data_3E25
#
_model_server_result.job_id            hzjk0d3exg-PlC8lcdqtvw 
_model_server_result.datetime_utc      '2025-06-24 04:33:33' 
_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          3e25 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":339}' 
#
_entry.id    3E25 
#
_exptl.entry_id    3E25 
_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    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            3E25 
_cell.length_a            100.309 
_cell.length_b            100.309 
_cell.length_c            127.035 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3E25 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41' 
#
_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 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 6_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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
metalc ? metalc1 A OD2 ASP 136 A ASP 136 1_555 B MG MG . A MG 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc2 B MG MG . A MG 338 1_555 C O1A UDP . A UDP 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
metalc ? metalc3 B MG MG . A MG 338 1_555 C O1B UDP . A UDP 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
#
_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 375 n n 
N1 C6 UDP sing 376 n n 
N1 C1' UDP sing 377 n n 
C2 N3 UDP sing 378 n n 
C2 O2 UDP doub 379 n n 
N3 C4 UDP sing 380 n n 
N3 HN3 UDP sing 381 n n 
C4 C5 UDP sing 382 n n 
C4 O4 UDP doub 383 n n 
C5 C6 UDP doub 384 n n 
C5 H5 UDP sing 385 n n 
C6 H6 UDP sing 386 n n 
C1' C2' UDP sing 387 n n 
C1' O4' UDP sing 388 n n 
C1' H1' UDP sing 389 n n 
C2' O2' UDP sing 390 n n 
C2' C3' UDP sing 391 n n 
C2' H2' UDP sing 392 n n 
O2' HO2' UDP sing 393 n n 
C3' C4' UDP sing 394 n n 
C3' O3' UDP sing 395 n n 
C3' H3' UDP sing 396 n n 
C4' O4' UDP sing 397 n n 
C4' C5' UDP sing 398 n n 
C4' H4' UDP sing 399 n n 
O3' HO3' UDP sing 400 n n 
C5' O5' UDP sing 401 n n 
C5' "H5'1" UDP sing 402 n n 
C5' "H5'2" UDP sing 403 n n 
O5' PA UDP sing 404 n n 
PA O1A UDP doub 405 n n 
PA O2A UDP sing 406 n n 
PA O3A UDP sing 407 n n 
O2A HOA2 UDP sing 408 n n 
O3A PB UDP sing 409 n n 
PB O1B UDP doub 410 n n 
PB O2B UDP sing 411 n n 
PB O3B UDP sing 412 n n 
O2B HOB2 UDP sing 413 n n 
O3B HOB3 UDP sing 414 n n 
#
_atom_sites.entry_id                     3E25 
_atom_sites.fract_transf_matrix[1][1]    0.009969 
_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]    0.009969 
_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]    0.007872 
_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
B 2 MG A 1 338 1 MG MG . 
C 3 UDP A 1 339 1 UDP UDP . 
D 4 3PG A 1 340 1 3PG MP3 . 
E 5 HOH A 1 341 1 HOH HOH . 
E 5 HOH A 2 342 2 HOH HOH . 
E 5 HOH A 3 343 3 HOH HOH . 
E 5 HOH A 4 344 4 HOH HOH . 
E 5 HOH A 5 345 5 HOH HOH . 
E 5 HOH A 6 346 6 HOH HOH . 
E 5 HOH A 7 347 7 HOH HOH . 
E 5 HOH A 8 348 8 HOH HOH . 
E 5 HOH A 9 349 9 HOH HOH . 
E 5 HOH A 10 350 10 HOH HOH . 
E 5 HOH A 11 351 11 HOH HOH . 
E 5 HOH A 12 352 12 HOH HOH . 
E 5 HOH A 13 353 13 HOH HOH . 
E 5 HOH A 14 354 14 HOH HOH . 
E 5 HOH A 15 355 15 HOH HOH . 
E 5 HOH A 16 356 16 HOH HOH . 
E 5 HOH A 17 357 17 HOH HOH . 
E 5 HOH A 18 358 18 HOH HOH . 
E 5 HOH A 19 359 19 HOH HOH . 
E 5 HOH A 20 360 20 HOH HOH . 
E 5 HOH A 21 361 21 HOH HOH . 
E 5 HOH A 22 362 22 HOH HOH . 
E 5 HOH A 23 363 23 HOH HOH . 
E 5 HOH A 24 364 24 HOH HOH . 
E 5 HOH A 25 365 25 HOH HOH . 
E 5 HOH A 26 366 26 HOH HOH . 
E 5 HOH A 27 367 27 HOH HOH . 
E 5 HOH A 28 368 28 HOH HOH . 
E 5 HOH A 29 369 29 HOH HOH . 
E 5 HOH A 30 370 30 HOH HOH . 
E 5 HOH A 31 371 31 HOH HOH . 
E 5 HOH A 32 372 32 HOH HOH . 
E 5 HOH A 33 373 33 HOH HOH . 
E 5 HOH A 34 374 34 HOH HOH . 
E 5 HOH A 35 375 35 HOH HOH . 
E 5 HOH A 36 376 36 HOH HOH . 
E 5 HOH A 37 377 37 HOH HOH . 
E 5 HOH A 38 378 38 HOH HOH . 
E 5 HOH A 39 379 39 HOH HOH . 
E 5 HOH A 40 380 40 HOH HOH . 
E 5 HOH A 41 381 41 HOH HOH . 
E 5 HOH A 42 382 42 HOH HOH . 
E 5 HOH A 43 383 43 HOH HOH . 
E 5 HOH A 44 384 44 HOH HOH . 
E 5 HOH A 45 385 46 HOH HOH . 
E 5 HOH A 46 386 47 HOH HOH . 
E 5 HOH A 47 387 48 HOH HOH . 
E 5 HOH A 48 388 49 HOH HOH . 
E 5 HOH A 49 389 50 HOH HOH . 
E 5 HOH A 50 390 51 HOH HOH . 
E 5 HOH A 51 391 52 HOH HOH . 
E 5 HOH A 52 392 53 HOH HOH . 
E 5 HOH A 53 393 55 HOH HOH . 
E 5 HOH A 54 394 56 HOH HOH . 
E 5 HOH A 55 395 57 HOH HOH . 
E 5 HOH A 56 396 58 HOH HOH . 
E 5 HOH A 57 397 59 HOH HOH . 
E 5 HOH A 58 398 60 HOH HOH . 
E 5 HOH A 59 399 61 HOH HOH . 
E 5 HOH A 60 400 63 HOH HOH . 
E 5 HOH A 61 401 64 HOH HOH . 
E 5 HOH A 62 402 65 HOH HOH . 
E 5 HOH A 63 403 67 HOH HOH . 
E 5 HOH A 64 404 68 HOH HOH . 
E 5 HOH A 65 405 69 HOH HOH . 
E 5 HOH A 66 406 70 HOH HOH . 
E 5 HOH A 67 407 71 HOH HOH . 
E 5 HOH A 68 408 72 HOH HOH . 
E 5 HOH A 69 409 73 HOH HOH . 
E 5 HOH A 70 410 74 HOH HOH . 
E 5 HOH A 71 411 75 HOH HOH . 
E 5 HOH A 72 412 76 HOH HOH . 
E 5 HOH A 73 413 77 HOH HOH . 
E 5 HOH A 74 414 78 HOH HOH . 
E 5 HOH A 75 415 79 HOH HOH . 
E 5 HOH A 76 416 80 HOH HOH . 
E 5 HOH A 77 417 82 HOH HOH . 
E 5 HOH A 78 418 83 HOH HOH . 
E 5 HOH A 79 419 84 HOH HOH . 
E 5 HOH A 80 420 85 HOH HOH . 
