data_7ZI9
#
_model_server_result.job_id            FLy1ufb4TQUxzoYnJ3NtXw 
_model_server_result.datetime_utc      '2024-11-17 04:26:16' 
_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          7zi9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    7ZI9 
#
_exptl.entry_id    7ZI9 
_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            7ZI9 
_cell.length_a            69.051 
_cell.length_b            69.051 
_cell.length_c            121.638 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7ZI9 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc2 A O SER 65 A SER 45 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc3 A O TRP 68 A TRP 48 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc4 D NA NA . A NA 303 1_555 E O HOH . A HOH 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc5 D NA NA . A NA 303 1_555 E O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? 
#
_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 436 n n 
N1 C6 UDP sing 437 n n 
N1 C1' UDP sing 438 n n 
C2 N3 UDP sing 439 n n 
C2 O2 UDP doub 440 n n 
N3 C4 UDP sing 441 n n 
N3 HN3 UDP sing 442 n n 
C4 C5 UDP sing 443 n n 
C4 O4 UDP doub 444 n n 
C5 C6 UDP doub 445 n n 
C5 H5 UDP sing 446 n n 
C6 H6 UDP sing 447 n n 
C1' C2' UDP sing 448 n n 
C1' O4' UDP sing 449 n n 
C1' H1' UDP sing 450 n n 
C2' O2' UDP sing 451 n n 
C2' C3' UDP sing 452 n n 
C2' H2' UDP sing 453 n n 
O2' HO2' UDP sing 454 n n 
C3' C4' UDP sing 455 n n 
C3' O3' UDP sing 456 n n 
C3' H3' UDP sing 457 n n 
C4' O4' UDP sing 458 n n 
C4' C5' UDP sing 459 n n 
C4' H4' UDP sing 460 n n 
O3' HO3' UDP sing 461 n n 
C5' O5' UDP sing 462 n n 
C5' "H5'1" UDP sing 463 n n 
C5' "H5'2" UDP sing 464 n n 
O5' PA UDP sing 465 n n 
PA O1A UDP doub 466 n n 
PA O2A UDP sing 467 n n 
PA O3A UDP sing 468 n n 
O2A HOA2 UDP sing 469 n n 
O3A PB UDP sing 470 n n 
PB O1B UDP doub 471 n n 
PB O2B UDP sing 472 n n 
PB O3B UDP sing 473 n n 
O2B HOB2 UDP sing 474 n n 
O3B HOB3 UDP sing 475 n n 
#
_atom_sites.entry_id                     7ZI9 
_atom_sites.fract_transf_matrix[1][1]    0.014482 
_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]    0.014482 
_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]    0.008221 
_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 J6M A 1 302 302 J6M LIG . 
D 4 NA A 1 303 1 NA NA . 
E 5 HOH A 1 401 110 HOH HOH . 
E 5 HOH A 2 402 4 HOH HOH . 
E 5 HOH A 3 403 107 HOH HOH . 
E 5 HOH A 4 404 90 HOH HOH . 
E 5 HOH A 5 405 108 HOH HOH . 
E 5 HOH A 6 406 75 HOH HOH . 
E 5 HOH A 7 407 32 HOH HOH . 
E 5 HOH A 8 408 111 HOH HOH . 
E 5 HOH A 9 409 35 HOH HOH . 
E 5 HOH A 10 410 29 HOH HOH . 
E 5 HOH A 11 411 72 HOH HOH . 
E 5 HOH A 12 412 82 HOH HOH . 
E 5 HOH A 13 413 1 HOH HOH . 
E 5 HOH A 14 414 28 HOH HOH . 
E 5 HOH A 15 415 66 HOH HOH . 
E 5 HOH A 16 416 102 HOH HOH . 
E 5 HOH A 17 417 92 HOH HOH . 
E 5 HOH A 18 418 61 HOH HOH . 
E 5 HOH A 19 419 116 HOH HOH . 
E 5 HOH A 20 420 97 HOH HOH . 
E 5 HOH A 21 421 18 HOH HOH . 
E 5 HOH A 22 422 50 HOH HOH . 
E 5 HOH A 23 423 44 HOH HOH . 
E 5 HOH A 24 424 64 HOH HOH . 
E 5 HOH A 25 425 52 HOH HOH . 
E 5 HOH A 26 426 48 HOH HOH . 
E 5 HOH A 27 427 22 HOH HOH . 
E 5 HOH A 28 428 41 HOH HOH . 
