data_6ZLJ # _model_server_result.job_id BO8Z2ipr7wvMqsSYiBnEnQ _model_server_result.datetime_utc '2024-11-30 17:30:44' _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":"D","auth_seq_id":402}' # _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 . . . D 3 -4.649 17.687 -7.766 1 25.15 ? O2 UGF 402 A 1 HETATM 2 C C2 UGF . . . D 3 -3.636 16.992 -7.664 1 26.48 ? C2 UGF 402 A 1 HETATM 3 N N3 UGF . . . D 3 -2.378 17.598 -7.723 1 25.91 ? N3 UGF 402 A 1 HETATM 4 C C4 UGF . . . D 3 -1.211 16.898 -7.646 1 27.19 ? C4 UGF 402 A 1 HETATM 5 O O4 UGF . . . D 3 -0.119 17.484 -7.75 1 28.39 ? O4 UGF 402 A 1 HETATM 6 C C5 UGF . . . D 3 -1.317 15.508 -7.506 1 27.19 ? C5 UGF 402 A 1 HETATM 7 C C6 UGF . . . D 3 -2.568 14.908 -7.429 1 24.29 ? C6 UGF 402 A 1 HETATM 8 N N1 UGF . . . D 3 -3.72 15.65 -7.511 1 26.88 ? N1 UGF 402 A 1 HETATM 9 C C1D UGF . . . D 3 -5.031 15.021 -7.404 1 25.76 ? C1D UGF 402 A 1 HETATM 10 O O4D UGF . . . D 3 -5.076 14.712 -5.987 1 25.26 ? O4D UGF 402 A 1 HETATM 11 C C2D UGF . . . D 3 -5.182 13.756 -8.171 1 27.11 ? C2D UGF 402 A 1 HETATM 12 O O2D UGF . . . D 3 -5.784 14.111 -9.45 1 28.08 ? O2D UGF 402 A 1 HETATM 13 C C3D UGF . . . D 3 -6.172 12.982 -7.278 1 25.79 ? C3D UGF 402 A 1 HETATM 14 O O3D UGF . . . D 3 -7.573 13.289 -7.681 1 29.4 ? O3D UGF 402 A 1 HETATM 15 C C4D UGF . . . D 3 -5.9 13.5 -5.878 1 27.14 ? C4D UGF 402 A 1 HETATM 16 C C5D UGF . . . D 3 -5.12 12.54 -4.985 1 26.55 ? C5D UGF 402 A 1 HETATM 17 O O5D UGF . . . D 3 -4.068 12.029 -5.76 1 26.46 ? O5D UGF 402 A 1 HETATM 18 P PA UGF . . . D 3 -2.841 11.133 -5.011 1 28.35 ? PA UGF 402 A 1 HETATM 19 O O1A UGF . . . D 3 -1.763 10.813 -5.986 1 29.39 ? O1A UGF 402 A 1 HETATM 20 O O2A UGF . . . D 3 -2.674 11.571 -3.589 1 28.36 ? O2A UGF 402 A 1 HETATM 21 O O3A UGF . . . D 3 -3.659 9.724 -4.745 1 28.37 ? O3A UGF 402 A 1 HETATM 22 P PB UGF . . . D 3 -4.516 8.822 -5.799 1 30.75 ? PB UGF 402 A 1 HETATM 23 O O1B UGF . . . D 3 -5.866 8.756 -5.227 1 34.36 ? O1B UGF 402 A 1 HETATM 24 O O2B UGF . . . D 3 -4.294 9.118 -7.229 1 35.83 ? O2B UGF 402 A 1 HETATM 25 O O3B UGF . . . D 3 -3.684 7.468 -5.736 1 32.98 ? O3B UGF 402 A 1 HETATM 26 C C1' UGF . . . D 3 -3.242 6.914 -4.487 1 39.39 ? C1' UGF 402 A 1 HETATM 27 O O5' UGF . . . D 3 -4.179 6.072 -3.891 1 38.87 ? O5' UGF 402 A 1 HETATM 28 C C5' UGF . . . D 3 -4.565 5.019 -4.735 1 45.41 ? C5' UGF 402 A 1 HETATM 29 C C6' UGF . . . D 3 -5.683 4.209 -4.031 1 45.04 ? C6' UGF 402 A 1 HETATM 30 O "O'P" UGF . . . D 3 -6.238 4.713 -3.029 1 44.28 ? "O'P" UGF 402 A 1 HETATM 31 O "O'Q" UGF . . . D 3 -5.967 3.108 -4.533 1 51.85 ? "O'Q" UGF 402 A 1 HETATM 32 C C4' UGF . . . D 3 -3.333 4.13 -4.983 1 41.02 ? C4' UGF 402 A 1 HETATM 33 F F4' UGF . . . D 3 -3.747 3.14 -5.867 1 40.71 ? F4' UGF 402 A 1 HETATM 34 C C3' UGF . . . D 3 -2.139 4.953 -5.505 1 37.97 ? C3' UGF 402 A 1 HETATM 35 O O3' UGF . . . D 3 -0.943 4.196 -5.341 1 37.39 ? O3' UGF 402 A 1 HETATM 36 C C2' UGF . . . D 3 -1.937 6.153 -4.684 1 37.58 ? C2' UGF 402 A 1 HETATM 37 O O2' UGF . . . D 3 -1.007 7.016 -5.372 1 38.57 ? O2' UGF 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 407 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 37 #