data_6ZLJ # _model_server_result.job_id uqcYDF9d4DfpN0ShCE3FgQ _model_server_result.datetime_utc '2024-11-07 18:59:31' _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 6zlj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":802}' # _entry.id 6ZLJ # _exptl.entry_id 6ZLJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 582.276 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{R},3~{S},4~{R},5~{R},6~{R})-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidany l)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-fluoranyl-4,5-bis(oxidanyl)oxane-2-carboxylic acid' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 97.25 _cell.angle_beta 98.18 _cell.angle_gamma 109.93 _cell.entry_id 6ZLJ _cell.length_a 42.199 _cell.length_b 58.222 _cell.length_c 64.439 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZLJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 1_455 x-1,y,z 1 0 0 0 1 0 0 0 1 -42.199 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C15 H21 F N2 O17 P2' _chem_comp.formula_weight 582.276 _chem_comp.id UGF _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{R},3~{S},4~{R},5~{R},6~{R})-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidany l)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-fluoranyl-4,5-bis(oxidanyl)oxane-2-carboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'UDP-4-Deoxy-4-Fluoro-Glucuronic acid' # 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 O2D C2D UGF sing 433 n n C2D C1D UGF sing 434 n n C2D C3D UGF sing 435 n n O2 C2 UGF doub 436 n n O4 C4 UGF doub 437 n n N3 C2 UGF sing 438 n n N3 C4 UGF sing 439 n n O3D C3D UGF sing 440 n n C2 N1 UGF sing 441 n n C4 C5 UGF sing 442 n n N1 C6 UGF sing 443 n n N1 C1D UGF sing 444 n n C5 C6 UGF doub 445 n n C1D O4D UGF sing 446 n n C3D C4D UGF sing 447 n n O2B PB UGF doub 448 n n O1A PA UGF doub 449 n n O4D C4D UGF sing 450 n n F4' C4' UGF sing 451 n n C4D C5D UGF sing 452 n n PB O3B UGF sing 453 n n PB O1B UGF sing 454 n n PB O3A UGF sing 455 n n O5D PA UGF sing 456 n n O5D C5D UGF sing 457 n n O3B C1' UGF sing 458 n n C3' O3' UGF sing 459 n n C3' C4' UGF sing 460 n n C3' C2' UGF sing 461 n n O2' C2' UGF sing 462 n n PA O3A UGF sing 463 n n PA O2A UGF sing 464 n n C4' C5' UGF sing 465 n n C5' C6' UGF sing 466 n n C5' O5' UGF sing 467 n n C2' C1' UGF sing 468 n n "O'Q" C6' UGF doub 469 n n C1' O5' UGF sing 470 n n C6' "O'P" UGF sing 471 n n N3 H1 UGF sing 472 n n C5 H2 UGF sing 473 n n C6 H3 UGF sing 474 n n C1D H4 UGF sing 475 n n C2D H5 UGF sing 476 n n O2D H6 UGF sing 477 n n C3D H7 UGF sing 478 n n O3D H8 UGF sing 479 n n C4D H9 UGF sing 480 n n C5D H10 UGF sing 481 n n C5D H11 UGF sing 482 n n O2A H12 UGF sing 483 n n O1B H13 UGF sing 484 n n C1' H14 UGF sing 485 n n C5' H15 UGF sing 486 n n "O'P" H16 UGF sing 487 n n C4' H17 UGF sing 488 n n C3' H18 UGF sing 489 n n O3' H19 UGF sing 490 n n C2' H20 UGF sing 491 n n O2' H21 