data_8SFT # _model_server_result.job_id YSm9MJds3c9jLMHeY5FV-w _model_server_result.datetime_utc '2025-09-19 08:43:07' _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 8sft # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":502}' # _entry.id 8SFT # _exptl.entry_id 8SFT _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 8SFT _cell.length_a 83.277 _cell.length_b 159.906 _cell.length_c 163.311 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SFT _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_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,F,G,H,I,J,K,L,M,N,O,AA 1 1 B,P,Q,R,S,T,U,V,W,BA 2 1 C,X,Y,CA 3 1 D,Z,DA 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 Q N N ? 2 Y N N ? 2 Z 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 395 n n N1 C6 UDP sing 396 n n N1 C1' UDP sing 397 n n C2 N3 UDP sing 398 n n C2 O2 UDP doub 399 n n N3 C4 UDP sing 400 n n N3 HN3 UDP sing 401 n n C4 C5 UDP sing 402 n n C4 O4 UDP doub 403 n n C5 C6 UDP doub 404 n n C5 H5 UDP sing 405 n n C6 H6 UDP sing 406 n n C1' C2' UDP sing 407 n n C1' O4' UDP sing 408 n n C1' H1' UDP sing 409 n n C2' O2' UDP sing 410 n n C2' C3' UDP sing 411 n n C2' H2' UDP sing 412 n n O2' HO2' UDP sing 413 n n C3' C4' UDP sing 414 n n C3' O3' UDP sing 415 n n C3' H3' UDP sing 416 n n C4' O4' UDP sing 417 n n C4' C5' UDP sing 418 n n C4' H4' UDP sing 419 n n O3' HO3' UDP sing 420 n n C5' O5' UDP sing 421 n n C5' "H5'1" UDP sing 422 n n C5' "H5'2" UDP sing 423 n n O5' PA UDP sing 424 n n PA O1A UDP doub 425 n n PA O2A UDP sing 426 n n PA O3A UDP sing 427 n n O2A HOA2 UDP sing 428 n n O3A PB UDP sing 429 n n PB O1B UDP doub 430 n n PB O2B UDP sing 431 n n PB O3B UDP sing 432 n n O2B HOB2 UDP sing 433 n n O3B HOB3 UDP sing 434 n n # _atom_sites.entry_id 8SFT _atom_sites.fract_transf_matrix[1][1] 0.012008 _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] 0.006254 _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] 0.006123 _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 1 501 501 UDP UDP . F 3 KMP A 1 502 503 KMP KMP . G 4 SO4 A 1 503 504 SO4 SO4 . H 5 UNL A 1 504 538 UNL UNK . I 5 UNL A 1 505 539 UNL UNK . J 5 UNL A 1 506 540 UNL UNK . K 5 UNL A 1 507 541 UNL UNK . L 5 UNL A 1 508 542 UNL UNK . M 5 UNL A 1 509 543 UNL UNK . N 5 UNL A 1 510 547 UNL UNK . O 5 UNL A 1 511 548 UNL UNK . P 3 KMP B 1 501 501 KMP KMP . Q 2 UDP B 1 502 502 UDP UDP . R 4 SO4 B 1 503 504 SO4 SO4 . S 5 UNL B 1 504 544 UNL UNK . T 5 UNL B 1 505 545 UNL UNK . U 5 UNL B 1 506 546 UNL UNK . V 5 UNL B 1 507 549 UNL UNK . W 5 UNL B 1 508 550 UNL UNK . X 3 KMP C 1 501 501 KMP KMP . Y 2 UDP C 1 502 502 UDP UDP . Z 2 UDP D 1 501 501 UDP UDP . AA 6 HOH A 1 601 57 HOH HOH . AA 6 HOH A 2 602 230 HOH HOH . AA 6 HOH A 3 603 222 HOH HOH . AA 6 HOH A 4 604 146 HOH HOH . AA 6 HOH A 5 605 47 HOH HOH . AA 6 HOH A 6 606 124 HOH HOH . AA 6 HOH A 7 607 73 HOH HOH . AA 6 HOH A 8 608 232 HOH HOH . AA 6 HOH A 9 609 308 HOH HOH . AA 6 HOH A 10 610 287 HOH HOH . AA 6 HOH A 11 611 77 HOH HOH . AA 6 HOH A 12 612 88 HOH HOH . AA 6 HOH A 13 613 135 HOH HOH . AA 6 HOH A 14 614 142 HOH HOH . AA 6 HOH A 15 615 251 HOH HOH . AA 6 HOH A 16 616 32 HOH HOH . AA 6 HOH A 17 617 60 HOH HOH . AA 6 HOH A 18 618 36 HOH HOH . AA 6 HOH A 19 619 68 HOH HOH . AA 6 HOH A 20 620 7 HOH HOH . AA 6 HOH A 21 621 401 HOH HOH . AA 6 HOH A 22 622 80 HOH HOH . AA 6 HOH A 23 623 452 HOH HOH . AA 6 HOH A 24 624 216 HOH HOH . AA 6 HOH A 25 625 326 HOH HOH . AA 6 HOH A 26 626 78 HOH HOH . AA 6 HOH A 27 627 386 HOH HOH . AA 6 HOH A 28 628 44 HOH HOH . AA 6 HOH A 29 629 162 HOH HOH . AA 6 HOH A 30 630 31 HOH HOH . AA 6 HOH A 31 631 214 HOH HOH . AA 6 HOH A 32 632 2 HOH HOH . AA 6 HOH A 33 633 471 HOH HOH . AA 6 HOH A 34 634 469 HOH HOH . AA 6 HOH A 35 635 63 HOH HOH . AA 6 HOH A 36 636 49 HOH HOH . AA 6 HOH A 37 637 53 HOH HOH . AA 6 HOH A 38 638 90 HOH HOH . AA 6 HOH A 39 639 108 HOH HOH . AA 6 HOH A 40 640 518 HOH HOH . AA 6 HOH A 41 641 172 HOH HOH . AA 6 HOH A 42 642 472 HOH HOH . AA 6 HOH A 43 643 520 HOH HOH . AA 6 HOH A 44 644 5 HOH HOH . AA 6 HOH A 45 645 341 HOH HOH . AA 6 HOH A 46 646 184 HOH HOH . AA 6 HOH A 47 647 389 HOH HOH . AA 6 HOH A 48 648 150 HOH HOH . AA 6 HOH A 49 649 4 HOH HOH . AA 6 HOH A 50 650 464 HOH HOH . AA 6 HOH A 51 651 252 HOH HOH . AA 6 HOH A 52 652 311 HOH HOH . AA 6 HOH A 53 653 512 HOH HOH . BA 6 HOH B 1 601 263 HOH HOH . BA 6 HOH B 2 602 69 HOH HOH . BA 6 HOH B 3 603 470 HOH HOH . BA 6 HOH B 4 604 281 HOH HOH . BA 6 HOH B 5 605 52 HOH HOH . BA 6 HOH B 6 606 5 HOH HOH . BA 6 HOH B 7 607 226 HOH HOH . BA 6 HOH B 8 608 137 HOH HOH . BA 6 HOH B 9 609 179 HOH HOH . BA 6 HOH B 10 610 70 HOH HOH . BA 6 HOH B 11 611 56 HOH HOH . BA 6 HOH B 12 612 109 HOH HOH . BA 6 HOH B 13 613 534 HOH HOH . BA 6 HOH B 14 614 168 HOH HOH . BA 6 HOH B 15 615 443 HOH HOH . BA 6 HOH B 16 616 2 HOH HOH . BA 6 HOH B 17 617 301 HOH HOH . BA 6 HOH B 18 618 186 HOH HOH . BA 6 HOH B 19 619 8 HOH HOH . BA 6 HOH B 20 620 210 HOH HOH . BA 6 HOH B 21 621 505 HOH HOH . BA 6 HOH B 22 622 96 HOH HOH . BA 6 HOH B 23 623 42 HOH HOH . BA 6 HOH B 24 624 113 HOH HOH . BA 6 HOH B 25 625 369 HOH HOH . BA 6 HOH B 26 626 12 HOH HOH . BA 6 HOH B 27 627 296 HOH HOH . BA 6 HOH B 28 628 155 HOH HOH . BA 6 HOH B 29 629 1 HOH HOH . BA 6 HOH B 30 630 199 HOH HOH . BA 6 HOH B 31 631 495 HOH HOH . BA 6 HOH B 32 632 416 HOH HOH . BA 6 HOH B 33 633 238 HOH HOH . BA 6 HOH B 34 