E 5 HOH A 29 429 45 HOH HOH . 
E 5 HOH A 30 430 11 HOH HOH . 
E 5 HOH A 31 431 80 HOH HOH . 
E 5 HOH A 32 432 43 HOH HOH . 
E 5 HOH A 33 433 9 HOH HOH . 
E 5 HOH A 34 434 23 HOH HOH . 
E 5 HOH A 35 435 19 HOH HOH . 
E 5 HOH A 36 436 70 HOH HOH . 
E 5 HOH A 37 437 33 HOH HOH . 
E 5 HOH A 38 438 85 HOH HOH . 
E 5 HOH A 39 439 26 HOH HOH . 
E 5 HOH A 40 440 59 HOH HOH . 
E 5 HOH A 41 441 31 HOH HOH . 
E 5 HOH A 42 442 109 HOH HOH . 
E 5 HOH A 43 443 100 HOH HOH . 
E 5 HOH A 44 444 14 HOH HOH . 
E 5 HOH A 45 445 20 HOH HOH . 
E 5 HOH A 46 446 5 HOH HOH . 
E 5 HOH A 47 447 10 HOH HOH . 
E 5 HOH A 48 448 57 HOH HOH . 
E 5 HOH A 49 449 71 HOH HOH . 
E 5 HOH A 50 450 37 HOH HOH . 
E 5 HOH A 51 451 13 HOH HOH . 
E 5 HOH A 52 452 27 HOH HOH . 
E 5 HOH A 53 453 15 HOH HOH . 
E 5 HOH A 54 454 17 HOH HOH . 
E 5 HOH A 55 455 88 HOH HOH . 
E 5 HOH A 56 456 8 HOH HOH . 
E 5 HOH A 57 457 7 HOH HOH . 
E 5 HOH A 58 458 21 HOH HOH . 
E 5 HOH A 59 459 79 HOH HOH . 
E 5 HOH A 60 460 67 HOH HOH . 
E 5 HOH A 61 461 46 HOH HOH . 
E 5 HOH A 62 462 12 HOH HOH . 
E 5 HOH A 63 463 56 HOH HOH . 
E 5 HOH A 64 464 69 HOH HOH . 
E 5 HOH A 65 465 38 HOH HOH . 
E 5 HOH A 66 466 24 HOH HOH . 
E 5 HOH A 67 467 58 HOH HOH . 
E 5 HOH A 68 468 76 HOH HOH . 
E 5 HOH A 69 469 65 HOH HOH . 
E 5 HOH A 70 470 40 HOH HOH . 
E 5 HOH A 71 471 6 HOH HOH . 
E 5 HOH A 72 472 77 HOH HOH . 
E 5 HOH A 73 473 54 HOH HOH . 
E 5 HOH A 74 474 49 HOH HOH . 
E 5 HOH A 75 475 104 HOH HOH . 
E 5 HOH A 76 476 81 HOH HOH . 
E 5 HOH A 77 477 2 HOH HOH . 
E 5 HOH A 78 478 60 HOH HOH . 
E 5 HOH A 79 479 87 HOH HOH . 
E 5 HOH A 80 480 39 HOH HOH . 
E 5 HOH A 81 481 16 HOH HOH . 
E 5 HOH A 82 482 3 HOH HOH . 
E 5 HOH A 83 483 47 HOH HOH . 
E 5 HOH A 84 484 112 HOH HOH . 
E 5 HOH A 85 485 25 HOH HOH . 
E 5 HOH A 86 486 73 HOH HOH . 
E 5 HOH A 87 487 42 HOH HOH . 
E 5 HOH A 88 488 53 HOH HOH . 
E 5 HOH A 89 489 113 HOH HOH . 
E 5 HOH A 90 490 51 HOH HOH . 
E 5 HOH A 91 491 36 HOH HOH . 
E 5 HOH A 92 492 99 HOH HOH . 
E 5 HOH A 93 493 101 HOH HOH . 
E 5 HOH A 94 494 89 HOH HOH . 
E 5 HOH A 95 495 98 HOH HOH . 
E 5 HOH A 96 496 103 HOH HOH . 
E 5 HOH A 97 497 106 HOH HOH . 
E 5 HOH A 98 498 117 HOH HOH . 
E 5 HOH A 99 499 91 HOH HOH . 
E 5 HOH A 100 500 118 HOH HOH . 
E 5 HOH A 101 501 74 HOH HOH . 
E 5 HOH A 102 502 94 HOH HOH . 
E 5 HOH A 103 503 84 HOH HOH . 
E 5 HOH A 104 504 30 HOH HOH . 
E 5 HOH A 105 505 62 HOH HOH . 
E 5 HOH A 106 506 55 HOH HOH . 
E 5 HOH A 107 507 114 HOH HOH . 
E 5 HOH A 108 508 105 HOH HOH . 
E 5 HOH A 109 509 96 HOH HOH . 
E 5 HOH A 110 510 93 HOH HOH . 
E 5 HOH A 111 511 34 HOH HOH . 
E 5 HOH A 112 512 115 HOH HOH . 
E 5 HOH A 113 513 68 HOH HOH . 
E 5 HOH A 114 514 63 HOH HOH . 
E 5 HOH A 115 515 78 HOH HOH . 
E 5 HOH A 116 516 95 HOH HOH . 
E 5 HOH A 117 517 83 HOH HOH . 
E 5 HOH A 118 518 86 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 -28.342 -25.77 17.676 1 41.51 ? N1 UDP 301 A 1 
HETATM 2 C C2 UDP . . . B 2 -29.477 -25.804 18.511 1 43.04 ? C2 UDP 301 A 1 
HETATM 3 N N3 UDP . . . B 2 -29.638 -24.895 19.459 1 42.75 ? N3 UDP 301 A 1 
HETATM 4 C C4 UDP . . . B 2 -28.73 -23.938 19.63 1 40.46 ? C4 UDP 301 A 1 
HETATM 5 C C5 UDP . . . B 2 -27.547 -23.879 18.861 1 37.54 ? C5 UDP 301 A 1 
HETATM 6 C C6 UDP . . . B 2 -27.387 -24.821 17.863 1 41.44 ? C6 UDP 301 A 1 
HETATM 7 O O2 UDP . . . B 2 -30.36 -26.653 18.355 1 45.16 ? O2 UDP 301 A 1 
HETATM 8 O O4 UDP . . . B 2 -28.915 -23.138 20.542 1 46.92 ? O4 UDP 301 A 1 
HETATM 9 C C1' UDP . . . B 2 -28.16 -26.776 16.632 1 40.57 ? C1' UDP 301 A 1 
HETATM 10 C C2' UDP . . . B 2 -28.142 -26.214 15.218 1 40.86 ? C2' UDP 301 A 1 
HETATM 11 O O2' UDP . . . B 2 -29.427 -26.019 14.618 1 41.16 ? O2' UDP 301 A 1 
HETATM 12 C C3' UDP . . . B 2 -27.343 -27.278 14.483 1 42.04 ? C3' UDP 301 A 1 
HETATM 13 C C4' UDP . . . B 2 -26.353 -27.77 15.536 1 36.49 ? C4' UDP 301 A 1 
HETATM 14 O O4' UDP . . . B 2 -26.882 -27.41 16.837 1 36.34 ? O4' UDP 301 A 1 
HETATM 15 O O3' UDP . . . B 2 -28.155 -28.362 13.991 1 41.76 ? O3' UDP 301 A 1 
HETATM 16 C C5' UDP . . . B 2 -25 -27.156 15.317 1 37.98 ? C5' UDP 301 A 1 
HETATM 17 O O5' UDP . . . B 2 -25.064 -25.722 15.255 1 33.97 ? O5' UDP 301 A 1 
HETATM 18 P PA UDP . . . B 2 -24.149 -24.908 14.271 1 33.87 ? PA UDP 301 A 1 
HETATM 19 O O1A UDP . . . B 2 -24.306 -25.346 12.904 1 32.49 ? O1A UDP 301 A 1 
HETATM 20 O O2A UDP . . . B 2 -24.506 -23.441 14.454 1 33.84 ? O2A UDP 301 A 1 
HETATM 21 O O3A UDP . . . B 2 -22.683 -25.186 14.914 1 28.82 ? O3A UDP 301 A 1 
HETATM 22 P PB UDP . . . B 2 -21.251 -24.627 14.351 1 30.02 ? PB UDP 301 A 1 
HETATM 23 O O1B UDP . . . B 2 -21.477 -23.552 13.288 1 28.14 ? O1B UDP 301 A 1 
HETATM 24 O O2B UDP . . . B 2 -20.532 -25.88 13.897 1 30.72 ? O2B UDP 301 A 1 
HETATM 25 O O3B UDP . . . B 2 -20.638 -24.17 15.633 1 27.42 ? O3B UDP 301 A 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#