UGF sing 492 n n # _atom_sites.entry_id 6ZLJ _atom_sites.fract_transf_matrix[1][1] 0.023697 _atom_sites.fract_transf_matrix[1][2] 0.00859 _atom_sites.fract_transf_matrix[1][3] 0.005111 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018269 _atom_sites.fract_transf_matrix[2][3] 0.003491 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015962 _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 NAD A 1 401 401 NAD NAD . D 3 UGF A 1 402 402 UGF UGF . E 2 NAD B 1 801 801 NAD NAD . F 3 UGF B 1 802 802 UGF UGF . G 4 HOH A 1 501 501 HOH HOH . G 4 HOH A 2 502 502 HOH HOH . G 4 HOH A 3 503 503 HOH HOH . G 4 HOH A 4 504 508 HOH HOH . G 4 HOH A 5 505 505 HOH HOH . G 4 HOH A 6 506 506 HOH HOH . G 4 HOH A 7 507 504 HOH HOH . G 4 HOH A 8 508 507 HOH HOH . G 4 HOH A 9 509 510 HOH HOH . G 4 HOH A 10 510 509 HOH HOH . G 4 HOH A 11 511 512 HOH HOH . G 4 HOH A 12 512 511 HOH HOH . G 4 HOH A 13 513 513 HOH HOH . G 4 HOH A 14 514 514 HOH HOH . G 4 HOH A 15 515 518 HOH HOH . G 4 HOH A 16 516 517 HOH HOH . G 4 HOH A 17 517 520 HOH HOH . G 4 HOH A 18 518 519 HOH HOH . G 4 HOH A 19 519 516 HOH HOH . G 4 HOH A 20 520 515 HOH HOH . G 4 HOH A 21 521 521 HOH HOH . G 4 HOH A 22 522 524 HOH HOH . G 4 HOH A 23 523 523 HOH HOH . G 4 HOH A 24 524 522 HOH HOH . G 4 HOH A 25 525 525 HOH HOH . G 4 HOH A 26 526 526 HOH HOH . G 4 HOH A 27 527 527 HOH HOH . G 4 HOH A 28 528 528 HOH HOH . G 4 HOH A 29 529 536 HOH HOH . G 4 HOH A 30 530 529 HOH HOH . G 4 HOH A 31 531 531 HOH HOH . G 4 HOH A 32 532 530 HOH HOH . G 4 HOH A 33 533 532 HOH HOH . G 4 HOH A 34 534 534 HOH HOH . G 4 HOH A 35 535 535 HOH HOH . G 4 HOH A 36 536 540 HOH HOH . G 4 HOH A 37 537 539 HOH HOH . G 4 HOH A 38 538 542 HOH HOH . G 4 HOH A 39 539 533 HOH HOH . G 4 HOH A 40 540 537 HOH HOH . G 4 HOH A 41 541 545 HOH HOH . G 4 HOH A 42 542 538 HOH HOH . G 4 HOH A 43 543 546 HOH HOH . G 4 HOH A 44 544 547 HOH HOH . G 4 HOH A 45 545 543 HOH HOH . G 4 HOH A 46 546 544 HOH HOH . G 4 HOH A 47 547 541 HOH HOH . G 4 HOH A 48 548 553 HOH HOH . G 4 HOH A 49 549 548 HOH HOH . G 4 HOH A 50 550 554 HOH HOH . G 4 HOH A 51 551 552 HOH HOH . G 4 HOH A 52 552 550 HOH HOH . G 4 HOH A 53 553 551 HOH HOH . G 4 HOH A 54 554 549 HOH HOH . G 4 HOH A 55 555 558 HOH HOH . G 4 HOH A 56 556 557 HOH HOH . G 4 HOH A 57 557 555 HOH HOH . G 4 HOH A 58 558 556 HOH HOH . G 4 HOH A 59 559 561 HOH HOH . G 4 HOH A 60 560 562 HOH HOH . G 4 HOH A 61 561 559 HOH HOH . G 4 HOH A 62 562 560 HOH HOH . G 4 HOH A 63 563 963 HOH HOH . G 4 HOH A 64 564 564 HOH HOH . G 4 HOH A 65 565 563 HOH HOH . G 4 HOH A 66 566 565 HOH HOH . G 4 HOH A 67 567 566 HOH HOH . G 4 HOH A 68 568 569 HOH HOH . G 4 HOH A 69 569 570 HOH HOH . G 4 HOH A 70 570 568 HOH HOH . G 4 HOH A 71 571 567 HOH HOH . G 4 HOH A 72 572 976 HOH HOH . G 4 HOH A 73 573 571 HOH HOH . G 4 HOH A 74 574 572 HOH HOH . G 4 HOH A 75 575 573 HOH HOH . G 4 HOH A 76 576 574 HOH HOH . G 4 HOH A 77 577 575 HOH HOH . G 4 HOH A 78 578 576 HOH HOH . G 4 HOH A 79 579 577 HOH HOH . G 4 HOH A 80 580 578 HOH HOH . H 4 HOH B 1 901 901 HOH HOH . H 4 HOH B 2 902 902 HOH HOH . H 4 HOH B 3 903 903 HOH HOH . H 4 HOH B 4 904 904 HOH HOH . H 4 HOH B 5 905 906 HOH HOH . H 4 HOH B 6 906 905 HOH HOH . H 4 HOH B 7 907 908 HOH HOH . H 4 HOH B 8 908 907 HOH HOH . H 4 HOH B 9 909 911 HOH HOH . H 4 HOH B 10 910 910 HOH HOH . H 4 HOH B 11 911 912 HOH HOH . H 4 HOH B 12 912 914 HOH HOH . H 4 HOH B 13 913 909 HOH HOH . H 4 HOH B 14 914 913 HOH HOH . H 4 HOH B 15 915 917 HOH HOH . H 4 HOH B 16 916 916 HOH HOH . H 4 HOH B 17 917 915 HOH HOH . H 4 HOH B 18 918 926 HOH HOH . H 4 HOH B 19 919 918 HOH HOH . H 4 HOH B 20 920 921 HOH HOH . H 4 HOH B 21 921 920 HOH HOH . H 4 HOH B 22 922 923 HOH HOH . H 4 HOH B 23 923 927 HOH HOH . H 4 HOH B 24 924 922 HOH HOH . H 4 HOH B 25 925 925 HOH HOH . H 4 HOH B 26 926 932 HOH HOH . H 4 HOH B 27 927 931 HOH HOH . H 4 HOH B 28 928 928 HOH HOH . H 4 HOH B 29 929 919 HOH HOH . H 4 HOH B 30 930 929 HOH HOH . H 4 HOH B 31 931 933 HOH HOH . H 4 HOH B 32 932 924 HOH HOH . H 4 HOH B 33 933 930 HOH HOH . H 4 HOH B 34 934 936 HOH HOH . H 4 HOH B 35 935 935 HOH HOH . H 4 HOH B 36 936 934 HOH HOH . H 4 HOH B 37 937 937 HOH HOH . H 4 HOH B 38 938 938 HOH HOH . H 4 HOH B 39 939 940 HOH HOH . H 4 HOH B 40 940 942 HOH HOH . H 4 HOH B 41 941 939 HOH HOH . H 4 HOH B 42 942 946 HOH HOH . H 4 HOH B 43 943 947 HOH HOH . H 4 HOH B 44 944 945 HOH HOH . H 4 HOH B 45 945 944 HOH HOH . H 4 HOH B 46 946 943 HOH HOH . H 4 HOH B 47 947 950 HOH HOH . H 4 HOH B 48 948 948 HOH HOH . H 4 HOH B 49 949 951 HOH HOH . H 4 HOH B 50 950 941 HOH HOH . H 4 HOH B 51 951 953 HOH HOH . H 4 HOH B 52 952 949 HOH HOH . H 4 HOH B 53 953 952 HOH HOH . H 4 HOH B 54 954 955 HOH HOH . H 4 HOH B 55 955 954 HOH HOH . H 4 HOH B 56 956 956 HOH HOH . H 4 HOH B 57 957 959 HOH HOH . H 4 HOH B 58 958 957 HOH HOH . H 4 HOH B 59 959 958 HOH HOH . H 4 HOH B 60 960 962 HOH HOH . H 4 HOH B 61 961 961 HOH HOH . H 4 HOH B 62 962 960 HOH HOH . H 4 HOH B 63 963 965 HOH HOH . H 4 HOH B 64 964 966 HOH HOH . H 4 HOH B 65 965 964 HOH HOH . H 4 HOH B 66 966 967 HOH HOH . H 4 HOH B 67 967 969 HOH HOH . H 4 HOH B 68 968 968 HOH HOH . H 4 HOH B 69 969 971 HOH HOH . H 4 HOH B 70 970 972 HOH HOH . H 4 HOH B 71 971 970 HOH HOH . H 4 HOH B 72 972 977 HOH HOH . H 4 HOH B 73 973 975 HOH HOH . H 4 HOH B 74 974 973 HOH HOH . H 4 HOH B 75 975 974 HOH HOH . H 4 HOH B 76 976 979 HOH HOH . H 4 HOH B 77 977 978 HOH HOH . H 4 HOH B 78 978 980 HOH HOH . H 4 HOH B 79 979 981 HOH HOH . H 4 HOH B 80 980 982 HOH HOH . H 4 HOH B 81 981 983 HOH HOH . H 4 HOH B 82 982 985 HOH HOH . H 4 HOH B 83 983 984 HOH HOH . H 4 HOH B 84 984 987 HOH HOH . H 4 HOH B 85 985 986 HOH HOH . H 4 HOH B 86 986 988 HOH HOH . H 4 HOH B 87 987 989 HOH HOH . H 4 HOH B 88 988 990 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 O O2 UGF . . . F 3 30.702 -34.702 -20.627 1 32.86 ? O2 UGF 802 B 1 HETATM 2 C C2 UGF . . . F 3 31.418 -34.082 -21.419 1 31.07 ? C2 UGF 802 B 1 HETATM 3 N N3 UGF . . . F 3 32.304 -34.819 -22.155 1 29.83 ? N3 UGF 802 B 1 HETATM 4 C C4 UGF . . . F 3 33.143 -34.254 -23.096 1 29.84 ? C4 UGF 802 B 1 HETATM 5 O O4 UGF . . . F 3 33.928 -34.964 -23.734 1 30.59 ? O4 UGF 802 B 1 HETATM 6 C C5 UGF . . . F 3 33.113 -32.877 -23.22 1 27.59 ? C5 UGF 802 B 1 HETATM 7 C C6 UGF . . . F 3 32.21 -32.134 -22.461 1 27.9 ? C6 UGF 802 B 1 HETATM 8 N N1 UGF . . . F 3 31.363 -32.744 -21.548 1 28.6 ? N1 UGF 802 B 1 HETATM 9 C C1D UGF . . . F 3 30.389 -31.979 -20.745 1 30.85 ? C1D UGF 802 B 1 HETATM 10 O O4D UGF . . . F 3 29.457 -31.554 -21.69 1 31.98 ? O4D UGF 802 B 1 HETATM 11 C C2D UGF . . . F 3 30.91 -30.724 -20.142 1 31.64 ? C2D UGF 802 B 1 HETATM 12 O O2D UGF . . . F 3 31.447 -31.024 -18.84 1 34.57 ? O2D UGF 802 B 1 HETATM 13 C C3D UGF . . . F 3 29.699 -29.889 -20.067 1 30.23 ? C3D UGF 802 B 1 HETATM 14 O O3D UGF . . . F 3 28.976 -30.163 -18.906 1 33.4 ? O3D UGF 802 B 1 HETATM 15 C C4D UGF . . . F 3 28.889 -30.321 -21.23 1 30.29 ? C4D UGF 802 B 1 HETATM 16 C C5D UGF . . . F 3 28.952 -29.294 -22.415 1 30.44 ? C5D UGF 802 B 1 HETATM 17 O O5D UGF . . . F 3 30.304 -29.057 -22.737 1 32.62 ? O5D UGF 802 B 1 HETATM 18 P PA UGF . . . F 3 30.6 -28.224 -24.18 1 33.4 ? PA UGF 802 B 1 HETATM 19 O O1A UGF . . . F 3 32.042 -28.107 -24.246 1 34.98 ? O1A UGF 802 B 1 HETATM 20 O O2A UGF . . . F 3 29.799 -28.767 -25.2 1 36.38 ? O2A UGF 802 B 1 HETATM 21 O O3A UGF . . . F 3 29.871 -26.789 -23.785 1 35.65 ? O3A UGF 802 B 1 HETATM 22 P PB UGF . . . F 3 30.045 -25.807 -22.509 1 35.27 ? PB UGF 802 B 1 HETATM 23 O O1B UGF . . . F 3 28.724 -25.483 -21.92 1 37.89 ? O1B UGF 802 B 1 HETATM 24 O O2B UGF . . . F 3 31.16 -26.173 -21.654 1 37.22 ? O2B UGF 802 B 1 HETATM 25 O O3B UGF . . . F 3 30.796 -24.482 -23.253 1 35.86 ? O3B UGF 802 B 1 HETATM 26 C C1' UGF . . . F 3 30.35 -23.857 -24.455 1 40.57 ? C1' UGF 802 B 1 HETATM 27 O O5' UGF . . . F 3 29.393 -22.874 -24.218 1 43.7 ? O5' UGF 802 B 1 HETATM 28 C C5' UGF . . . F 3 29.842 -21.977 -23.214 1 46.14 ? C5' UGF 802 B 1 HETATM 29 C C6' UGF . . . F 3 28.649 -21.153 -22.637 1 48.93 ? C6' UGF 802 B 1 HETATM 30 O "O'P" UGF . . . F 3 27.656 -20.877 -23.357 1 38.96 ? "O'P" UGF 802 B 1 HETATM 31 O "O'Q" UGF . . . F 3 28.754 -20.843 -21.436 1 59.74 ? "O'Q" UGF 802 B 1 HETATM 32 C C4' UGF . . . F 3 30.855 -21.115 -23.97 1 45.72 ? C4' UGF 802 B 1 HETATM 33 F F4' UGF . . . F 3 31.233 -20.109 -23.23 1 41.11 ? F4' UGF 802 B 1 HETATM 34 C C3' UGF . . . F 3 32.051 -22.021 -24.462 1 43.16 ? C3' UGF 802 B 1 HETATM 35 O O3' UGF . . . F 3 32.844 -21.335 -25.404 1 43.04 ? O3' UGF 802 B 1 HETATM 36 C C2' UGF . . . F 3 31.544 -23.237 -25.184 1 39.72 ? C2' UGF 802 B 1 HETATM 37 O O2' UGF . . . F 3 32.577 -24.191 -25.207 1 38.29 ? O2' UGF 802 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 37 #