634 284 HOH HOH . BA 6 HOH B 35 635 58 HOH HOH . BA 6 HOH B 36 636 138 HOH HOH . BA 6 HOH B 37 637 81 HOH HOH . BA 6 HOH B 38 638 121 HOH HOH . BA 6 HOH B 39 639 195 HOH HOH . BA 6 HOH B 40 640 156 HOH HOH . BA 6 HOH B 41 641 28 HOH HOH . BA 6 HOH B 42 642 102 HOH HOH . BA 6 HOH B 43 643 465 HOH HOH . BA 6 HOH B 44 644 493 HOH HOH . BA 6 HOH B 45 645 38 HOH HOH . BA 6 HOH B 46 646 523 HOH HOH . BA 6 HOH B 47 647 283 HOH HOH . BA 6 HOH B 48 648 431 HOH HOH . BA 6 HOH B 49 649 278 HOH HOH . BA 6 HOH B 50 650 131 HOH HOH . BA 6 HOH B 51 651 325 HOH HOH . BA 6 HOH B 52 652 442 HOH HOH . BA 6 HOH B 53 653 171 HOH HOH . BA 6 HOH B 54 654 407 HOH HOH . BA 6 HOH B 55 655 3 HOH HOH . BA 6 HOH B 56 656 241 HOH HOH . BA 6 HOH B 57 657 521 HOH HOH . BA 6 HOH B 58 658 212 HOH HOH . BA 6 HOH B 59 659 535 HOH HOH . BA 6 HOH B 60 660 479 HOH HOH . BA 6 HOH B 61 661 6 HOH HOH . BA 6 HOH B 62 662 513 HOH HOH . BA 6 HOH B 63 663 552 HOH HOH . BA 6 HOH B 64 664 269 HOH HOH . BA 6 HOH B 65 665 551 HOH HOH . CA 6 HOH C 1 601 4 HOH HOH . CA 6 HOH C 2 602 10 HOH HOH . CA 6 HOH C 3 603 253 HOH HOH . CA 6 HOH C 4 604 59 HOH HOH . CA 6 HOH C 5 605 285 HOH HOH . CA 6 HOH C 6 606 351 HOH HOH . CA 6 HOH C 7 607 46 HOH HOH . CA 6 HOH C 8 608 537 HOH HOH . CA 6 HOH C 9 609 182 HOH HOH . CA 6 HOH C 10 610 180 HOH HOH . CA 6 HOH C 11 611 99 HOH HOH . CA 6 HOH C 12 612 314 HOH HOH . CA 6 HOH C 13 613 267 HOH HOH . CA 6 HOH C 14 614 43 HOH HOH . CA 6 HOH C 15 615 1 HOH HOH . CA 6 HOH C 16 616 527 HOH HOH . CA 6 HOH C 17 617 19 HOH HOH . CA 6 HOH C 18 618 528 HOH HOH . CA 6 HOH C 19 619 196 HOH HOH . CA 6 HOH C 20 620 118 HOH HOH . CA 6 HOH C 21 621 122 HOH HOH . CA 6 HOH C 22 622 101 HOH HOH . CA 6 HOH C 23 623 553 HOH HOH . CA 6 HOH C 24 624 189 HOH HOH . CA 6 HOH C 25 625 82 HOH HOH . CA 6 HOH C 26 626 259 HOH HOH . CA 6 HOH C 27 627 54 HOH HOH . CA 6 HOH C 28 628 85 HOH HOH . CA 6 HOH C 29 629 274 HOH HOH . CA 6 HOH C 30 630 524 HOH HOH . CA 6 HOH C 31 631 271 HOH HOH . CA 6 HOH C 32 632 229 HOH HOH . CA 6 HOH C 33 633 79 HOH HOH . CA 6 HOH C 34 634 205 HOH HOH . CA 6 HOH C 35 635 498 HOH HOH . CA 6 HOH C 36 636 342 HOH HOH . CA 6 HOH C 37 637 504 HOH HOH . CA 6 HOH C 38 638 525 HOH HOH . CA 6 HOH C 39 639 484 HOH HOH . DA 6 HOH D 1 601 405 HOH HOH . DA 6 HOH D 2 602 425 HOH HOH . DA 6 HOH D 3 603 6 HOH HOH . DA 6 HOH D 4 604 147 HOH HOH . DA 6 HOH D 5 605 14 HOH HOH . DA 6 HOH D 6 606 13 HOH HOH . DA 6 HOH D 7 607 499 HOH HOH . DA 6 HOH D 8 608 144 HOH HOH . DA 6 HOH D 9 609 107 HOH HOH . DA 6 HOH D 10 610 48 HOH HOH . DA 6 HOH D 11 611 517 HOH HOH . DA 6 HOH D 12 612 136 HOH HOH . DA 6 HOH D 13 613 39 HOH HOH . DA 6 HOH D 14 614 310 HOH HOH . DA 6 HOH D 15 615 332 