data_8INO
#
_model_server_result.job_id            WSZvs5dNqWsxFn9srnENAQ 
_model_server_result.datetime_utc      '2025-06-21 04:21:26' 
_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          8ino 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":502}' 
#
_entry.id    8INO 
#
_exptl.entry_id    8INO 
_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            8INO 
_cell.length_a            45.608 
_cell.length_b            52.2 
_cell.length_c            200.701 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8INO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             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 
#
_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 443 n n 
N1 C6 UDP sing 444 n n 
N1 C1' UDP sing 445 n n 
C2 N3 UDP sing 446 n n 
C2 O2 UDP doub 447 n n 
N3 C4 UDP sing 448 n n 
N3 HN3 UDP sing 449 n n 
C4 C5 UDP sing 450 n n 
C4 O4 UDP doub 451 n n 
C5 C6 UDP doub 452 n n 
C5 H5 UDP sing 453 n n 
C6 H6 UDP sing 454 n n 
C1' C2' UDP sing 455 n n 
C1' O4' UDP sing 456 n n 
C1' H1' UDP sing 457 n n 
C2' O2' UDP sing 458 n n 
C2' C3' UDP sing 459 n n 
C2' H2' UDP sing 460 n n 
O2' HO2' UDP sing 461 n n 
C3' C4' UDP sing 462 n n 
C3' O3' UDP sing 463 n n 
C3' H3' UDP sing 464 n n 
C4' O4' UDP sing 465 n n 
C4' C5' UDP sing 466 n n 
C4' H4' UDP sing 467 n n 
O3' HO3' UDP sing 468 n n 
C5' O5' UDP sing 469 n n 
C5' "H5'1" UDP sing 470 n n 
C5' "H5'2" UDP sing 471 n n 
O5' PA UDP sing 472 n n 
PA O1A UDP doub 473 n n 
PA O2A UDP sing 474 n n 
PA O3A UDP sing 475 n n 
O2A HOA2 UDP sing 476 n n 
O3A PB UDP sing 477 n n 
PB O1B UDP doub 478 n n 
PB O2B UDP sing 479 n n 
PB O3B UDP sing 480 n n 
O2B HOB2 UDP sing 481 n n 
O3B HOB3 UDP sing 482 n n 
#
_atom_sites.entry_id                     8INO 
_atom_sites.fract_transf_matrix[1][1]    0.021926 
_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]    0.019157 
_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]    0.004983 
_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 Q30 A 1 501 501 Q30 PEG . 
C 3 UDP A 1 502 502 UDP UDP . 
D 4 TRS A 1 503 503 TRS TRS . 
E 5 HOH A 1 601 42 HOH HOH . 
E 5 HOH A 2 602 77 HOH HOH . 
E 5 HOH A 3 603 65 HOH HOH . 
E 5 HOH A 4 604 63 HOH HOH . 
E 5 HOH A 5 605 50 HOH HOH . 
E 5 HOH A 6 606 35 HOH HOH . 
E 5 HOH A 7 607 69 HOH HOH . 
E 5 HOH A 8 608 59 HOH HOH . 
E 5 HOH A 9 609 44 HOH HOH . 
E 5 HOH A 10 610 78 HOH HOH . 
E 5 HOH A 11 611 43 HOH HOH . 
E 5 HOH A 12 612 106 HOH HOH . 
E 5 HOH A 13 613 3 HOH HOH . 
E 5 HOH A 14 614 112 HOH HOH . 
E 5 HOH A 15 615 80 HOH HOH . 
E 5 HOH A 16 616 12 HOH HOH . 
E 5 HOH A 17 617 37 HOH HOH . 
E 5 HOH A 18 618 68 HOH HOH . 
E 5 HOH A 19 619 36 HOH HOH . 
E 5 HOH A 20 620 120 HOH HOH . 
E 5 HOH A 21 621 71 HOH HOH . 
E 5 HOH A 22 622 1 HOH HOH . 
E 5 HOH A 23 623 70 HOH HOH . 
E 5 HOH A 24 624 13 HOH HOH . 