E 5 HOH A 81 421 86 HOH HOH . 
E 5 HOH A 82 422 87 HOH HOH . 
E 5 HOH A 83 423 88 HOH HOH . 
E 5 HOH A 84 424 89 HOH HOH . 
E 5 HOH A 85 425 90 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 . . . C 3 15.466 -13.537 4.966 0.66 35.14 ? N1 UDP 339 A 1 
HETATM 2 C C2 UDP . . . C 3 14.013 -13.594 5.086 0.66 37.42 ? C2 UDP 339 A 1 
HETATM 3 N N3 UDP . . . C 3 13.426 -14.6 5.784 0.66 36.22 ? N3 UDP 339 A 1 
HETATM 4 C C4 UDP . . . C 3 14.202 -15.561 6.377 0.66 32.09 ? C4 UDP 339 A 1 
HETATM 5 C C5 UDP . . . C 3 15.589 -15.509 6.279 0.66 31.93 ? C5 UDP 339 A 1 
HETATM 6 C C6 UDP . . . C 3 16.205 -14.476 5.556 0.66 33.3 ? C6 UDP 339 A 1 
HETATM 7 O O2 UDP . . . C 3 13.157 -12.643 4.513 0.66 41.43 ? O2 UDP 339 A 1 
HETATM 8 O O4 UDP . . . C 3 13.591 -16.626 7.035 0.66 31.55 ? O4 UDP 339 A 1 
HETATM 9 C C1' UDP . . . C 3 16.182 -12.523 4.185 0.66 35.34 ? C1' UDP 339 A 1 
HETATM 10 C C2' UDP . . . C 3 15.696 -12.368 2.793 0.66 37.89 ? C2' UDP 339 A 1 
HETATM 11 O O2' UDP . . . C 3 15.904 -13.392 1.845 0.66 40.18 ? O2' UDP 339 A 1 
HETATM 12 C C3' UDP . . . C 3 16.174 -10.959 2.488 0.66 37.7 ? C3' UDP 339 A 1 
HETATM 13 C C4' UDP . . . C 3 15.91 -10.219 3.85 0.66 42.49 ? C4' UDP 339 A 1 
HETATM 14 O O4' UDP . . . C 3 16.222 -11.279 4.815 0.66 39.38 ? O4' UDP 339 A 1 
HETATM 15 O O3' UDP . . . C 3 17.414 -10.751 1.9 0.66 33.37 ? O3' UDP 339 A 1 
HETATM 16 C C5' UDP . . . C 3 14.58 -9.477 3.985 0.66 44.09 ? C5' UDP 339 A 1 
HETATM 17 O O5' UDP . . . C 3 13.516 -10.148 3.385 0.66 45.36 ? O5' UDP 339 A 1 
HETATM 18 P PA UDP . . . C 3 12.388 -9.267 2.592 0.66 57.47 ? PA UDP 339 A 1 
HETATM 19 O O1A UDP . . . C 3 13.06 -8.624 1.222 0.66 58.95 ? O1A UDP 339 A 1 
HETATM 20 O O2A UDP . . . C 3 11.285 -10.168 2.255 0.66 56.4 ? O2A UDP 339 A 1 
HETATM 21 O O3A UDP . . . C 3 11.914 -8.025 3.574 0.66 54.26 ? O3A UDP 339 A 1 
HETATM 22 P PB UDP . . . C 3 11.091 -6.729 2.936 0.66 67.42 ? PB UDP 339 A 1 
HETATM 23 O O1B UDP . . . C 3 12.171 -5.608 2.36 0.66 61.25 ? O1B UDP 339 A 1 
HETATM 24 O O2B UDP . . . C 3 10.21 -7.199 1.866 0.66 58.91 ? O2B UDP 339 A 1 
HETATM 25 O O3B UDP . . . C 3 10.194 -5.983 4.108 0.66 62.72 ? O3B UDP 339 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           449 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           25 
#