data_7ZIB
#
_model_server_result.job_id            TQv89fBEtpZEtQO4Is0oDg 
_model_server_result.datetime_utc      '2024-11-22 21:35:31' 
_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          7zib 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    7ZIB 
#
_exptl.entry_id    7ZIB 
_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    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            7ZIB 
_cell.length_a            68.506 
_cell.length_b            68.506 
_cell.length_c            120.334 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7ZIB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        91 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 2 2' 
#
_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' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 O LYS 62 A LYS 42 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc2 A O SER 65 A SER 45 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc3 A O TRP 68 A TRP 48 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc4 D NA NA . A NA 303 1_555 E O HOH . A HOH 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
#
_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 440 n n 
N1 C6 UDP sing 441 n n 
N1 C1' UDP sing 442 n n 
C2 N3 UDP sing 443 n n 
C2 O2 UDP doub 444 n n 
N3 C4 UDP sing 445 n n 
N3 HN3 UDP sing 446 n n 
C4 C5 UDP sing 447 n n 
C4 O4 UDP doub 448 n n 
C5 C6 UDP doub 449 n n 
C5 H5 UDP sing 450 n n 
C6 H6 UDP sing 451 n n 
C1' C2' UDP sing 452 n n 
C1' O4' UDP sing 453 n n 
C1' H1' UDP sing 454 n n 
C2' O2' UDP sing 455 n n 
C2' C3' UDP sing 456 n n 
C2' H2' UDP sing 457 n n 
O2' HO2' UDP sing 458 n n 
C3' C4' UDP sing 459 n n 
C3' O3' UDP sing 460 n n 
C3' H3' UDP sing 461 n n 
C4' O4' UDP sing 462 n n 
C4' C5' UDP sing 463 n n 
C4' H4' UDP sing 464 n n 
O3' HO3' UDP sing 465 n n 
C5' O5' UDP sing 466 n n 
C5' "H5'1" UDP sing 467 n n 
C5' "H5'2" UDP sing 468 n n 
O5' PA UDP sing 469 n n 
PA O1A UDP doub 470 n n 
PA O2A UDP sing 471 n n 
PA O3A UDP sing 472 n n 
O2A HOA2 UDP sing 473 n n 
O3A PB UDP sing 474 n n 
PB O1B UDP doub 475 n n 
PB O2B UDP sing 476 n n 
PB O3B UDP sing 477 n n 
O2B HOB2 UDP sing 478 n n 
O3B HOB3 UDP sing 479 n n 
#
_atom_sites.entry_id                     7ZIB 
_atom_sites.fract_transf_matrix[1][1]    0.014597 
_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]    0.014597 
_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]    0.00831 
_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 UDP A 1 301 301 UDP UDP . 
C 3 J7I A 1 302 302 J7I LIG . 
D 4 NA A 1 303 1 NA NA . 
E 5 HOH A 1 401 52 HOH HOH . 
E 5 HOH A 2 402 40 HOH HOH . 
E 5 HOH A 3 403 22 HOH HOH . 
E 5 HOH A 4 404 49 HOH HOH . 
E 5 HOH A 5 405 24 HOH HOH . 
E 5 HOH A 6 406 58 HOH HOH . 
E 5 HOH A 7 407 20 HOH HOH . 
E 5 HOH A 8 408 23 HOH HOH . 
E 5 HOH A 9 409 30 HOH HOH . 
E 5 HOH A 10 410 50 HOH HOH . 
E 5 HOH A 11 411 48 HOH HOH . 
E 5 HOH A 12 412 65 HOH HOH . 
E 5 HOH A 13 413 39 HOH HOH . 
E 5 HOH A 14 414 57 HOH HOH . 
E 5 HOH A 15 415 64 HOH HOH . 
E 5 HOH A 16 416 42 HOH HOH . 
E 5 HOH A 17 417 25 HOH HOH . 
E 5 HOH A 18 418 33 HOH HOH . 
E 5 HOH A 19 419 37 HOH HOH . 
E 5 HOH A 20 420 1 HOH HOH . 
E 5 HOH A 21 421 3 HOH HOH . 
E 5 HOH A 22 422 36 HOH HOH . 
E 5 HOH A 23 423 27 HOH HOH . 
E 5 HOH A 24 424 10 HOH HOH . 
E 5 HOH A 25 425 46 HOH HOH . 
E 5 HOH A 26 426 41 HOH HOH . 
E 5 HOH A 27 427 11 HOH HOH . 
E 5 HOH A 28 428 5 HOH HOH . 
E 5 HOH A 29 429 26 HOH HOH . 
E 5 HOH A 30 430 4 HOH HOH . 
E 5 HOH A 31 431 62 HOH HOH . 
E 5 HOH A 32 432 9 HOH HOH . 
E 5 HOH A 33 433 8 HOH HOH . 
E 5 HOH A 34 434 13 HOH HOH . 
E 5 HOH A 35 435 6 HOH HOH . 
E 5 HOH A 36 436 63 HOH HOH . 
E 5 HOH A 37 437 34 HOH HOH . 
E 5 HOH A 38 438 15 HOH HOH . 
E 5 HOH A 39 439 28 HOH HOH . 
E 5 HOH A 40 440 44 HOH HOH . 
E 5 HOH A 41 441 51 HOH HOH . 
E 5 HOH A 42 442 55 HOH HOH . 
E 5 HOH A 43 443 19 HOH HOH . 
E 5 HOH A 44 444 68 HOH HOH . 
E 5 HOH A 45 445 70 HOH HOH . 
E 5 HOH A 46 446 47 HOH HOH . 
E 5 HOH A 47 447 16 HOH HOH . 
E 5 HOH A 48 448 59 HOH HOH . 
E 5 HOH A 49 449 38 HOH HOH . 
E 5 HOH A 50 450 2 HOH HOH . 
E 5 HOH A 51 451 12 HOH HOH . 
E 5 HOH A 52 452 56 HOH HOH . 
E 5 HOH A 53 453 53 HOH HOH . 
E 5 HOH A 54 454 17 HOH HOH . 
E 5 HOH A 55 455 29 HOH HOH . 
E 5 HOH A 56 456 69 HOH HOH . 
E 5 HOH A 57 457 60 HOH HOH . 
E 5 HOH A 58 458 61 HOH HOH . 
E 5 HOH A 59 459 66 HOH HOH . 
E 5 HOH A 60 460 7 HOH HOH . 
E 5 HOH A 61 461 54 HOH HOH . 
E 5 HOH A 62 462 31 HOH HOH . 
E 5 HOH A 63 463 14 HOH HOH . 
E 5 HOH A 64 464 67 HOH HOH . 
E 5 HOH A 65 465 45 HOH HOH . 
E 5 HOH A 66 466 43 HOH HOH . 
E 5 HOH A 67 467 21 HOH HOH . 
E 5 HOH A 68 468 18 HOH HOH . 
E 5 HOH A 69 469 35 HOH HOH . 
E 5 HOH A 70 470 32 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 . . . B 2 -28.024 -25.687 17.598 1 47.47 ? N1 UDP 301 A 1 
HETATM 2 C C2 UDP . . . B 2 -29.173 -25.642 18.394 1 46.38 ? C2 UDP 301 A 1 
HETATM 3 N N3 UDP . . . B 2 -29.271 -24.708 19.337 1 47.4 ? N3 UDP 301 A 1 
HETATM 4 C C4 UDP . . . B 2 -28.296 -23.828 19.573 1 49.75 ? C4 UDP 301 A 1 
HETATM 5 C C5 UDP . . . B 2 -27.127 -23.851 18.816 1 50.03 ? C5 UDP 301 A 1 
HETATM 6 C C6 UDP . . . B 2 -27.023 -24.801 17.809 1 52.28 ? C6 UDP 301 A 1 
HETATM 7 O O2 UDP . . . B 2 -30.097 -26.439 18.189 1 50.94 ? O2 UDP 301 A 1 
HETATM 8 O O4 UDP . . . B 2 -28.405 -22.986 20.479 1 53.64 ? O4 UDP 301 A 1 
HETATM 9 C C1' UDP . . . B 2 -27.873 -26.678 16.559 1 46.22 ? C1' UDP 301 A 1 
HETATM 10 C C2' UDP . . . B 2 -27.857 -26.062 15.172 1 46.85 ? C2' UDP 301 A 1 
HETATM 11 O O2' UDP . . . B 2 -29.145 -25.842 14.59 1 47.07 ? O2' UDP 301 A 1 
HETATM 12 C C3' UDP . . . B 2 -27.018 -27.091 14.444 1 47.96 ? C3' UDP 301 A 1 
HETATM 13 C C4' UDP . . . B 2 -26.029 -27.593 15.49 1 42.23 ? C4' UDP 301 A 1 
HETATM 14 O O4' UDP . . . B 2 -26.581 -27.289 16.776 1 39.99 ? O4' UDP 301 A 1 
HETATM 15 O O3' UDP . . . B 2 -27.777 -28.21 14.04 1 46.88 ? O3' UDP 301 A 1 
HETATM 16 C C5' UDP . . . B 2 -24.663 -26.941 15.366 1 45.29 ? C5' UDP 301 A 1 
HETATM 17 O O5' UDP . . . B 2 -24.716 -25.513 15.277 1 39.77 ? O5' UDP 301 A 1 
HETATM 18 P PA UDP . . . B 2 -23.838 -24.767 14.153 1 37.36 ? PA UDP 301 A 1 
HETATM 19 O O1A UDP . . . B 2 -23.965 -25.457 12.922 1 39.75 ? O1A UDP 301 A 1 
HETATM 20 O O2A UDP . . . B 2 -24.156 -23.286 14.288 1 41.88 ? O2A UDP 301 A 1 
HETATM 21 O O3A UDP . . . B 2 -22.392 -25.079 14.835 1 34.27 ? O3A UDP 301 A 1 
HETATM 22 P PB UDP . . . B 2 -20.928 -24.552 14.37 1 35 ? PB UDP 301 A 1 
HETATM 23 O O1B UDP . . . B 2 -21.201 -23.514 13.282 1 34.28 ? O1B UDP 301 A 1 
HETATM 24 O O2B UDP . . . B 2 -20.297 -25.82 13.83 1 35.46 ? O2B UDP 301 A 1 
HETATM 25 O O3B UDP . . . B 2 -20.297 -24.104 15.697 1 32.22 ? O3B UDP 301 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           300 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#