E 5 HOH A 25 625 10 HOH HOH . 
E 5 HOH A 26 626 66 HOH HOH . 
E 5 HOH A 27 627 2 HOH HOH . 
E 5 HOH A 28 628 110 HOH HOH . 
E 5 HOH A 29 629 9 HOH HOH . 
E 5 HOH A 30 630 90 HOH HOH . 
E 5 HOH A 31 631 24 HOH HOH . 
E 5 HOH A 32 632 113 HOH HOH . 
E 5 HOH A 33 633 60 HOH HOH . 
E 5 HOH A 34 634 14 HOH HOH . 
E 5 HOH A 35 635 11 HOH HOH . 
E 5 HOH A 36 636 38 HOH HOH . 
E 5 HOH A 37 637 8 HOH HOH . 
E 5 HOH A 38 638 56 HOH HOH . 
E 5 HOH A 39 639 31 HOH HOH . 
E 5 HOH A 40 640 28 HOH HOH . 
E 5 HOH A 41 641 54 HOH HOH . 
E 5 HOH A 42 642 26 HOH HOH . 
E 5 HOH A 43 643 73 HOH HOH . 
E 5 HOH A 44 644 119 HOH HOH . 
E 5 HOH A 45 645 108 HOH HOH . 
E 5 HOH A 46 646 20 HOH HOH . 
E 5 HOH A 47 647 19 HOH HOH . 
E 5 HOH A 48 648 6 HOH HOH . 
E 5 HOH A 49 649 23 HOH HOH . 
E 5 HOH A 50 650 86 HOH HOH . 
E 5 HOH A 51 651 57 HOH HOH . 
E 5 HOH A 52 652 5 HOH HOH . 
E 5 HOH A 53 653 72 HOH HOH . 
E 5 HOH A 54 654 87 HOH HOH . 
E 5 HOH A 55 655 117 HOH HOH . 
E 5 HOH A 56 656 75 HOH HOH . 
E 5 HOH A 57 657 67 HOH HOH . 
E 5 HOH A 58 658 64 HOH HOH . 
E 5 HOH A 59 659 22 HOH HOH . 
E 5 HOH A 60 660 32 HOH HOH . 
E 5 HOH A 61 661 30 HOH HOH . 
E 5 HOH A 62 662 4 HOH HOH . 
E 5 HOH A 63 663 105 HOH HOH . 
E 5 HOH A 64 664 15 HOH HOH . 
E 5 HOH A 65 665 34 HOH HOH . 
E 5 HOH A 66 666 53 HOH HOH . 
E 5 HOH A 67 667 7 HOH HOH . 
E 5 HOH A 68 668 52 HOH HOH . 
E 5 HOH A 69 669 18 HOH HOH . 
E 5 HOH A 70 670 85 HOH HOH . 
E 5 HOH A 71 671 102 HOH HOH . 
E 5 HOH A 72 672 107 HOH HOH . 
E 5 HOH A 73 673 29 HOH HOH . 
E 5 HOH A 74 674 55 HOH HOH . 
E 5 HOH A 75 675 116 HOH HOH . 
E 5 HOH A 76 676 21 HOH HOH . 
E 5 HOH A 77 677 58 HOH HOH . 
E 5 HOH A 78 678 115 HOH HOH . 
E 5 HOH A 79 679 41 HOH HOH . 
E 5 HOH A 80 680 61 HOH HOH . 
E 5 HOH A 81 681 45 HOH HOH . 
E 5 HOH A 82 682 88 HOH HOH . 
E 5 HOH A 83 683 46 HOH HOH . 
E 5 HOH A 84 684 92 HOH HOH . 
E 5 HOH A 85 685 16 HOH HOH . 
E 5 HOH A 86 686 39 HOH HOH . 
E 5 HOH A 87 687 48 HOH HOH . 
E 5 HOH A 88 688 17 HOH HOH . 
E 5 HOH A 89 689 47 HOH HOH . 
E 5 HOH A 90 690 118 HOH HOH . 
E 5 HOH A 91 691 76 HOH HOH . 
