQX
#
_model_server_result.job_id            fDnlylvyOOYkM0DbnlLFPg 
_model_server_result.datetime_utc      '2024-11-21 23:19:04' 
_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          7uqx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":801}' 
#
_entry.id    7UQX 
#
_exptl.entry_id    7UQX 
_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    2 
_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            7UQX 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7UQX 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 F N N 
#
_pdbx_entity_branch.entity_id    3 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
3 n C NAG 1 C 1 NAG B 801 NAG 
3 n C NAG 2 C 2 NAG B 802 NAG 
3 n C BMA 3 C 3 BMA B 803 BMA 
#
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 A SG CYS 72 A CYS 98 1_555 A SG CYS 77 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 83 A CYS 109 1_555 A SG CYS 126 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 272 A CYS 298 1_555 A SG CYS 286 A CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 A SG CYS 308 A CYS 334 1_555 A SG CYS 329 A CYS 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 626 A CYS 652 1_555 A SG CYS 678 A CYS 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf6 B SG CYS 41 B CYS 85 1_555 B SG CYS 46 B CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf7 B SG CYS 52 B CYS 96 1_555 B SG CYS 107 B CYS 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf8 B SG CYS 274 B CYS 318 1_555 B SG CYS 295 B CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf9 B SG CYS 582 B CYS 626 1_555 B SG CYS 632 B CYS 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
covale ? covale1 A ND2 ASN 304 A ASN 330 1_555 E C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale2 B ND2 ASN 593 B ASN 637 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
metalc ? metalc1 F O1A UDP . B UDP 801 1_555 G MN MN . B MN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? 
metalc ? metalc2 F O2B UDP . B UDP 801 1_555 G MN MN . B MN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? 
#
_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 410 n n 
N1 C6 UDP sing 411 n n 
N1 C1' UDP sing 412 n n 
C2 N3 UDP sing 413 n n 
C2 O2 UDP doub 414 n n 
N3 C4 UDP sing 415 n n 
N3 HN3 UDP sing 416 n n 
C4 C5 UDP sing 417 n n 
C4 O4 UDP doub 418 n n 
C5 C6 UDP doub 419 n n 
C5 H5 UDP sing 420 n n 
C6 H6 UDP sing 421 n n 
C1' C2' UDP sing 422 n n 
C1' O4' UDP sing 423 n n 
C1' H1' UDP sing 424 n n 
C2' O2' UDP sing 425 n n 
C2' C3' UDP sing 426 n n 
C2' H2' UDP sing 427 n n 
O2' HO2' UDP sing 428 n n 
C3' C4' UDP sing 429 n n 
C3' O3' UDP sing 430 n n 
C3' H3' UDP sing 431 n n 
C4' O4' UDP sing 432 n n 
C4' C5' UDP sing 433 n n 
C4' H4' UDP sing 434 n n 
O3' HO3' UDP sing 435 n n 
C5' O5' UDP sing 436 n n 
C5' "H5'1" UDP sing 437 n n 
C5' "H5'2" UDP sing 438 n n 
O5' PA UDP sing 439 n n 
PA O1A UDP doub 440 n n 
PA O2A UDP sing 441 n n 
PA O3A UDP sing 442 n n 
O2A HOA2 UDP sing 443 n n 
O3A PB UDP sing 444 n n 
PB O1B UDP doub 445 n n 
PB O2B UDP sing 446 n n 
PB O3B UDP sing 447 n n 
O2B HOB2 UDP sing 448 n n 
O3B HOB3 UDP sing 449 n n 
#
_atom_sites.entry_id                     7UQX 
_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 1 801 801 UDP UDP . 
E 5 NAG A 1 802 901 NAG NAG . 
F 4 UDP B 1 801 804 UDP UDP . 
G 6 MN B 1 802 805 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 . . . D 4 131.655 122.001 105.027 1 92.17 ? N1 UDP 801 A 1 
HETATM 2 C C2 UDP . . . D 4 131.481 122.472 103.739 1 92.17 ? C2 UDP 801 A 1 
HETATM 3 N N3 UDP . . . D 4 132.45 122.089 102.845 1 92.17 ? N3 UDP 801 A 1 
HETATM 4 C C4 UDP . . . D 4 133.552 121.298 103.106 1 92.17 ? C4 UDP 801 A 1 
HETATM 5 C C5 UDP . . . D 4 133.661 120.85 104.461 1 92.17 ? C5 UDP 801 A 1 
HETATM 6 C C6 UDP . . . D 4 132.728 121.208 105.361 1 92.17 ? C6 UDP 801 A 1 
HETATM 7 O O2 UDP . . . D 4 130.538 123.179 103.412 1 92.17 ? O2 UDP 801 A 1 
HETATM 8 O O4 UDP . . . D 4 134.348 121.034 102.192 1 92.17 ? O4 UDP 801 A 1 
HETATM 9 C C1' UDP . . . D 4 130.649 122.376 106.032 1 92.17 ? C1' UDP 801 A 1 
HETATM 10 C C2' UDP . . . D 4 129.355 121.57 105.927 1 92.17 ? C2' UDP 801 A 1 
HETATM 11 O O2' UDP . . . D 4 128.436 122.214 105.052 1 92.17 ? O2' UDP 801 A 1 
HETATM 12 C C3' UDP . . . D 4 128.874 121.588 107.377 1 92.17 ? C3' UDP 801 A 1 
HETATM 13 C C4' UDP . . . D 4 130.183 121.497 108.158 1 92.17 ? C4' UDP 801 A 1 
HETATM 14 O O4' UDP . . . D 4 131.184 122.116 107.317 1 92.17 ? O4' UDP 801 A 1 
HETATM 15 O O3' UDP . . . D 4 128.175 122.787 107.691 1 92.17 ? O3' UDP 801 A 1 
HETATM 16 C C5' UDP . . . D 4 130.621 120.1 108.519 1 92.17 ? C5' UDP 801 A 1 
HETATM 17 O O5' UDP . . . D 4 132.063 120.04 108.503 1 92.17 ? O5' UDP 801 A 1 
HETATM 18 P PA UDP . . . D 4 132.913 120.39 109.789 1 92.17 ? PA UDP 801 A 1 
HETATM 19 O O1A UDP . . . D 4 133.068 121.864 109.817 1 92.17 ? O1A UDP 801 A 1 
HETATM 20 O O2A UDP . . . D 4 134.19 119.556 109.847 1 92.17 ? O2A UDP 801 A 1 
HETATM 21 O O3A UDP . . . D 4 132.014 119.911 111.004 1 92.17 ? O3A UDP 801 A 1 
HETATM 22 P PB UDP . . . D 4 132.524 119.864 112.503 1 92.17 ? PB UDP 801 A 1 
HETATM 23 O O1B UDP . . . D 4 133.535 121.009 112.56 1 92.17 ? O1B UDP 801 A 1 
HETATM 24 O O2B UDP . . . D 4 133.257 118.523 112.578 1 92.17 ? O2B UDP 801 A 1 
HETATM 25 O O3B UDP . . . D 4 131.404 119.994 113.481 1 92.17 ? O3B UDP 801 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           327 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           25 
#