data_4ZYJ # _model_server_result.job_id Bz-7x_O6PsopQuCzeqeXCA _model_server_result.datetime_utc '2025-01-02 19:33:53' _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 4zyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 4ZYJ # _exptl.entry_id 4ZYJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 4ZYJ _cell.length_a 100.483 _cell.length_b 134.667 _cell.length_c 144.294 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZYJ _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,I,J,K,L _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 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A TYD doub 334 n n PA O2A TYD sing 335 n n PA O3A TYD sing 336 n n PA O5' TYD sing 337 n n O2A HOA2 TYD sing 338 n n O3A PB TYD sing 339 n n PB O1B TYD doub 340 n n PB O2B TYD sing 341 n n PB O3B TYD sing 342 n n O2B HOB2 TYD sing 343 n n O3B HOB3 TYD sing 344 n n O5' C5' TYD sing 345 n n C5' C4' TYD sing 346 n n C5' "H5'1" TYD sing 347 n n C5' "H5'2" TYD sing 348 n n C4' O4' TYD sing 349 n n C4' C3' TYD sing 350 n n C4' H4' TYD sing 351 n n O4' C1' TYD sing 352 n n C3' O3' TYD sing 353 n n C3' C2' TYD sing 354 n n C3' H3' TYD sing 355 n n O3' HO3' TYD sing 356 n n C2' C1' TYD sing 357 n n C2' "H2'1" TYD sing 358 n n C2' "H2'2" TYD sing 359 n n C1' N1 TYD sing 360 n n C1' H1' TYD sing 361 n n N1 C2 TYD sing 362 n y N1 C6 TYD sing 363 n y C2 O2 TYD doub 364 n n C2 N3 TYD sing 365 n y N3 C4 TYD sing 366 n y N3 HN3 TYD sing 367 n n C4 O4 TYD doub 368 n n C4 C5 TYD sing 369 n y C5 C5M TYD sing 370 n n C5 C6 TYD doub 371 n y C5M H51 TYD sing 372 n n C5M H52 TYD sing 373 n n C5M H53 TYD sing 374 n n C6 H6 TYD sing 375 n n # _atom_sites.entry_id 4ZYJ _atom_sites.fract_transf_matrix[1][1] 0.009952 _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] 0.007426 _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] 0.00693 _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 TYD A 1 501 2 TYD TYD . F 2 TYD B 1 501 1 TYD TYD . G 2 TYD C 1 501 3 TYD TYD . H 2 TYD D 1 501 4 TYD TYD . I 3 HOH A 1 601 36 HOH HOH . I 3 HOH A 2 602 37 HOH HOH . I 3 HOH A 3 603 91 HOH HOH . I 3 HOH A 4 604 82 HOH HOH . I 3 HOH A 5 605 16 HOH HOH . I 3 HOH A 6 606 25 HOH HOH . I 3 HOH A 7 607 38 HOH HOH . I 3 HOH A 8 608 4 HOH HOH . I 3 HOH A 9 609 97 HOH HOH . I 3 HOH A 10 610 20 HOH HOH . I 3 HOH A 11 611 14 HOH HOH . I 3 HOH A 12 612 59 HOH HOH . I 3 HOH A 13 613 17 HOH HOH . I 3 HOH A 14 614 5 HOH HOH . I 3 HOH A 15 615 3 HOH HOH . I 3 HOH A 16 616 72 HOH HOH . I 3 HOH A 17 617 15 HOH HOH . I 3 HOH A 18 618 29 HOH HOH . I 3 HOH A 19 619 39 HOH HOH . I 3 HOH A 20 620 35 HOH HOH . I 3 HOH A 21 621 98 HOH HOH . I 3 HOH A 22 622 22 HOH HOH . I 3 HOH A 23 623 26 HOH HOH . I 3 HOH A 24 624 58 HOH HOH . I 3 HOH A 25 625 96 HOH HOH . I 3 HOH A 26 626 54 HOH HOH . I 3 HOH A 27 627 13 HOH HOH . I 3 HOH A 28 628 51 HOH HOH . I 3 HOH A 29 629 100 HOH HOH . I 3 HOH A 30 630 65 HOH HOH . I 3 HOH A 31 631 67 HOH HOH . I 3 HOH A 32 632 103 HOH HOH . I 3 HOH A 33 633 40 HOH HOH . I 3 HOH A 34 634 95 HOH HOH . I 3 HOH A 35 635 1 HOH HOH . I 3 HOH A 36 636 2 HOH HOH . I 3 HOH A 37 637 68 HOH HOH . I 3 HOH A 38 638 27 HOH HOH . I 3 HOH A 39 639 66 HOH HOH . I 3 HOH A 40 640 102 HOH HOH . I 3 HOH A 41 641 52 HOH HOH . I 3 HOH A 42 642 99 HOH HOH . I 3 HOH A 43 643 111 HOH HOH . J 3 HOH B 1 601 76 HOH HOH . J 3 HOH B 2 602 24 HOH HOH . J 3 HOH B 3 603 8 HOH HOH . J 3 HOH B 4 604 56 HOH HOH . J 3 HOH B 5 605 77 HOH HOH . J 3 HOH B 6 606 88 HOH HOH . J 3 HOH B 7 607 32 HOH HOH . J 3 HOH B 8 608 70 HOH HOH . J 3 HOH B 9 609 6 HOH HOH . J 3 HOH B 10 610 73 HOH HOH . J 3 HOH B 11 611 7 HOH HOH . J 3 HOH B 12 612 104 HOH HOH . J 3 HOH B 13 613 55 HOH HOH . J 3 HOH B 14 614 62 HOH HOH . J 3 HOH B 15 615 101 HOH HOH . J 3 HOH B 16 616 23 HOH HOH . J 3 HOH B 17 617 28 HOH HOH . J 3 HOH B 18 618 53 HOH HOH . J 3 HOH B 19 619 34 HOH HOH . J 3 HOH B 20 620 69 HOH HOH . J 3 HOH B 21 621 30 HOH HOH . K 3 HOH C 1 601 42 HOH HOH . K 3 HOH C 2 602 44 HOH HOH . K 3 HOH C 3 603 41 HOH HOH . K 3 HOH C 4 604 9 HOH HOH . K 3 HOH C 5 605 71 HOH HOH . K 3 HOH C 6 606 74 HOH HOH . K 3 HOH C 7 607 109 HOH HOH . K 3 HOH C 8 608 43 HOH HOH . K 3 HOH C 9 609 11 HOH HOH . K 3 HOH C 10 610 63 HOH HOH . K 3 HOH C 11 611 10 HOH HOH . K 3 HOH C 12 612 83 HOH HOH . K 3 HOH C 13 613 50 HOH HOH . K 3 HOH C 14 614 85 HOH HOH . K 3 HOH C 15 615 108 HOH HOH . K 3 HOH C 16 616 105 HOH HOH . K 3 HOH C 17 617 107 HOH HOH . K 3 HOH C 18 618 106 HOH HOH . K 3 HOH C 19 619 84 HOH HOH . K 3 HOH C 20 620 75 HOH HOH . K 3 HOH C 21 621 110 HOH HOH . K 3 HOH C 22 622 60 HOH HOH . L 3 HOH D 1 601 49 HOH HOH . L 3 HOH D 2 602 57 HOH HOH . L 3 HOH D 3 603 92 HOH HOH . L 3 HOH D 4 604 47 HOH HOH . L 3 HOH D 5 605 48 HOH HOH . L 3 HOH D 6 606 33 HOH HOH . L 3 HOH D 7 607 79 HOH HOH . L 3 HOH D 8 608 31 HOH HOH . L 3 HOH D 9 609 18 HOH HOH . L 3 HOH D 10 610 45 HOH HOH . L 3 HOH D 11 611 21 HOH HOH . L 3 HOH D 12 612 