data_5DJS
#
_model_server_result.job_id            hj5yoq4pGpHJSTwQjUbywg 
_model_server_result.datetime_utc      '2025-02-05 11:50:20' 
_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          5djs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":601}' 
#
_entry.id    5DJS 
#
_exptl.entry_id    5DJS 
_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    4 
_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            5DJS 
_cell.length_a            70.188 
_cell.length_b            216.361 
_cell.length_c            216.406 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DJS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I 1 1 
B,F,J 2 1 
C,G,K 3 1 
D,H,L 4 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N 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 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     5DJS 
_atom_sites.fract_transf_matrix[1][1]    0.014247 
_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]    0.004622 
_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]    0.004621 
_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
E 2 UDP A 1 601 1 UDP UDP . 
F 2 UDP B 1 601 1 UDP UDP . 
G 2 UDP C 1 601 1 UDP UDP . 
H 2 UDP D 1 601 1 UDP UDP . 
I 3 HOH A 1 701 58 HOH HOH . 
I 3 HOH A 2 702 71 HOH HOH . 
I 3 HOH A 3 703 70 HOH HOH . 
I 3 HOH A 4 704 61 HOH HOH . 
I 3 HOH A 5 705 98 HOH HOH . 
I 3 HOH A 6 706 4 HOH HOH . 
I 3 HOH A 7 707 13 HOH HOH . 
I 3 HOH A 8 708 82 HOH HOH . 
I 3 HOH A 9 709 6 HOH HOH . 
I 3 HOH A 10 710 115 HOH HOH . 
I 3 HOH A 11 711 9 HOH HOH . 
I 3 HOH A 12 712 114 HOH HOH . 
I 3 HOH A 13 713 60 HOH HOH . 
I 3 HOH A 14 714 81 HOH HOH . 
I 3 HOH A 15 715 116 HOH HOH . 
I 3 HOH A 16 716 26 HOH HOH . 
I 3 HOH A 17 717 51 HOH HOH . 
I 3 HOH A 18 718 117 HOH HOH . 
I 3 HOH A 19 719 130 HOH HOH . 
I 3 HOH A 20 720 120 HOH HOH . 
I 3 HOH A 21 721 79 HOH HOH . 
I 3 HOH A 22 722 24 HOH HOH . 
I 3 HOH A 23 723 95 HOH HOH . 
I 3 HOH A 24 724 31 HOH HOH . 
I 3 HOH A 25 725 69 HOH HOH . 
I 3 HOH A 26 726 29 HOH HOH . 
I 3 HOH A 27 727 101 HOH HOH . 
I 3 HOH A 28 728 132 HOH HOH . 
I 3 HOH A 29 729 77 HOH HOH . 
I 3 HOH A 30 730 133 HOH HOH . 
I 3 HOH A 31 731 123 HOH HOH . 
J 3 HOH B 1 701 93 HOH HOH . 
J 3 HOH B 2 702 92 HOH HOH . 
J 3 HOH B 3 703 1 HOH HOH . 
J 3 HOH B 4 704 5 HOH HOH . 
J 3 HOH B 5 705 66 HOH HOH . 
J 3 HOH B 6 706 49 HOH HOH . 
J 3 HOH B 7 707 42 HOH HOH . 
J 3 HOH B 8 708 113 HOH HOH . 
J 3 HOH B 9 709 43 HOH HOH . 
J 3 HOH B 10 710 34 HOH HOH . 
J 3 HOH B 11 711 121 HOH HOH . 
J 3 HOH B 12 712 90 HOH HOH . 
J 3 HOH B 13 713 129 HOH HOH . 
J 3 HOH B 14 714 38 HOH HOH . 
J 3 HOH B 15 715 67 HOH HOH . 
J 3 HOH B 16 716 56 HOH HOH . 
J 3 HOH B 17 717 45 HOH HOH . 
J 3 HOH B 18 718 57 HOH HOH . 
J 3 HOH B 19 719 89 HOH HOH . 
J 3 HOH B 20 720 86 HOH HOH . 
J 3 HOH B 21 721 19 HOH HOH . 
J 3 HOH B 22 722 46 HOH HOH . 
J 3 HOH B 23 723 44 HOH HOH . 
J 3 HOH B 24 724 128 HOH HOH . 
J 3 HOH B 25 725 11 HOH HOH . 
J 3 HOH B 26 726 112 HOH HOH . 
J 3 HOH B 27 727 63 HOH HOH . 
J 3 HOH B 28 728 55 HOH HOH . 
J 3 HOH B 29 729 36 HOH HOH . 
J 3 HOH B 30 730 52 HOH HOH . 
J 3 HOH B 31 731 97 HOH HOH . 
J 3 HOH B 32 732 41 HOH HOH . 
J 3 HOH B 33 733 76 HOH HOH . 
J 3 HOH B 34 734 78 HOH HOH . 
K 3 HOH C 1 701 85 HOH HOH . 
K 3 HOH C 2 702 32 HOH HOH . 
K 3 HOH C 3 703 91 HOH HOH . 
K 3 HOH C 4 704 125 HOH HOH . 
K 3 HOH C 5 705 126 HOH HOH . 
K 3 HOH C 6 706 100 HOH HOH . 
K 3 HOH C 7 707 22 HOH HOH . 
K 3 HOH C 8 708 8 HOH HOH . 
K 3 HOH C 9 709 27 HOH HOH . 
K 3 HOH C 10 710 75 HOH HOH . 
K 3 HOH C 11 711 84 HOH HOH . 
K 3 HOH C 12 712 16 HOH HOH . 
K 3 HOH C 13 713 68 HOH HOH . 
K 3 HOH C 14 714 96 HOH HOH . 
K 3 HOH C 15 715 37 HOH HOH . 
K 3 HOH C 16 716 48 HOH HOH . 
K 3 HOH C 17 717 10 HOH HOH . 
K 3 HOH C 18 718 3 HOH HOH . 
K 3 HOH C 19 719 14 HOH HOH . 
K 3 HOH C 20 720 94 HOH HOH . 
K 3 HOH C 21 721 35 HOH HOH . 
K 3 HOH C 22 722 47 HOH HOH . 
K 3 HOH C 23 723 39 HOH HOH . 
K 3 HOH C 24 724 23 HOH HOH . 
K 3 HOH C 25 725 25 HOH HOH . 
K 3 HOH C 26 726 17 HOH HOH . 
K 3 HOH C 27 727 65 HOH HOH . 
K 3 HOH C 28 728 99 HOH HOH . 
K 3 HOH C 29 729 74 HOH HOH . 
K 3 HOH C 30 730 20 HOH HOH . 
K 3 HOH C 31 731 53 HOH HOH . 
K 3 HOH C 32 732 18 HOH HOH . 
K 3 HOH C 33 733 102 HOH HOH . 
K 3 HOH C 34 734 72 HOH HOH . 
K 3 HOH C 35 735 124 HOH HOH . 
L 3 HOH D 1 701 131 HOH HOH . 
L 3 HOH D 2 702 62 HOH HOH . 
L 3 HOH D 3 703 119 HOH HOH . 
L 3 HOH D 4 704 118 HOH HOH . 
L 3 HOH D 5 705 107 HOH HOH . 
L 3 HOH D 6 706 30 HOH HOH . 
L 3 HOH D 7 707 127 HOH HOH . 
L 3 HOH D 8 708 88 HOH HOH . 
L 3 HOH D 9 709 28 HOH HOH . 
L 3 HOH D 10 710 111 HOH HOH . 
L 3 HOH D 11 711 110 HOH HOH . 
L 3 HOH D 12 712 83 HOH HOH . 
L 3 HOH D 13 713 2 HOH HOH . 
L 3 HOH D 14 714 108 HOH HOH . 
L 3 HOH D 15 715 7 HOH HOH . 
L 3 HOH D 16 716 109 HOH HOH . 
L 3 HOH D 17 717 50 HOH HOH . 
L 3 HOH D 18 718 64 HOH HOH . 
L 3 HOH D 19 719 104 HOH HOH . 
L 3 HOH D 20 720 33 HOH HOH . 
L 3 HOH D 21 721 59 HOH HOH . 
L 3 HOH D 22 722 15 HOH HOH . 
L 3 HOH D 23 723 80 HOH HOH . 
L 3 HOH D 24 724 105 HOH HOH . 
L 3 HOH D 25 725 40 HOH HOH . 
L 3 HOH D 26 726 106 HOH HOH . 
L 3 HOH D 27 727 87 HOH HOH . 
L 3 HOH D 28 728 21 HOH HOH . 
L 3 HOH D 29 729 12 HOH HOH . 
L 3 HOH D 30 730 73 HOH HOH . 
L 3 HOH D 31 731 103 HOH HOH . 
L 3 HOH D 32 732 122 HOH HOH . 
L 3 HOH D 33 733 54 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 . . . H 2 1.544 -31.309 70.633 0.7 74.42 ? N1 UDP 601 D 1 
HETATM 2 C C2 UDP . . . H 2 0.23 -31.575 70.164 0.7 69.55 ? C2 UDP 601 D 1 
HETATM 3 N N3 UDP . . . H 2 -0.013 -31.608 68.844 0.7 67.34 ? N3 UDP 601 D 1 
HETATM 4 C C4 UDP . . . H 2 0.968 -31.397 67.953 0.7 65.79 ? C4 UDP 601 D 1 
HETATM 5 C C5 UDP . . . H 2 2.268 -31.138 68.37 0.7 67.12 ? C5 UDP 601 D 1 
HETATM 6 C C6 UDP . . . H 2 2.535 -31.099 69.735 0.7 71.46 ? C6 UDP 601 D 1 
HETATM 7 O O2 UDP . . . H 2 -0.715 -31.778 70.958 0.7 66.19 ? O2 UDP 601 D 1 
HETATM 8 O O4 UDP . . . H 2 0.715 -31.437 66.743 0.7 62.69 ? O4 UDP 601 D 1 
HETATM 9 C C1' UDP . . . H 2 1.834 -31.274 72.08 0.7 80 ? C1' UDP 601 D 1 
HETATM 10 C C2' UDP . . . H 2 2.746 -32.436 72.452 0.7 82.45 ? C2' UDP 601 D 1 
HETATM 11 O O2' UDP . . . H 2 2.206 -33.12 73.59 0.7 84.51 ? O2' UDP 601 D 1 
HETATM 12 C C3' UDP . . . H 2 4.091 -31.781 72.728 0.7 82.04 ? C3' UDP 601 D 1 
HETATM 13 C C4' UDP . . . H 2 3.727 -30.364 73.158 0.7 78.52 ? C4' UDP 601 D 1 
HETATM 14 O O4' UDP . . . H 2 2.512 -30.064 72.458 0.7 82.05 ? O4' UDP 601 D 1 
HETATM 15 O O3' UDP . . . H 2 4.821 -32.457 73.748 0.7 87.28 ? O3' UDP 601 D 1 
HETATM 16 C C5' UDP . . . H 2 4.765 -29.263 72.922 0.7 72.84 ? C5' UDP 601 D 1 
HETATM 17 O O5' UDP . . . H 2 5.94 -29.681 72.221 0.7 66.92 ? O5' UDP 601 D 1 
HETATM 18 P PA UDP . . . H 2 6.775 -28.592 71.356 0.7 61.99 ? PA UDP 601 D 1 
HETATM 19 O O1A UDP . . . H 2 6.302 -28.727 69.928 0.7 59.61 ? O1A UDP 601 D 1 
HETATM 20 O O2A UDP . . . H 2 6.652 -27.275 72.09 0.7 60.27 ? O2A UDP 601 D 1 
HETATM 21 O O3A UDP . . . H 2 8.331 -29.049 71.366 0.7 60.5 ? O3A UDP 601 D 1 
HETATM 22 P PB UDP . . . H 2 9.218 -29.248 72.709 0.7 60.07 ? PB UDP 601 D 1 
HETATM 23 O O1B UDP . . . H 2 10.33 -30.181 72.328 0.7 56.01 ? O1B UDP 601 D 1 
HETATM 24 O O2B UDP . . . H 2 8.292 -29.911 73.679 0.7 65.14 ? O2B UDP 601 D 1 
HETATM 25 O O3B UDP . . . H 2 9.636 -27.852 73.097 0.7 59.8 ? O3B UDP 601 D 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           392 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#