data_7ZI3
#
_model_server_result.job_id            6cU6lkRE6QqK0IyMFX5qbg 
_model_server_result.datetime_utc      '2024-11-13 06:07:35' 
_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          7zi3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    7ZI3 
#
_exptl.entry_id    7ZI3 
_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            7ZI3 
_cell.length_a            68.94 
_cell.length_b            68.94 
_cell.length_c            120.763 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7ZI3 
_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                      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 O LYS 62 A LYS 42 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? 
metalc ? metalc2 A O SER 65 A SER 45 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc3 A O TRP 68 A TRP 48 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc4 D NA NA . A NA 303 1_555 E O HOH . A HOH 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
#
_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 439 n n 
N1 C6 UDP sing 440 n n 
N1 C1' UDP sing 441 n n 
C2 N3 UDP sing 442 n n 
C2 O2 UDP doub 443 n n 
N3 C4 UDP sing 444 n n 
N3 HN3 UDP sing 445 n n 
C4 C5 UDP sing 446 n n 
C4 O4 UDP doub 447 n n 
C5 C6 UDP doub 448 n n 
C5 H5 UDP sing 449 n n 
C6 H6 UDP sing 450 n n 
C1' C2' UDP sing 451 n n 
C1' O4' UDP sing 452 n n 
C1' H1' UDP sing 453 n n 
C2' O2' UDP sing 454 n n 
C2' C3' UDP sing 455 n n 
C2' H2' UDP sing 456 n n 
O2' HO2' UDP sing 457 n n 
C3' C4' UDP sing 458 n n 
C3' O3' UDP sing 459 n n 
C3' H3' UDP sing 460 n n 
C4' O4' UDP sing 461 n n 
C4' C5' UDP sing 462 n n 
C4' H4' UDP sing 463 n n 
O3' HO3' UDP sing 464 n n 
C5' O5' UDP sing 465 n n 
C5' "H5'1" UDP sing 466 n n 
C5' "H5'2" UDP sing 467 n n 
O5' PA UDP sing 468 n n 
PA O1A UDP doub 469 n n 
PA O2A UDP sing 470 n n 
PA O3A UDP sing 471 n n 
O2A HOA2 UDP sing 472 n n 
O3A PB UDP sing 473 n n 
PB O1B UDP doub 474 n n 
PB O2B UDP sing 475 n n 
PB O3B UDP sing 476 n n 
O2B HOB2 UDP sing 477 n n 
O3B HOB3 UDP sing 478 n n 
#
_atom_sites.entry_id                     7ZI3 
_atom_sites.fract_transf_matrix[1][1]    0.014505 
_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]    0.014505 
_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]    0.008281 
_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 J98 A 1 301 301 J98 LIG . 
C 3 UDP A 1 302 302 UDP UDP . 
D 4 NA A 1 303 1 NA NA . 
E 5 HOH A 1 401 62 HOH HOH . 
E 5 HOH A 2 402 19 HOH HOH . 
E 5 HOH A 3 403 64 HOH HOH . 
E 5 HOH A 4 404 46 HOH HOH . 
E 5 HOH A 5 405 52 HOH HOH . 
E 5 HOH A 6 406 42 HOH HOH . 
E 5 HOH A 7 407 65 HOH HOH . 
E 5 HOH A 8 408 18 HOH HOH . 
E 5 HOH A 9 409 53 HOH HOH . 
E 5 HOH A 10 410 45 HOH HOH . 
E 5 HOH A 11 411 29 HOH HOH . 
E 5 HOH A 12 412 40 HOH HOH . 
E 5 HOH A 13 413 27 HOH HOH . 
E 5 HOH A 14 414 39 HOH HOH . 
E 5 HOH A 15 415 50 HOH HOH . 
E 5 HOH A 16 416 51 HOH HOH . 
E 5 HOH A 17 417 25 HOH HOH . 
E 5 HOH A 18 418 49 HOH HOH . 
E 5 HOH A 19 419 4 HOH HOH . 
E 5 HOH A 20 420 8 HOH HOH . 
E 5 HOH A 21 421 48 HOH HOH . 
E 5 HOH A 22 422 36 HOH HOH . 
E 5 HOH A 23 423 24 HOH HOH . 
E 5 HOH A 24 424 26 HOH HOH . 
E 5 HOH A 25 425 14 HOH HOH . 
E 5 HOH A 26 426 5 HOH HOH . 
E 5 HOH A 27 427 61 HOH HOH . 
E 5 HOH A 28 428 6 HOH HOH . 
E 5 HOH A 29 429 56 HOH HOH . 
E 5 HOH A 30 430 21 HOH HOH . 
E 5 HOH A 31 431 44 HOH HOH . 
E 5 HOH A 32 432 47 HOH HOH . 
E 5 HOH A 33 433 30 HOH HOH . 
E 5 HOH A 34 434 2 HOH HOH . 
E 5 HOH A 35 435 57 HOH HOH . 
E 5 HOH A 36 436 43 HOH HOH . 
E 5 HOH A 37 437 55 HOH HOH . 
E 5 HOH A 38 438 1 HOH HOH . 