86 HOH HOH . L 3 HOH D 13 613 64 HOH HOH . L 3 HOH D 14 614 80 HOH HOH . L 3 HOH D 15 615 46 HOH HOH . L 3 HOH D 16 616 87 HOH HOH . L 3 HOH D 17 617 90 HOH HOH . L 3 HOH D 18 618 81 HOH HOH . L 3 HOH D 19 619 89 HOH HOH . L 3 HOH D 20 620 12 HOH HOH . L 3 HOH D 21 621 94 HOH HOH . L 3 HOH D 22 622 19 HOH HOH . L 3 HOH D 23 623 112 HOH HOH . L 3 HOH D 24 624 61 HOH HOH . L 3 HOH D 25 625 113 HOH HOH . L 3 HOH D 26 626 93 HOH HOH . L 3 HOH D 27 627 78 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 P PA TYD . . . F 2 -73.392 6.279 -6.085 1 144.56 ? PA TYD 501 B 1 HETATM 2 O O1A TYD . . . F 2 -73.905 7.274 -7.096 1 142.39 ? O1A TYD 501 B 1 HETATM 3 O O2A TYD . . . F 2 -73.664 4.81 -6.357 1 125.14 ? O2A TYD 501 B 1 HETATM 4 O O3A TYD . . . F 2 -73.964 6.685 -4.615 1 160.26 ? O3A TYD 501 B 1 HETATM 5 P PB TYD . . . F 2 -75.33 6.137 -3.917 1 175.79 ? PB TYD 501 B 1 HETATM 6 O O1B TYD . . . F 2 -76.464 6.642 -4.782 1 167.96 ? O1B TYD 501 B 1 HETATM 7 O O2B TYD . . . F 2 -75.315 6.751 -2.537 1 176.02 ? O2B TYD 501 B 1 HETATM 8 O O3B TYD . . . F 2 -75.185 4.632 -3.885 1 173.36 ? O3B TYD 501 B 1 HETATM 9 O O5' TYD . . . F 2 -71.789 6.518 -5.931 1 127.29 ? O5' TYD 501 B 1 HETATM 10 C C5' TYD . . . F 2 -71.194 7.816 -5.954 1 96 ? C5' TYD 501 B 1 HETATM 11 C C4' TYD . . . F 2 -70.455 8.051 -7.269 1 80.99 ? C4' TYD 501 B 1 HETATM 12 O O4' TYD . . . F 2 -70.005 6.836 -7.882 1 76.76 ? O4' TYD 501 B 1 HETATM 13 C C3' TYD . . . F 2 -71.311 8.733 -8.313 1 76.04 ? C3' TYD 501 B 1 HETATM 14 O O3' TYD . . . F 2 -70.52 9.768 -8.912 1 78.24 ? O3' TYD 501 B 1 HETATM 15 C C2' TYD . . . F 2 -71.581 7.668 -9.363 1 75.34 ? C2' TYD 501 B 1 HETATM 16 C C1' TYD . . . F 2 -70.346 6.791 -9.283 1 67.57 ? C1' TYD 501 B 1 HETATM 17 N N1 TYD . . . F 2 -70.526 5.401 -9.734 1 59.45 ? N1 TYD 501 B 1 HETATM 18 C C2 TYD . . . F 2 -69.812 4.895 -10.851 1 61.26 ? C2 TYD 501 B 1 HETATM 19 O O2 TYD . . . F 2 -69.041 5.663 -11.477 1 67.79 ? O2 TYD 501 B 1 HETATM 20 N N3 TYD . . . F 2 -69.951 3.604 -11.256 1 60.34 ? N3 TYD 501 B 1 HETATM 21 C C4 TYD . . . F 2 -70.745 2.74 -10.582 1 62.83 ? C4 TYD 501 B 1 HETATM 22 O O4 TYD . . . F 2 -70.873 1.542 -10.947 1 60.14 ? O4 TYD 501 B 1 HETATM 23 C C5 TYD . . . F 2 -71.49 3.243 -9.398 1 57.54 ? C5 TYD 501 B 1 HETATM 24 C C5M TYD . . . F 2 -72.404 2.361 -8.588 1 59.56 ? C5M TYD 501 B 1 HETATM 25 C C6 TYD . . . F 2 -71.327 4.574 -9.044 1 59.4 ? C6 TYD 501 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #