data_4Q1F
#
_model_server_result.job_id            0EciobXjHWi7YUfSA13PIQ 
_model_server_result.datetime_utc      '2024-11-22 20:40:54' 
_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          4q1f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    4Q1F 
#
_exptl.entry_id    4Q1F 
_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    2 
_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            4Q1F 
_cell.length_a            68.782 
_cell.length_b            68.782 
_cell.length_c            121.278 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Q1F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_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,F,G,H 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E 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 419 n n 
N1 C6 UDP sing 420 n n 
N1 C1' UDP sing 421 n n 
C2 N3 UDP sing 422 n n 
C2 O2 UDP doub 423 n n 
N3 C4 UDP sing 424 n n 
N3 HN3 UDP sing 425 n n 
C4 C5 UDP sing 426 n n 
C4 O4 UDP doub 427 n n 
C5 C6 UDP doub 428 n n 
C5 H5 UDP sing 429 n n 
C6 H6 UDP sing 430 n n 
C1' C2' UDP sing 431 n n 
C1' O4' UDP sing 432 n n 
C1' H1' UDP sing 433 n n 
C2' O2' UDP sing 434 n n 
C2' C3' UDP sing 435 n n 
C2' H2' UDP sing 436 n n 
O2' HO2' UDP sing 437 n n 
C3' C4' UDP sing 438 n n 
C3' O3' UDP sing 439 n n 
C3' H3' UDP sing 440 n n 
C4' O4' UDP sing 441 n n 
C4' C5' UDP sing 442 n n 
C4' H4' UDP sing 443 n n 
O3' HO3' UDP sing 444 n n 
C5' O5' UDP sing 445 n n 
C5' "H5'1" UDP sing 446 n n 
C5' "H5'2" UDP sing 447 n n 
O5' PA UDP sing 448 n n 
PA O1A UDP doub 449 n n 
PA O2A UDP sing 450 n n 
PA O3A UDP sing 451 n n 
O2A HOA2 UDP sing 452 n n 
O3A PB UDP sing 453 n n 
PB O1B UDP doub 454 n n 
PB O2B UDP sing 455 n n 
PB O3B UDP sing 456 n n 
O2B HOB2 UDP sing 457 n n 
O3B HOB3 UDP sing 458 n n 
#
_atom_sites.entry_id                     4Q1F 
_atom_sites.fract_transf_matrix[1][1]    0.014539 
_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]    0.014539 
_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]    0.008246 
_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
C 2 UDP A 1 301 302 UDP UDP . 
D 3 2XN A 1 302 303 2XN 2XN . 
E 2 UDP B 1 301 302 UDP UDP . 
F 3 2XN B 1 302 303 2XN 2XN . 
G 4 HOH A 1 401 1 HOH HOH . 
G 4 HOH A 2 402 2 HOH HOH . 
G 4 HOH A 3 403 3 HOH HOH . 
G 4 HOH A 4 404 4 HOH HOH . 
G 4 HOH A 5 405 5 HOH HOH . 
G 4 HOH A 6 406 6 HOH HOH . 
G 4 HOH A 7 407 7 HOH HOH . 
G 4 HOH A 8 408 9 HOH HOH . 
G 4 HOH A 9 409 10 HOH HOH . 
G 4 HOH A 10 410 11 HOH HOH . 
G 4 HOH A 11 411 12 HOH HOH . 
G 4 HOH A 12 412 13 HOH HOH . 
G 4 HOH A 13 413 14 HOH HOH . 
G 4 HOH A 14 414 16 HOH HOH . 
G 4 HOH A 15 415 18 HOH HOH . 
G 4 HOH A 16 416 19 HOH HOH . 
G 4 HOH A 17 417 20 HOH HOH . 
G 4 HOH A 18 418 21 HOH HOH . 
G 4 HOH A 19 419 22 HOH HOH . 
G 4 HOH A 20 420 23 HOH HOH . 
G 4 HOH A 21 421 25 HOH HOH . 
G 4 HOH A 22 422 26 HOH HOH . 
G 4 HOH A 23 423 27 HOH HOH . 
G 4 HOH A 24 424 28 HOH HOH . 
G 4 HOH A 25 425 29 HOH HOH . 
G 4 HOH A 26 426 30 HOH HOH . 
G 4 HOH A 27 427 31 HOH HOH . 
G 4 HOH A 28 428 32 HOH HOH . 
G 4 HOH A 29 429 35 HOH HOH . 
G 4 HOH A 30 430 38 HOH HOH . 
G 4 HOH A 31 431 39 HOH HOH . 
G 4 HOH A 32 432 40 HOH HOH . 
G 4 HOH A 33 433 43 HOH HOH . 
G 4 HOH A 34 434 44 HOH HOH . 
G 4 HOH A 35 435 45 HOH HOH . 
G 4 HOH A 36 436 46 HOH HOH . 
G 4 HOH A 37 437 47 HOH HOH . 
G 4 HOH A 38 438 49 HOH HOH . 
G 4 HOH A 39 439 50 HOH HOH . 
G 4 HOH A 40 440 52 HOH HOH . 
G 4 HOH A 41 441 53 HOH HOH . 
G 4 HOH A 42 442 54 HOH HOH . 
G 4 HOH A 43 443 55 HOH HOH . 
G 4 HOH A 44 444 56 HOH HOH . 
G 4 HOH A 45 445 58 HOH HOH . 
G 4 HOH A 46 446 119 HOH HOH . 
G 4 HOH A 47 447 120 HOH HOH . 
G 4 HOH A 48 448 122 HOH HOH . 
G 4 HOH A 49 449 127 HOH HOH . 
G 4 HOH A 50 450 128 HOH HOH . 
G 4 HOH A 51 451 131 HOH HOH . 
G 4 HOH A 52 452 133 HOH HOH . 
G 4 HOH A 53 453 134 HOH HOH . 
G 4 HOH A 54 454 135 HOH HOH . 
G 4 HOH A 55 455 137 HOH HOH . 
G 4 HOH A 56 456 140 HOH HOH . 
G 4 HOH A 57 457 143 HOH HOH . 
G 4 HOH A 58 458 144 HOH HOH . 
G 4 HOH A 59 459 151 HOH HOH . 
G 4 HOH A 60 460 153 HOH HOH . 
G 4 HOH A 61 461 155 HOH HOH . 
G 4 HOH A 62 462 156 HOH HOH . 
G 4 HOH A 63 463 157 HOH HOH . 
G 4 HOH A 64 464 161 HOH HOH . 
G 4 HOH A 65 465 162 HOH HOH . 
G 4 HOH A 66 466 164 HOH HOH . 
G 4 HOH A 67 467 166 HOH HOH . 
G 4 HOH A 68 468 168 HOH HOH . 
G 4 HOH A 69 469 170 HOH HOH . 
G 4 HOH A 70 470 172 HOH HOH . 
G 4 HOH A 71 471 175 HOH HOH . 
G 4 HOH A 72 472 176 HOH HOH . 
G 4 HOH A 73 473 177 HOH HOH . 
G 4 HOH A 74 474 179 HOH HOH . 
G 4 HOH A 75 475 182 HOH HOH . 
G 4 HOH A 76 476 183 HOH HOH . 
G 4 HOH A 77 477 184 HOH HOH . 
G 4 HOH A 78 478 186 HOH HOH . 
G 4 HOH A 79 479 192 HOH HOH . 
G 4 HOH A 80 480 195 HOH HOH . 
G 4 HOH A 81 481 197 HOH HOH . 
G 4 HOH A 82 482 198 HOH HOH . 
H 4 HOH B 1 401 24 HOH HOH . 
H 4 HOH B 2 402 33 HOH HOH . 
H 4 HOH B 3 403 59 HOH HOH . 
H 4 HOH B 4 404 60 HOH HOH . 
H 4 HOH B 5 405 61 HOH HOH . 
H 4 HOH B 6 406 62 HOH HOH . 
H 4 HOH B 7 407 63 HOH HOH . 
H 4 HOH B 8 408 64 HOH HOH . 
H 4 HOH B 9 409 65 HOH HOH . 
H 4 HOH B 10 410 66 HOH HOH . 
H 4 HOH B 11 411 67 HOH HOH . 
H 4 HOH B 12 412 68 HOH HOH . 
H 4 HOH B 13 413 70 HOH HOH . 
H 4 HOH B 14 414 71 HOH HOH . 
H 4 HOH B 15 415 72 HOH HOH . 
H 4 HOH B 16 416 73 HOH HOH . 
H 4 HOH B 17 417 74 HOH HOH . 
H 4 HOH B 18 418 75 HOH HOH . 
H 4 HOH B 19 419 76 HOH HOH . 
H 4 HOH B 20 420 77 HOH HOH . 
H 4 HOH B 21 421 78 HOH HOH . 
H 4 HOH B 22 422 79 HOH HOH . 
H 4 HOH B 23 423 80 HOH HOH . 
H 4 HOH B 24 424 81 HOH HOH . 
H 4 HOH B 25 425 82 HOH HOH . 
H 4 HOH B 26 426 83 HOH HOH . 
H 4 HOH B 27 427 84 HOH HOH . 
H 4 HOH B 28 428 85 HOH HOH . 
H 4 HOH B 29 429 86 HOH HOH . 
H 4 HOH B 30 430 87 HOH HOH . 
H 4 HOH B 31 431 88 HOH HOH . 
H 4 HOH B 32 432 89 HOH HOH . 
H 4 HOH B 33 433 90 HOH HOH . 
H 4 HOH B 34 434 91 HOH HOH . 
H 4 HOH B 35 435 92 HOH HOH . 
H 4 HOH B 36 436 93 HOH HOH . 
H 4 HOH B 37 437 94 HOH HOH . 
H 4 HOH B 38 438 95 HOH HOH . 
H 4 HOH B 39 439 97 HOH HOH . 
H 4 HOH B 40 440 98 HOH HOH . 
H 4 HOH B 41 441 99 HOH HOH . 
H 4 HOH B 42 442 100 HOH HOH . 
H 4 HOH B 43 443 101 HOH HOH . 
H 4 HOH B 44 444 102 HOH HOH . 
H 4 HOH B 45 445 103 HOH HOH . 
H 4 HOH B 46 446 104 HOH HOH . 
H 4 HOH B 47 447 105 HOH HOH . 
H 4 HOH B 48 448 106 HOH HOH . 
H 4 HOH B 49 449 107 HOH HOH . 
H 4 HOH B 50 450 109 HOH HOH . 
H 4 HOH B 51 451 110 HOH HOH . 
H 4 HOH B 52 452 112 HOH HOH . 
H 4 HOH B 53 453 113 HOH HOH . 
H 4 HOH B 54 454 114 HOH HOH . 
H 4 HOH B 55 455 115 HOH HOH . 
H 4 HOH B 56 456 116 HOH HOH . 
H 4 HOH B 57 457 117 HOH HOH . 
H 4 HOH B 58 458 121 HOH HOH . 
H 4 HOH B 59 459 123 HOH HOH . 
H 4 HOH B 60 460 125 HOH HOH . 
H 4 HOH B 61 461 129 HOH HOH . 
H 4 HOH B 62 462 130 HOH HOH . 
H 4 HOH B 63 463 132 HOH HOH . 
H 4 HOH B 64 464 136 HOH HOH . 
H 4 HOH B 65 465 138 HOH HOH . 
H 4 HOH B 66 466 141 HOH HOH . 
H 4 HOH B 67 467 145 HOH HOH . 
H 4 HOH B 68 468 146 HOH HOH . 
H 4 HOH B 69 469 149 HOH HOH . 
H 4 HOH B 70 470 152 HOH HOH . 
H 4 HOH B 71 471 158 HOH HOH . 
H 4 HOH B 72 472 160 HOH HOH . 
H 4 HOH B 73 473 163 HOH HOH . 
H 4 HOH B 74 474 165 HOH HOH . 
H 4 HOH B 75 475 167 HOH HOH . 
H 4 HOH B 76 476 169 HOH HOH . 
H 4 HOH B 77 477 171 HOH HOH . 
H 4 HOH B 78 478 173 HOH HOH . 
H 4 HOH B 79 479 178 HOH HOH . 
H 4 HOH B 80 480 180 HOH HOH . 
H 4 HOH B 81 481 181 HOH HOH . 
H 4 HOH B 82 482 185 HOH HOH . 
H 4 HOH B 83 483 187 HOH HOH . 
H 4 HOH B 84 484 188 HOH HOH . 
H 4 HOH B 85 485 189 HOH HOH . 
H 4 HOH B 86 486 190 HOH HOH . 
H 4 HOH B 87 487 193 HOH HOH . 
H 4 HOH B 88 488 194 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 2 29.435 -25.111 -16.076 1 51.93 ? N1 UDP 301 A 1 
HETATM 2 C C2 UDP . . . C 2 30.574 -25.188 -16.853 1 57.69 ? C2 UDP 301 A 1 
HETATM 3 N N3 UDP . . . C 2 30.741 -24.338 -17.927 1 54.81 ? N3 UDP 301 A 1 
HETATM 4 C C4 UDP . . . C 2 29.765 -23.409 -18.22 1 55.64 ? C4 UDP 301 A 1 
HETATM 5 C C5 UDP . . . C 2 28.621 -23.34 -17.433 1 56.65 ? C5 UDP 301 A 1 
HETATM 6 C C6 UDP . . . C 2 28.396 -24.322 -16.475 1 54.44 ? C6 UDP 301 A 1 
HETATM 7 O O2 UDP . . . C 2 31.441 -26.02 -16.588 1 58.84 ? O2 UDP 301 A 1 
HETATM 8 O O4 UDP . . . C 2 29.908 -22.647 -19.175 1 56.95 ? O4 UDP 301 A 1 
HETATM 9 C C1' UDP . . . C 2 29.278 -26.036 -14.938 1 50.59 ? C1' UDP 301 A 1 
HETATM 10 C C2' UDP . . . C 2 29.253 -25.283 -13.618 1 52.21 ? C2' UDP 301 A 1 
HETATM 11 O O2' UDP . . . C 2 30.523 -25.272 -13.01 1 52.58 ? O2' UDP 301 A 1 
HETATM 12 C C3' UDP . . . C 2 28.257 -26.054 -12.776 1 55.16 ? C3' UDP 301 A 1 
HETATM 13 C C4' UDP . . . C 2 27.476 -26.918 -13.755 1 52.5 ? C4' UDP 301 A 1 
HETATM 14 O O4' UDP . . . C 2 28.059 -26.747 -15.031 1 50.14 ? O4' UDP 301 A 1 
HETATM 15 O O3' UDP . . . C 2 28.946 -26.874 -11.861 1 51.83 ? O3' UDP 301 A 1 
HETATM 16 C C5' UDP . . . C 2 26.014 -26.497 -13.81 1 51 ? C5' UDP 301 A 1 
HETATM 17 O O5' UDP . . . C 2 25.979 -25.137 -14.178 1 46.41 ? O5' UDP 301 A 1 
HETATM 18 P PA UDP . . . C 2 24.943 -24.106 -13.504 1 43.5 ? PA UDP 301 A 1 
HETATM 19 O O1A UDP . . . C 2 24.845 -24.415 -12.06 1 44.52 ? O1A UDP 301 A 1 
HETATM 20 O O2A UDP . . . C 2 25.383 -22.71 -13.714 1 43.25 ? O2A UDP 301 A 1 
HETATM 21 O O3A UDP . . . C 2 23.527 -24.401 -14.215 1 45.36 ? O3A UDP 301 A 1 
HETATM 22 P PB UDP . . . C 2 22.132 -23.931 -13.552 1 38.7 ? PB UDP 301 A 1 
HETATM 23 O O1B UDP . . . C 2 22.424 -22.985 -12.457 1 43.72 ? O1B UDP 301 A 1 
HETATM 24 O O2B UDP . . . C 2 21.407 -25.09 -12.988 1 41.79 ? O2B UDP 301 A 1 
HETATM 25 O O3B UDP . . . C 2 21.288 -23.275 -14.573 1 35.12 ? O3B UDP 301 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#