E 5 HOH A 39 439 35 HOH HOH . 
E 5 HOH A 40 440 63 HOH HOH . 
E 5 HOH A 41 441 15 HOH HOH . 
E 5 HOH A 42 442 58 HOH HOH . 
E 5 HOH A 43 443 11 HOH HOH . 
E 5 HOH A 44 444 33 HOH HOH . 
E 5 HOH A 45 445 22 HOH HOH . 
E 5 HOH A 46 446 10 HOH HOH . 
E 5 HOH A 47 447 28 HOH HOH . 
E 5 HOH A 48 448 17 HOH HOH . 
E 5 HOH A 49 449 7 HOH HOH . 
E 5 HOH A 50 450 37 HOH HOH . 
E 5 HOH A 51 451 12 HOH HOH . 
E 5 HOH A 52 452 3 HOH HOH . 
E 5 HOH A 53 453 32 HOH HOH . 
E 5 HOH A 54 454 60 HOH HOH . 
E 5 HOH A 55 455 54 HOH HOH . 
E 5 HOH A 56 456 34 HOH HOH . 
E 5 HOH A 57 457 41 HOH HOH . 
E 5 HOH A 58 458 9 HOH HOH . 
E 5 HOH A 59 459 16 HOH HOH . 
E 5 HOH A 60 460 23 HOH HOH . 
E 5 HOH A 61 461 59 HOH HOH . 
E 5 HOH A 62 462 38 HOH HOH . 
E 5 HOH A 63 463 20 HOH HOH . 
E 5 HOH A 64 464 31 HOH HOH . 
E 5 HOH A 65 465 13 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 -28.373 -25.74 17.537 1 56.47 ? N1 UDP 302 A 1 
HETATM 2 C C2 UDP . . . C 3 -29.525 -25.704 18.359 1 59.4 ? C2 UDP 302 A 1 
HETATM 3 N N3 UDP . . . C 3 -29.643 -24.787 19.317 1 57.41 ? N3 UDP 302 A 1 
HETATM 4 C C4 UDP . . . C 3 -28.675 -23.892 19.513 1 56.42 ? C4 UDP 302 A 1 
HETATM 5 C C5 UDP . . . C 3 -27.506 -23.905 18.748 1 53.96 ? C5 UDP 302 A 1 
HETATM 6 C C6 UDP . . . C 3 -27.379 -24.845 17.734 1 55.31 ? C6 UDP 302 A 1 
HETATM 7 O O2 UDP . . . C 3 -30.445 -26.52 18.189 1 58.82 ? O2 UDP 302 A 1 
HETATM 8 O O4 UDP . . . C 3 -28.795 -23.07 20.424 1 59.45 ? O4 UDP 302 A 1 
HETATM 9 C C1' UDP . . . C 3 -28.247 -26.746 16.493 1 55.31 ? C1' UDP 302 A 1 
HETATM 10 C C2' UDP . . . C 3 -28.255 -26.203 15.079 1 61.19 ? C2' UDP 302 A 1 
HETATM 11 O O2' UDP . . . C 3 -29.568 -25.978 14.536 1 63.08 ? O2' UDP 302 A 1 
HETATM 12 C C3' UDP . . . C 3 -27.468 -27.295 14.357 1 64.97 ? C3' UDP 302 A 1 
HETATM 13 C C4' UDP . . . C 3 -26.481 -27.768 15.419 1 57.88 ? C4' UDP 302 A 1 
HETATM 14 O O4' UDP . . . C 3 -26.964 -27.334 16.692 1 52.52 ? O4' UDP 302 A 1 
HETATM 15 O O3' UDP . . . C 3 -28.262 -28.411 13.918 1 59.79 ? O3' UDP 302 A 1 
HETATM 16 C C5' UDP . . . C 3 -25.111 -27.158 15.24 1 55.79 ? C5' UDP 302 A 1 
HETATM 17 O O5' UDP . . . C 3 -25.177 -25.746 15.202 1 53.48 ? O5' UDP 302 A 1 
HETATM 18 P PA UDP . . . C 3 -24.222 -24.886 14.246 1 49.45 ? PA UDP 302 A 1 
HETATM 19 O O1A UDP . . . C 3 -24.327 -25.409 12.932 1 45.98 ? O1A UDP 302 A 1 
HETATM 20 O O2A UDP . . . C 3 -24.548 -23.424 14.389 1 49.39 ? O2A UDP 302 A 1 
HETATM 21 O O3A UDP . . . C 3 -22.738 -25.214 14.788 1 44.34 ? O3A UDP 302 A 1 
HETATM 22 P PB UDP . . . C 3 -21.309 -24.656 14.281 1 46.65 ? PB UDP 302 A 1 
HETATM 23 O O1B UDP . . . C 3 -21.6 -23.622 13.189 1 46.42 ? O1B UDP 302 A 1 
HETATM 24 O O2B UDP . . . C 3 -20.644 -25.904 13.735 1 47.65 ? O2B UDP 302 A 1 
HETATM 25 O O3B UDP . . . C 3 -20.718 -24.152 15.547 1 43.6 ? O3B UDP 302 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#