data_7FGA
#
_model_server_result.job_id            b9dsXf4IyIoa--VjlADAow 
_model_server_result.datetime_utc      '2024-10-25 12:17:59' 
_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          7fga 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":401}' 
#
_entry.id    7FGA 
#
_exptl.entry_id    7FGA 
_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    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         120 
_cell.entry_id            7FGA 
_cell.length_a            157.712 
_cell.length_b            157.712 
_cell.length_c            187.803 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7FGA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I 1 1 
B,F,J 1 2 
C,G,K 2 1 
D,H,L 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' 5_555 y,-x+y,z+1/6 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 31.3005 
3 'crystal symmetry operation' 6_444 x-y-1,x-1,z-1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 -78.856 -136.582598 -31.3005 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   GLC 
_pdbx_entity_branch_link.comp_id_2                   Z9N 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O1 
_pdbx_entity_branch_link.leaving_atom_id_2           HO1 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 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
2 n E Z9N 1 E 1 Z9N A 402 LIG 
2 n E GLC 2 E 2 GLC A 402 LIG 
2 n F Z9N 1 F 1 Z9N B 501 LIG 
2 n F GLC 2 F 2 GLC B 501 LIG 
2 n G Z9N 1 G 1 Z9N C 402 LIG 
2 n G GLC 2 G 2 GLC C 402 LIG 
2 n H Z9N 1 H 1 Z9N D 501 LIG 
2 n H GLC 2 H 2 GLC D 501 LIG 
#
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
covale ? covale1 E O2 Z9N . E Z9N 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? 
covale ? covale2 F O2 Z9N . F Z9N 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? 
covale ? covale3 G O2 Z9N . G Z9N 1 1_555 G C1 GLC . G GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? 
covale ? covale4 H O2 Z9N . H Z9N 1 1_555 H C1 GLC . H GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? 
#
_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 380 n n 
N1 C6 UDP sing 381 n n 
N1 C1' UDP sing 382 n n 
C2 N3 UDP sing 383 n n 
C2 O2 UDP doub 384 n n 
N3 C4 UDP sing 385 n n 
N3 HN3 UDP sing 386 n n 
C4 C5 UDP sing 387 n n 
C4 O4 UDP doub 388 n n 
C5 C6 UDP doub 389 n n 
C5 H5 UDP sing 390 n n 
C6 H6 UDP sing 391 n n 
C1' C2' UDP sing 392 n n 
C1' O4' UDP sing 393 n n 
C1' H1' UDP sing 394 n n 
C2' O2' UDP sing 395 n n 
C2' C3' UDP sing 396 n n 
C2' H2' UDP sing 397 n n 
O2' HO2' UDP sing 398 n n 
C3' C4' UDP sing 399 n n 
C3' O3' UDP sing 400 n n 
C3' H3' UDP sing 401 n n 
C4' O4' UDP sing 402 n n 
C4' C5' UDP sing 403 n n 
C4' H4' UDP sing 404 n n 
O3' HO3' UDP sing 405 n n 
C5' O5' UDP sing 406 n n 
C5' "H5'1" UDP sing 407 n n 
C5' "H5'2" UDP sing 408 n n 
O5' PA UDP sing 409 n n 
PA O1A UDP doub 410 n n 
PA O2A UDP sing 411 n n 
PA O3A UDP sing 412 n n 
O2A HOA2 UDP sing 413 n n 
O3A PB UDP sing 414 n n 
PB O1B UDP doub 415 n n 
PB O2B UDP sing 416 n n 
PB O3B UDP sing 417 n n 
O2B HOB2 UDP sing 418 n n 
O3B HOB3 UDP sing 419 n n 
#
_atom_sites.entry_id                     7FGA 
_atom_sites.fract_transf_matrix[1][1]    0.006341 
_atom_sites.fract_transf_matrix[1][2]    0.003661 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007322 
_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]    0.005325 
_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 UDP A 1 401 401 UDP B4H . 
J 3 UDP B 1 401 401 UDP B4H . 
K 3 UDP C 1 401 401 UDP B4H . 
L 3 UDP D 1 401 401 UDP B4H . 
#
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 . . . L 3 78.315 -57.646 -20.54 1 52.41 ? N1 UDP 401 D 1 
HETATM 2 C C2 UDP . . . L 3 77.522 -56.874 -19.736 1 58.97 ? C2 UDP 401 D 1 
HETATM 3 N N3 UDP . . . L 3 77.814 -55.704 -19.395 1 61.3 ? N3 UDP 401 D 1 
HETATM 4 C C4 UDP . . . L 3 78.823 -55.091 -19.714 1 60.7 ? C4 UDP 401 D 1 
HETATM 5 C C5 UDP . . . L 3 79.767 -55.577 -20.48 1 56.81 ? C5 UDP 401 D 1 
HETATM 6 C C6 UDP . . . L 3 79.498 -56.927 -20.915 1 56.26 ? C6 UDP 401 D 1 
HETATM 7 O O2 UDP . . . L 3 76.503 -57.333 -19.342 1 60.95 ? O2 UDP 401 D 1 
HETATM 8 O O4 UDP . . . L 3 78.95 -53.988 -19.306 1 66.31 ? O4 UDP 401 D 1 
HETATM 9 C C1' UDP . . . L 3 78.01 -58.965 -20.937 1 52.45 ? C1' UDP 401 D 1 
HETATM 10 C C2' UDP . . . L 3 77.262 -58.966 -22.216 1 56.81 ? C2' UDP 401 D 1 
HETATM 11 O O2' UDP . . . L 3 75.829 -59.042 -21.955 1 62.03 ? O2' UDP 401 D 1 
HETATM 12 C C3' UDP . . . L 3 77.688 -60.139 -22.954 1 57.31 ? C3' UDP 401 D 1 
HETATM 13 C C4' UDP . . . L 3 78.956 -60.619 -22.355 1 55.95 ? C4' UDP 401 D 1 
HETATM 14 O O4' UDP . . . L 3 79.278 -59.758 -21.157 1 55.43 ? O4' UDP 401 D 1 
HETATM 15 O O3' UDP . . . L 3 76.674 -61.185 -22.854 1 58.51 ? O3' UDP 401 D 1 
HETATM 16 C C5' UDP . . . L 3 80.041 -60.51 -23.357 1 60.02 ? C5' UDP 401 D 1 
HETATM 17 O O5' UDP . . . L 3 79.489 -60.615 -24.639 1 63.51 ? O5' UDP 401 D 1 
HETATM 18 P PA UDP . . . L 3 80.473 -61.087 -25.871 1 73.37 ? PA UDP 401 D 1 
HETATM 19 O O1A UDP . . . L 3 79.964 -60.627 -27.16 1 72.64 ? O1A UDP 401 D 1 
HETATM 20 O O2A UDP . . . L 3 80.451 -62.536 -26.051 1 67.39 ? O2A UDP 401 D 1 
HETATM 21 O O3A UDP . . . L 3 81.995 -60.521 -25.591 1 68.11 ? O3A UDP 401 D 1 
HETATM 22 P PB UDP . . . L 3 83.244 -61.472 -25.089 1 66.53 ? PB UDP 401 D 1 
HETATM 23 O O1B UDP . . . L 3 84.297 -61.747 -26.327 1 49.23 ? O1B UDP 401 D 1 
HETATM 24 O O2B UDP . . . L 3 83.919 -60.86 -23.947 1 67.97 ? O2B UDP 401 D 1 
HETATM 25 O O3B UDP . . . L 3 82.773 -62.723 -24.501 1 55.19 ? O3B UDP 401 D 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#