data_7Q13
#
_model_server_result.job_id            4kzn-uTvLrPYhQAk4QRHfQ 
_model_server_result.datetime_utc      '2025-04-15 07:00:11' 
_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          7q13 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":802}' 
#
_entry.id    7Q13 
#
_exptl.entry_id    7Q13 
_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    4 
_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            7Q13 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7Q13 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,I,J,K,L,M,N,O,P,Q,R,S,T 
_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 J N N 
? 4 M N N 
? 4 P N N 
? 4 S N N 
#
_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 409 n n 
N1 C6 UDP sing 410 n n 
N1 C1' UDP sing 411 n n 
C2 N3 UDP sing 412 n n 
C2 O2 UDP doub 413 n n 
N3 C4 UDP sing 414 n n 
N3 HN3 UDP sing 415 n n 
C4 C5 UDP sing 416 n n 
C4 O4 UDP doub 417 n n 
C5 C6 UDP doub 418 n n 
C5 H5 UDP sing 419 n n 
C6 H6 UDP sing 420 n n 
C1' C2' UDP sing 421 n n 
C1' O4' UDP sing 422 n n 
C1' H1' UDP sing 423 n n 
C2' O2' UDP sing 424 n n 
C2' C3' UDP sing 425 n n 
C2' H2' UDP sing 426 n n 
O2' HO2' UDP sing 427 n n 
C3' C4' UDP sing 428 n n 
C3' O3' UDP sing 429 n n 
C3' H3' UDP sing 430 n n 
C4' O4' UDP sing 431 n n 
C4' C5' UDP sing 432 n n 
C4' H4' UDP sing 433 n n 
O3' HO3' UDP sing 434 n n 
C5' O5' UDP sing 435 n n 
C5' "H5'1" UDP sing 436 n n 
C5' "H5'2" UDP sing 437 n n 
O5' PA UDP sing 438 n n 
PA O1A UDP doub 439 n n 
PA O2A UDP sing 440 n n 
PA O3A UDP sing 441 n n 
O2A HOA2 UDP sing 442 n n 
O3A PB UDP sing 443 n n 
PB O1B UDP doub 444 n n 
PB O2B UDP sing 445 n n 
PB O3B UDP sing 446 n n 
O2B HOB2 UDP sing 447 n n 
O3B HOB3 UDP sing 448 n n 
#
_atom_sites.entry_id                     7Q13 
_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
I 3 G6P A 1 801 701 G6P G6P . 
J 4 UDP A 1 802 702 UDP UDP . 
K 5 GLC A 1 803 703 GLC GLC . 
L 3 G6P B 1 801 701 G6P G6P . 
M 4 UDP B 1 802 702 UDP UDP . 
N 5 GLC B 1 803 703 GLC GLC . 
O 3 G6P C 1 801 701 G6P G6P . 
P 4 UDP C 1 802 702 UDP UDP . 
Q 5 GLC C 1 803 703 GLC GLC . 
R 3 G6P D 1 801 701 G6P G6P . 
S 4 UDP D 1 802 702 UDP UDP . 
T 5 GLC D 1 803 703 GLC GLC . 
#
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 . . . S 4 191.795 145.825 157.078 1 29.04 ? N1 UDP 802 D 1 
HETATM 2 C C2 UDP . . . S 4 190.556 146.459 156.873 1 29.04 ? C2 UDP 802 D 1 
HETATM 3 N N3 UDP . . . S 4 189.595 146.376 157.787 1 29.04 ? N3 UDP 802 D 1 
HETATM 4 C C4 UDP . . . S 4 189.8 145.695 158.913 1 29.04 ? C4 UDP 802 D 1 
HETATM 5 C C5 UDP . . . S 4 191.012 145.053 159.147 1 29.04 ? C5 UDP 802 D 1 
HETATM 6 C C6 UDP . . . S 4 192.018 145.135 158.199 1 29.04 ? C6 UDP 802 D 1 
HETATM 7 O O2 UDP . . . S 4 190.346 147.108 155.83 1 29.04 ? O2 UDP 802 D 1 
HETATM 8 O O4 UDP . . . S 4 188.878 145.64 159.75 1 29.04 ? O4 UDP 802 D 1 
HETATM 9 C C1' UDP . . . S 4 192.831 145.937 156.056 1 29.04 ? C1' UDP 802 D 1 
HETATM 10 C C2' UDP . . . S 4 193.792 147.054 156.417 1 29.04 ? C2' UDP 802 D 1 
HETATM 11 O O2' UDP . . . S 4 193.497 148.239 155.675 1 29.04 ? O2' UDP 802 D 1 
HETATM 12 C C3' UDP . . . S 4 195.166 146.541 156.054 1 29.04 ? C3' UDP 802 D 1 
HETATM 13 C C4' UDP . . . S 4 194.966 145.089 155.679 1 29.04 ? C4' UDP 802 D 1 
HETATM 14 O O4' UDP . . . S 4 193.614 144.747 155.987 1 29.04 ? O4' UDP 802 D 1 
HETATM 15 O O3' UDP . . . S 4 195.684 147.277 154.947 1 29.04 ? O3' UDP 802 D 1 
HETATM 16 C C5' UDP . . . S 4 195.914 144.203 156.454 1 29.04 ? C5' UDP 802 D 1 
HETATM 17 O O5' UDP . . . S 4 196.971 143.831 155.583 1 29.04 ? O5' UDP 802 D 1 
HETATM 18 P PA UDP . . . S 4 198.28 143.117 156.173 1 29.04 ? PA UDP 802 D 1 
HETATM 19 O O1A UDP . . . S 4 199.396 143.303 155.179 1 29.04 ? O1A UDP 802 D 1 
HETATM 20 O O2A UDP . . . S 4 198.47 143.624 157.583 1 29.04 ? O2A UDP 802 D 1 
HETATM 21 O O3A UDP . . . S 4 197.907 141.549 156.254 1 29.04 ? O3A UDP 802 D 1 
HETATM 22 P PB UDP . . . S 4 196.928 140.771 155.233 1 29.04 ? PB UDP 802 D 1 
HETATM 23 O O1B UDP . . . S 4 197.091 141.439 153.89 1 29.04 ? O1B UDP 802 D 1 
HETATM 24 O O2B UDP . . . S 4 195.561 140.921 155.851 1 29.04 ? O2B UDP 802 D 1 
HETATM 25 O O3B UDP . . . S 4 197.454 139.36 155.274 1 29.04 ? O3B UDP 802 D 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           358 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#