data_6IH5 # _model_server_result.job_id F0x8JGr4GlaA6HIZ1lKS4g _model_server_result.datetime_utc '2025-02-05 16:49:44' _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 6ih5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 6IH5 # _exptl.entry_id 6IH5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 640.408 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2S,3S,4R,5S)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.35 _cell.angle_gamma 90 _cell.entry_id 6IH5 _cell.length_a 59.662 _cell.length_b 98.523 _cell.length_c 62.007 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H28 N5 O15 P2 1' _chem_comp.formula_weight 640.408 _chem_comp.id A7R _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2S,3S,4R,5S)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' _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 O03 C01 A7R sing 1 n n O10 P01 A7R doub 2 n n O04 C02 A7R sing 3 n n C01 C02 A7R sing 4 n n C01 C03 A7R sing 5 n n O12 P02 A7R doub 6 n n C09 C03 A7R sing 7 n n C09 O07 A7R sing 8 n n P01 O07 A7R sing 9 n n P01 O11 A7R sing 10 n n P01 O09 A7R sing 11 n n O13 P02 A7R sing 12 n n C02 C04 A7R sing 13 n n C03 O01 A7R sing 14 n n P02 O09 A7R sing 15 n n P02 O08 A7R sing 16 n n O01 C04 A7R sing 17 n n O15 C18 A7R doub 18 n n C04 N03 A7R sing 19 n n O08 C10 A7R sing 20 n n C18 N03 A7R sing 21 n n C18 N05 A7R sing 22 n n N03 C17 A7R sing 23 n n O05 C05 A7R sing 24 n n O06 C06 A7R sing 25 n n N05 C20 A7R doub 26 n n C14 C12 A7R doub 27 n y C14 C15 A7R sing 28 n y C10 C07 A7R sing 29 n n C17 C19 A7R doub 30 n n C12 N01 A7R sing 31 n y C15 C13 A7R doub 32 n y C20 C19 A7R sing 33 n n C20 N04 A7R sing 34 n n C05 C06 A7R sing 35 n n C05 C07 A7R sing 36 n n C06 C08 A7R sing 37 n n C07 O02 A7R sing 38 n n N01 C08 A7R sing 39 n n N01 C11 A7R doub 40 n y C13 C11 A7R sing 41 n y C13 C16 A7R sing 42 n n C08 O02 A7R sing 43 n n C16 O14 A7R doub 44 n n C16 N02 A7R sing 45 n n C01 H1 A7R sing 46 n n C02 H2 A7R sing 47 n n C03 H3 A7R sing 48 n n C04 H4 A7R sing 49 n n C05 H5 A7R sing 50 n n C06 H6 A7R sing 51 n n C07 H7 A7R sing 52 n n C08 H8 A7R sing 53 n n C09 H9 A7R sing 54 n n C09 H10 A7R sing 55 n n C10 H11 A7R sing 56 n n C10 H12 A7R sing 57 n n C11 H13 A7R sing 58 n n C12 H14 A7R sing 59 n n C14 H15 A7R sing 60 n n C15 H16 A7R sing 61 n n C17 H17 A7R sing 62 n n C19 H18 A7R sing 63 n n N02 H19 A7R sing 64 n n N02 H20 A7R sing 65 n n N04 H21 A7R sing 66 n n N04 H22 A7R sing 67 n n O03 H23 A7R sing 68 n n O04 H24 A7R sing 69 n n O05 H25 A7R sing 70 n n O06 H26 A7R sing 71 n n O11 H27 A7R sing 72 n n O13 H28 A7R sing 73 n n # _atom_sites.entry_id 6IH5 _atom_sites.fract_transf_matrix[1][1] 0.016761 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003669 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01015 _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] 0.016509 _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 A7R B 1 400 400 A7R NCD . D 3 HOH A 1 401 38 HOH HOH . D 3 HOH A 2 402 74 HOH HOH . D 3 HOH A 3 403 95 HOH HOH . D 3 HOH A 4 404 29 HOH HOH . D 3 HOH A 5 405 21 HOH HOH . D 3 HOH A 6 406 11 HOH HOH . D 3 HOH A 7 407 10 HOH HOH . D 3 HOH A 8 408 9 HOH HOH . D 3 HOH A 9 409 43 HOH HOH . D 3 HOH A 10 410 112 HOH HOH . D 3 HOH A 11 411 70 HOH HOH . D 3 HOH A 12 412 15 HOH HOH . D 3 HOH A 13 413 3 HOH HOH . D 3 HOH A 14 414 54 HOH HOH . D 3 HOH A 15 415 80 HOH HOH . D 3 HOH A 16 416 87 HOH HOH . D 3 HOH A 17 417 56 HOH HOH . D 3 HOH A 18 418 20 HOH HOH . D 3 HOH A 19 419 86 HOH HOH . D 3 HOH A 20 420 69 HOH HOH . D 3 HOH A 21 421 88 HOH HOH . D 3 HOH A 22 422 72 HOH HOH . D 3 HOH A 23 423 78 HOH HOH . D 3 HOH A 24 424 44 HOH HOH . D 3 HOH A 25 425 59 HOH HOH . D 3 HOH A 26 426 13 HOH HOH . D 3 HOH A 27 427 14 HOH HOH . D 3 HOH A 28 428 94 HOH HOH . D 3 HOH A 29 429 42 HOH HOH . D 3 HOH A 30 430 75 HOH HOH . D 3 HOH A 31 431 101 HOH HOH . D 3 HOH A 32 432 18 HOH HOH . D 3 HOH A 33 433 49 HOH HOH . D 3 HOH A 34 434 114 HOH HOH . D 3 HOH A 35 435 51 HOH HOH . D 3 HOH A 36 436 24 HOH HOH . D 3 HOH A 37 437 6 HOH HOH . D 3 HOH A 38 438 85 HOH HOH . D 3 HOH A 39 439 107 HOH HOH . D 3 HOH A 40 440 41 HOH HOH . D 3 HOH A 41 441 91 HOH HOH . D 3 HOH A 42 442 25 HOH HOH . D 3 HOH A 43 443 33 HOH HOH . D 3 HOH A 44 444 47 HOH HOH . D 3 HOH A 45 445 66 HOH HOH . D 3 HOH A 46 446 103 HOH HOH . D 3 HOH A 47 447 117 HOH HOH . D 3 HOH A 48 448 62 HOH HOH . D 3 HOH A 49 449 52 HOH HOH . D 3 HOH A 50 450 118 HOH HOH . D 3 HOH A 51 451 96 HOH HOH . D 3 HOH A 52 452 39 HOH HOH . D 3 HOH A 53 453 37 HOH HOH . E 3 HOH B 1 501 77 HOH HOH . E 3 HOH B 2 502 26 HOH HOH . E 3 HOH B 3 503 84 HOH HOH . E 3 HOH B 4 504 82 HOH HOH . E 3 HOH B 5 505 45 HOH HOH . E 3 HOH B 6 506 30 HOH HOH . E 3 HOH B 7 507 110 HOH HOH . E 3 HOH B 8 508 92 HOH HOH . E 3 HOH B 9 509 104 HOH HOH . E 3 HOH B 10 510 71 HOH HOH . E 3 HOH B 11 511 61 HOH HOH . E 3 HOH B 12 512 113 HOH HOH . E 3 HOH B 13 513 93 HOH HOH . E 3 HOH B 14 514 50 HOH HOH . E 3 HOH B 15 515 36 HOH HOH . E 3 HOH B 16 516 81 HOH HOH . E 3 HOH B 17 517 73 HOH HOH . E 3 HOH B 18 518 2 HOH HOH . E 3 HOH B 19 519 106 HOH HOH . E 3 HOH B 20 520 31 HOH HOH . E 3 HOH B 21 521 57 HOH HOH . E 3 HOH B 22 522 23 HOH HOH . E 3 HOH B 23 523 68 HOH HOH . E 3 HOH B 24 524 5 HOH HOH . E 3 HOH B 25 525 108 HOH HOH . E 3 HOH B 26 526 115 HOH HOH . E 3 HOH B 27 527 105 HOH HOH . E 3 HOH B 28 528 12 HOH HOH . E 3 HOH B 29 529 100 HOH HOH . E 3 HOH B 30 530 7 HOH HOH . E 3 HOH B 31 531 8 HOH HOH . E 3 HOH B 32 532 35 HOH HOH . E 3 HOH B 33 533 64 HOH HOH . E 3 HOH B 34 534 27 HOH HOH . E 3 HOH B 35 535 46 HOH HOH . E 3 HOH B 36 536 116 HOH HOH . E 3 HOH B 37 537 32 HOH HOH . E 3 HOH B 38 538 1 HOH HOH . E 3 HOH B 39 539 40 HOH HOH . E 3 HOH B 40 540 97 HOH HOH . E 3 HOH B 41 541 53 HOH HOH . E 3 HOH B 42 542 16 HOH HOH . E 3 HOH B 43 543 102 HOH HOH . E 3 HOH B 44 544 60 HOH HOH . E 3 HOH B 45 545 55 HOH HOH . E 3 HOH B 46 546 65 HOH HOH . E 3 HOH B 47 547 48 HOH HOH . E 3 HOH B 48 548 4 HOH HOH . E 3 HOH B 49 549 109 HOH HOH . E 3 HOH B 50 550 17 HOH HOH . E 3 HOH B 51 551 111 HOH HOH . E 3 HOH B 52 552 22 HOH HOH . E 3 HOH B 53 553 67 HOH HOH . E 3 HOH B 54 554 79 HOH HOH . E 3 HOH B 55 555 76 HOH HOH . E 3 HOH B 56 556 98 HOH HOH . E 3 HOH B 57 557 19 HOH HOH . E 3 HOH B 58 558 34 HOH HOH . E 3 HOH B 59 559 28 HOH HOH . E 3 HOH B 60 560 58 HOH HOH . E 3 HOH B 61 561 83 HOH HOH . E 3 HOH B 62 562 89 HOH HOH . E 3 HOH B 63 563 99 HOH HOH . E 3 HOH B 64 564 90 HOH HOH . E 3 HOH B 65 565 63 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 C C01 A7R . . . C 2 -29.826 31.745 -42.805 1 55.91 ? C01 A7R 400 B 1 HETATM 2 C C02 A7R . . . C 2 -30.722 30.83 -43.592 1 59.11 ? C02 A7R 400 B 1 HETATM 3 C C03 A7R . . . C 2 -29.189 32.417 -43.802 1 54.7 ? C03 A7R 400 B 1 HETATM 4 C C04 A7R . . . C 2 -30.665 31.62 -44.981 1 58.74 ? C04 A7R 400 B 1 HETATM 5 C C05 A7R . . . C 2 -24.512 36.919 -46.537 1 55.43 ? C05 A7R 400 B 1 HETATM 6 C C06 A7R . . . C 2 -23.922 38.002 -46.569 1 51.68 ? C06 A7R 400 B 1 HETATM 7 C C07 A7R . . . C 2 -23.403 35.844 -46.377 1 58.55 ? C07 A7R 400 B 1 HETATM 8 C C08 A7R . . . C 2 -22.426 37.735 -47.116 1 51.46 ? C08 A7R 400 B 1 HETATM 9 C C09 A7R . . . C 2 -28.397 33.528 -43.315 1 54.93 ? C09 A7R 400 B 1 HETATM 10 C C10 A7R . . . C 2 -23.246 35.462 -45.007 1 56.52 ? C10 A7R 400 B 1 HETATM 11 C C11 A7R . . . C 2 -20.969 39.657 -47.019 1 38.07 ? C11 A7R 400 B 1 HETATM 12 C C12 A7R . . . C 2 -20.997 38.139 -45.339 1 50.86 ? C12 A7R 400 B 1 HETATM 13 C C13 A7R . . . C 2 -19.993 40.407 -46.417 1 39.82 ? C13 A7R 400 B 1 HETATM 14 C C14 A7R . . . C 2 -20.026 38.818 -44.644 1 46.68 ? C14 A7R 400 B 1 HETATM 15 C C15 A7R . . . C 2 -19.532 39.959 -45.219 1 43.99 ? C15 A7R 400 B 1 HETATM 16 C C16 A7R . . . C 2 -19.386 41.698 -46.952 1 38.32 ? C16 A7R 400 B 1 HETATM 17 C C17 A7R . . . C 2 -30.668 30.611 -46.956 1 57.1 ? C17 A7R 400 B 1 HETATM 18 C C18 A7R . . . C 2 -32.714 31.385 -46.435 1 59.5 ? C18 A7R 400 B 1 HETATM 19 C C19 A7R . . . C 2 -31.142 30.116 -48.131 1 60.42 ? C19 A7R 400 B 1 HETATM 20 C C20 A7R . . . C 2 -32.464 30.315 -48.377 1 66.2 ? C20 A7R 400 B 1 HETATM 21 N N01 A7R . . . C 2 -21.435 38.559 -46.482 1 43.91 ? N01 A7R 400 B 1 HETATM 22 N N02 A7R . . . C 2 -20.202 42.662 -47.619 1 34.31 ? N02 A7R 400 B 1 HETATM 23 N N03 A7R . . . C 2 -31.45 31.238 -46.135 1 57.97 ? N03 A7R 400 B 1 HETATM 24 N N04 A7R . . . C 2 -33.011 29.822 -49.606 1 74.66 ? N04 A7R 400 B 1 HETATM 25 N N05 A7R . . . C 2 -33.218 30.943 -47.519 1 62.97 ? N05 A7R 400 B 1 HETATM 26 O O01 A7R . . . C 2 -30.315 32.853 -44.788 1 53.29 ? O01 A7R 400 B 1 HETATM 27 O O02 A7R . . . C 2 -22.189 36.464 -47.017 1 47.86 ? O02 A7R 400 B 1 HETATM 28 O O03 A7R . . . C 2 -30.611 32.508 -41.844 1 50.53 ? O03 A7R 400 B 1 HETATM 29 O O04 A7R . . . C 2 -31.865 30.487 -42.953 1 56.19 ? O04 A7R 400 B 1 HETATM 30 O O05 A7R . . . C 2 -25.492 36.755 -45.415 1 52.14 ? O05 A7R 400 B 1 HETATM 31 O O06 A7R . . . C 2 -23.788 38.709 -45.322 1 54.12 ? O06 A7R 400 B 1 HETATM 32 O O07 A7R . . . C 2 -27.077 33.19 -43.527 1 58.14 ? O07 A7R 400 B 1 HETATM 33 O O08 A7R . . . C 2 -24.11 36.118 -44.078 1 48.76 ? O08 A7R 400 B 1 HETATM 34 O O09 A7R . . . C 2 -24.786 33.955 -43.058 1 47.15 ? O09 A7R 400 B 1 HETATM 35 O O10 A7R . . . C 2 -25.997 32.919 -41.059 1 53.19 ? O10 A7R 400 B 1 HETATM 36 O O11 A7R . . . C 2 -25.206 31.723 -42.898 1 56.5 ? O11 A7R 400 B 1 HETATM 37 O O12 A7R . . . C 2 -25.51 36.226 -42.117 1 46.17 ? O12 A7R 400 B 1 HETATM 38 O O13 A7R . . . C 2 -23.236 35.446 -41.947 1 48.83 ? O13 A7R 400 B 1 HETATM 39 O O14 A7R . . . C 2 -18.254 41.922 -46.79 1 36.41 ? O14 A7R 400 B 1 HETATM 40 O O15 A7R . . . C 2 -33.474 31.899 -45.774 1 57.28 ? O15 A7R 400 B 1 HETATM 41 P P01 A7R . . . C 2 -25.845 32.94 -42.497 1 48.93 ? P01 A7R 400 B 1 HETATM 42 P P02 A7R . . . C 2 -24.456 35.461 -42.702 1 46.43 ? P02 A7R 400 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 42 #