E 5 HOH A 92 692 40 HOH HOH . 
E 5 HOH A 93 693 27 HOH HOH . 
E 5 HOH A 94 694 100 HOH HOH . 
E 5 HOH A 95 695 81 HOH HOH . 
E 5 HOH A 96 696 111 HOH HOH . 
E 5 HOH A 97 697 51 HOH HOH . 
E 5 HOH A 98 698 97 HOH HOH . 
E 5 HOH A 99 699 104 HOH HOH . 
E 5 HOH A 100 700 84 HOH HOH . 
E 5 HOH A 101 701 89 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 -4.684 20.885 80.424 1 23.24 ? N1 UDP 502 A 1 
HETATM 2 C C2 UDP . . . C 3 -3.595 20.339 80.942 1 23.86 ? C2 UDP 502 A 1 
HETATM 3 N N3 UDP . . . C 3 -2.91 20.904 81.906 1 25.35 ? N3 UDP 502 A 1 
HETATM 4 C C4 UDP . . . C 3 -3.313 22.062 82.37 1 24.92 ? C4 UDP 502 A 1 
HETATM 5 C C5 UDP . . . C 3 -4.45 22.699 81.861 1 24.96 ? C5 UDP 502 A 1 
HETATM 6 C C6 UDP . . . C 3 -5.144 22.055 80.838 1 23.09 ? C6 UDP 502 A 1 
HETATM 7 O O2 UDP . . . C 3 -3.133 19.112 80.494 1 23.49 ? O2 UDP 502 A 1 
HETATM 8 O O4 UDP . . . C 3 -2.551 22.633 83.366 1 26.13 ? O4 UDP 502 A 1 
HETATM 9 C C1' UDP . . . C 3 -5.383 20.202 79.339 1 23.46 ? C1' UDP 502 A 1 
HETATM 10 C C2' UDP . . . C 3 -6.809 19.758 79.69 1 25.38 ? C2' UDP 502 A 1 
HETATM 11 O O2' UDP . . . C 3 -6.775 18.514 80.283 1 20.26 ? O2' UDP 502 A 1 
HETATM 12 C C3' UDP . . . C 3 -7.389 19.744 78.253 1 26.07 ? C3' UDP 502 A 1 
HETATM 13 C C4' UDP . . . C 3 -6.881 20.803 77.638 1 24.55 ? C4' UDP 502 A 1 
HETATM 14 O O4' UDP . . . C 3 -5.521 21.108 78.401 1 24.71 ? O4' UDP 502 A 1 
HETATM 15 O O3' UDP . . . C 3 -6.858 18.506 77.595 1 25.04 ? O3' UDP 502 A 1 
HETATM 16 C C5' UDP . . . C 3 -7.732 22.064 77.727 1 24.82 ? C5' UDP 502 A 1 
HETATM 17 O O5' UDP . . . C 3 -8.844 21.799 76.92 1 24.98 ? O5' UDP 502 A 1 
HETATM 18 P PA UDP . . . C 3 -10.272 22.584 77.101 1 23.51 ? PA UDP 502 A 1 
HETATM 19 O O1A UDP . . . C 3 -11.276 22.015 76.114 1 24.03 ? O1A UDP 502 A 1 
HETATM 20 O O2A UDP . . . C 3 -10.763 22.378 78.521 1 27.34 -1 O2A UDP 502 A 1 
HETATM 21 O O3A UDP . . . C 3 -10.155 24.22 76.943 1 28.33 ? O3A UDP 502 A 1 
HETATM 22 P PB UDP . . . C 3 -9.212 25.069 75.895 1 27.58 ? PB UDP 502 A 1 
HETATM 23 O O1B UDP . . . C 3 -9.39 24.493 74.503 1 25.25 ? O1B UDP 502 A 1 
HETATM 24 O O2B UDP . . . C 3 -9.692 26.508 75.959 1 28.47 -1 O2B UDP 502 A 1 
HETATM 25 O O3B UDP . . . C 3 -7.75 24.995 76.34 1 26.92 ? O3B UDP 502 A 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#