HOH HOH . DA 6 HOH D 16 616 178 HOH HOH . DA 6 HOH D 17 617 30 HOH HOH . DA 6 HOH D 18 618 33 HOH HOH . DA 6 HOH D 19 619 97 HOH HOH . DA 6 HOH D 20 620 185 HOH HOH . DA 6 HOH D 21 621 265 HOH HOH . DA 6 HOH D 22 622 235 HOH HOH . DA 6 HOH D 23 623 87 HOH HOH . DA 6 HOH D 24 624 34 HOH HOH . DA 6 HOH D 25 625 515 HOH HOH . DA 6 HOH D 26 626 111 HOH HOH . DA 6 HOH D 27 627 200 HOH HOH . DA 6 HOH D 28 628 86 HOH HOH . DA 6 HOH D 29 629 514 HOH HOH . DA 6 HOH D 30 630 346 HOH HOH . DA 6 HOH D 31 631 529 HOH HOH . DA 6 HOH D 32 632 462 HOH HOH . DA 6 HOH D 33 633 329 HOH HOH . DA 6 HOH D 34 634 491 HOH HOH . DA 6 HOH D 35 635 488 HOH HOH . DA 6 HOH D 36 636 516 HOH HOH . DA 6 HOH D 37 637 231 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 . . . Q 2 31.607 -9.314 38.064 1 51.21 0 N1 UDP 502 B 1 HETATM 2 C C2 UDP . . . Q 2 32.465 -9.014 39.104 1 49.72 0 C2 UDP 502 B 1 HETATM 3 N N3 UDP . . . Q 2 32.056 -9.458 40.334 1 52.9 0 N3 UDP 502 B 1 HETATM 4 C C4 UDP . . . Q 2 30.903 -10.159 40.625 1 55.1 0 C4 UDP 502 B 1 HETATM 5 C C5 UDP . . . Q 2 30.066 -10.432 39.493 1 51.35 0 C5 UDP 502 B 1 HETATM 6 C C6 UDP . . . Q 2 30.44 -10.009 38.276 1 52.15 0 C6 UDP 502 B 1 HETATM 7 O O2 UDP . . . Q 2 33.51 -8.398 38.946 1 50.45 0 O2 UDP 502 B 1 HETATM 8 O O4 UDP . . . Q 2 30.674 -10.489 41.788 1 56.17 0 O4 UDP 502 B 1 HETATM 9 C C1' UDP . . . Q 2 31.998 -8.859 36.717 1 48.1 0 C1' UDP 502 B 1 HETATM 10 C C2' UDP . . . Q 2 32.774 -9.918 35.939 1 46.82 0 C2' UDP 502 B 1 HETATM 11 O O2' UDP . . . Q 2 34.142 -9.816 36.268 1 47.04 0 O2' UDP 502 B 1 HETATM 12 C C3' UDP . . . Q 2 32.47 -9.515 34.491 1 49.34 0 C3' UDP 502 B 1 HETATM 13 C C4' UDP . . . Q 2 31.063 -8.897 34.571 1 48.38 0 C4' UDP 502 B 1 HETATM 14 O O4' UDP . . . Q 2 30.829 -8.605 35.974 1 46.26 0 O4' UDP 502 B 1 HETATM 15 O O3' UDP . . . Q 2 33.417 -8.577 33.997 1 43.5 0 O3' UDP 502 B 1 HETATM 16 C C5' UDP . . . Q 2 29.941 -9.752 34.038 1 48.33 0 C5' UDP 502 B 1 HETATM 17 O O5' UDP . . . Q 2 29.942 -9.684 32.592 1 48.6 0 O5' UDP 502 B 1 HETATM 18 P PA UDP . . . Q 2 29.612 -11.005 31.747 1 51.28 0 PA UDP 502 B 1 HETATM 19 O O1A UDP . . . Q 2 29.758 -10.709 30.292 1 41.98 0 O1A UDP 502 B 1 HETATM 20 O O2A UDP . . . Q 2 30.373 -12.153 32.317 1 41.66 0 O2A UDP 502 B 1 HETATM 21 O O3A UDP . . . Q 2 28.058 -11.219 32.073 1 49.9 0 O3A UDP 502 B 1 HETATM 22 P PB UDP . . . Q 2 26.775 -10.246 32.116 1 48.68 0 PB UDP 502 B 1 HETATM 23 O O1B UDP . . . Q 2 26.964 -9.251 31.003 1 52.18 0 O1B UDP 502 B 1 HETATM 24 O O2B UDP . . . Q 2 25.582 -11.136 31.898 1 51.99 0 O2B UDP 502 B 1 HETATM 25 O O3B UDP . . . Q 2 26.782 -9.612 33.478 1 53.53 0 O3B UDP 502 B 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #