data_7FG9
#
_model_server_result.job_id            9OELL74CFaaA6vtW5UvgUg 
_model_server_result.datetime_utc      '2024-10-25 14:35:33' 
_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          7fg9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    7FG9 
#
_exptl.entry_id    7FG9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_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         120 
_cell.entry_id            7FG9 
_cell.length_a            177.643 
_cell.length_b            177.643 
_cell.length_c            57.034 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7FG9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 1 2 
#
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+1/2 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 28.517 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D 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 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     7FG9 
_atom_sites.fract_transf_matrix[1][1]    0.005629 
_atom_sites.fract_transf_matrix[1][2]    0.00325 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.0065 
_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]    0.017533 
_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
C 2 UDP A 1 401 401 UDP B4H . 
D 2 UDP B 1 401 401 UDP B4H . 
E 3 HOH A 1 501 55 HOH HOH . 
E 3 HOH A 2 502 13 HOH HOH . 
E 3 HOH A 3 503 64 HOH HOH . 
E 3 HOH A 4 504 37 HOH HOH . 
E 3 HOH A 5 505 52 HOH HOH . 
E 3 HOH A 6 506 58 HOH HOH . 
E 3 HOH A 7 507 6 HOH HOH . 
E 3 HOH A 8 508 61 HOH HOH . 
E 3 HOH A 9 509 23 HOH HOH . 
E 3 HOH A 10 510 59 HOH HOH . 
E 3 HOH A 11 511 14 HOH HOH . 
E 3 HOH A 12 512 67 HOH HOH . 
E 3 HOH A 13 513 42 HOH HOH . 
E 3 HOH A 14 514 39 HOH HOH . 
E 3 HOH A 15 515 57 HOH HOH . 
E 3 HOH A 16 516 24 HOH HOH . 
E 3 HOH A 17 517 9 HOH HOH . 
E 3 HOH A 18 518 53 HOH HOH . 
E 3 HOH A 19 519 29 HOH HOH . 
E 3 HOH A 20 520 66 HOH HOH . 
E 3 HOH A 21 521 35 HOH HOH . 
E 3 HOH A 22 522 34 HOH HOH . 
E 3 HOH A 23 523 2 HOH HOH . 
E 3 HOH A 24 524 49 HOH HOH . 
E 3 HOH A 25 525 60 HOH HOH . 
E 3 HOH A 26 526 40 HOH HOH . 
E 3 HOH A 27 527 48 HOH HOH . 
E 3 HOH A 28 528 36 HOH HOH . 
E 3 HOH A 29 529 32 HOH HOH . 
E 3 HOH A 30 530 41 HOH HOH . 
E 3 HOH A 31 531 21 HOH HOH . 
E 3 HOH A 32 532 15 HOH HOH . 
E 3 HOH A 33 533 46 HOH HOH . 
E 3 HOH A 34 534 50 HOH HOH . 
E 3 HOH A 35 535 43 HOH HOH . 
E 3 HOH A 36 536 16 HOH HOH . 
E 3 HOH A 37 537 38 HOH HOH . 
F 3 HOH B 1 501 7 HOH HOH . 
F 3 HOH B 2 502 18 HOH HOH . 
F 3 HOH B 3 503 45 HOH HOH . 
F 3 HOH B 4 504 22 HOH HOH . 
F 3 HOH B 5 505 5 HOH HOH . 
F 3 HOH B 6 506 27 HOH HOH . 
F 3 HOH B 7 507 62 HOH HOH . 
F 3 HOH B 8 508 56 HOH HOH . 
F 3 HOH B 9 509 12 HOH HOH . 
F 3 HOH B 10 510 54 HOH HOH . 
F 3 HOH B 11 511 30 HOH HOH . 
F 3 HOH B 12 512 26 HOH HOH . 
F 3 HOH B 13 513 19 HOH HOH . 
F 3 HOH B 14 514 8 HOH HOH . 
F 3 HOH B 15 515 20 HOH HOH . 
F 3 HOH B 16 516 17 HOH HOH . 
F 3 HOH B 17 517 11 HOH HOH . 
F 3 HOH B 18 518 25 HOH HOH . 
F 3 HOH B 19 519 28 HOH HOH . 
F 3 HOH B 20 520 47 HOH HOH . 
F 3 HOH B 21 521 63 HOH HOH . 
F 3 HOH B 22 522 10 HOH HOH . 
F 3 HOH B 23 523 65 HOH HOH . 
F 3 HOH B 24 524 44 HOH HOH . 
F 3 HOH B 25 525 68 HOH HOH . 
F 3 HOH B 26 526 51 HOH HOH . 
F 3 HOH B 27 527 31 HOH HOH . 
#
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 2 -56.922 54.66 -11.689 1 47.6 ? N1 UDP 401 B 1 
HETATM 2 C C2 UDP . . . D 2 -56.979 55.402 -12.848 1 51.2 ? C2 UDP 401 B 1 
HETATM 3 N N3 UDP . . . D 2 -58.075 55.812 -13.333 1 47.95 ? N3 UDP 401 B 1 
HETATM 4 C C4 UDP . . . D 2 -59.197 55.607 -12.874 1 48.22 ? C4 UDP 401 B 1 
HETATM 5 C C5 UDP . . . D 2 -59.425 54.911 -11.783 1 46.39 ? C5 UDP 401 B 1 
HETATM 6 C C6 UDP . . . D 2 -58.229 54.42 -11.152 1 42 ? C6 UDP 401 B 1 
HETATM 7 O O2 UDP . . . D 2 -55.938 55.671 -13.396 1 44.02 ? O2 UDP 401 B 1 
HETATM 8 O O4 UDP . . . D 2 -60.139 56.055 -13.451 1 47.47 ? O4 UDP 401 B 1 
HETATM 9 C C1' UDP . . . D 2 -55.716 54.212 -11.129 1 41.98 ? C1' UDP 401 B 1 
HETATM 10 C C2' UDP . . . D 2 -55.542 54.779 -9.774 1 43.27 ? C2' UDP 401 B 1 
HETATM 11 O O2' UDP . . . D 2 -54.951 56.103 -9.859 1 40.23 ? O2' UDP 401 B 1 
HETATM 12 C C3' UDP . . . D 2 -54.611 53.851 -9.172 1 46.85 ? C3' UDP 401 B 1 
HETATM 13 C C4' UDP . . . D 2 -55.026 52.502 -9.645 1 45.43 ? C4' UDP 401 B 1 
HETATM 14 O O4' UDP . . . D 2 -55.69 52.704 -10.987 1 47.61 ? O4' UDP 401 B 1 
HETATM 15 O O3' UDP . . . D 2 -53.304 54.161 -9.737 1 45.73 ? O3' UDP 401 B 1 
HETATM 16 C C5' UDP . . . D 2 -56.033 51.893 -8.749 1 40.51 ? C5' UDP 401 B 1 
HETATM 17 O O5' UDP . . . D 2 -55.376 51.094 -7.816 1 46.49 ? O5' UDP 401 B 1 
HETATM 18 P PA UDP . . . D 2 -55.778 51.147 -6.213 1 41.77 ? PA UDP 401 B 1 
HETATM 19 O O1A UDP . . . D 2 -56.181 52.49 -5.741 1 41.21 ? O1A UDP 401 B 1 
HETATM 20 O O2A UDP . . . D 2 -54.601 50.792 -5.433 1 39.94 ? O2A UDP 401 B 1 
HETATM 21 O O3A UDP . . . D 2 -56.997 50.123 -5.848 1 47.78 ? O3A UDP 401 B 1 
HETATM 22 P PB UDP . . . D 2 -57.388 48.769 -6.673 1 42.46 ? PB UDP 401 B 1 
HETATM 23 O O1B UDP . . . D 2 -58.286 49.075 -7.801 1 40.56 ? O1B UDP 401 B 1 
HETATM 24 O O2B UDP . . . D 2 -58.083 47.779 -5.547 1 46.74 ? O2B UDP 401 B 1 
HETATM 25 O O3B UDP . . . D 2 -56.21 48.166 -7.327 1 48.6 ? O3B UDP 401 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          16 
_model_server_stats.element_count           25 
#