data_8GFE # _model_server_result.job_id lpMgwvSjy1S4YUpHOph4gA _model_server_result.datetime_utc '2024-11-19 11:46:11' _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 8gfe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 8GFE # _exptl.entry_id 8GFE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 380.372 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-2-[(4-oxidanylidene-3~{H}-pyrido[1,2-a]pyrimidin-2-yl)methoxy]oxan-3-yl]ethanamide _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 90 _cell.angle_gamma 90 _cell.entry_id 8GFE _cell.length_a 175.474 _cell.length_b 175.474 _cell.length_c 175.474 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GFE _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 90 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 87 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 105 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 102 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.104 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C17 H22 N3 O7 1' _chem_comp.formula_weight 380.372 _chem_comp.id ZH8 _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-2-[(4-oxidanylidene-3~{H}-pyrido[1,2-a]pyrimidin-2-yl)methoxy]oxan-3-yl]ethanamide _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 C7 O4 ZH8 sing 405 n n C7 C6 ZH8 sing 406 n n O1 C2 ZH8 doub 407 n n C5 O3 ZH8 sing 408 n n C5 C6 ZH8 sing 409 n n C5 C4 ZH8 sing 410 n n O5 C6 ZH8 sing 411 n n O5 C8 ZH8 sing 412 n n O2 C4 ZH8 sing 413 n n C3 C4 ZH8 sing 414 n n C3 C8 ZH8 sing 415 n n C3 N1 ZH8 sing 416 n n O6 C8 ZH8 sing 417 n n O6 C9 ZH8 sing 418 n n C2 N1 ZH8 sing 419 n n C2 C1 ZH8 sing 420 n n C9 C10 ZH8 sing 421 n n C10 N3 ZH8 doub 422 n n C10 C11 ZH8 sing 423 n n N3 C17 ZH8 sing 424 n n C11 C12 ZH8 sing 425 n n C17 C16 ZH8 doub 426 n y C17 N2 ZH8 sing 427 n y C12 N2 ZH8 sing 428 n n C12 O7 ZH8 doub 429 n n C16 C15 ZH8 sing 430 n y N2 C13 ZH8 doub 431 n y C15 C14 ZH8 doub 432 n y C13 C14 ZH8 sing 433 n y C1 H1 ZH8 sing 434 n n C1 H2 ZH8 sing 435 n n C1 H3 ZH8 sing 436 n n N1 H4 ZH8 sing 437 n n C3 H5 ZH8 sing 438 n n C4 H6 ZH8 sing 439 n n O2 H7 ZH8 sing 440 n n C5 H8 ZH8 sing 441 n n O3 H9 ZH8 sing 442 n n C6 H10 ZH8 sing 443 n n C7 H11 ZH8 sing 444 n n C7 H12 ZH8 sing 445 n n O4 H13 ZH8 sing 446 n n C8 H14 ZH8 sing 447 n n C9 H15 ZH8 sing 448 n n C9 H16 ZH8 sing 449 n n C11 H17 ZH8 sing 450 n n C11 H18 ZH8 sing 451 n n C13 H19 ZH8 sing 452 n n C14 H20 ZH8 sing 453 n n C15 H21 ZH8 sing 454 n n C16 H22 ZH8 sing 455 n n # _atom_sites.entry_id 8GFE _atom_sites.fract_transf_matrix[1][1] 0.005699 _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] 0.005699 _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] 0.005699 _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 B 2 ZH8 A 1 601 1 ZH8 UNL . C 3 CIT A 1 602 2 CIT CIT . D 4 DMS A 1 603 3 DMS DMS . E 4 DMS A 1 604 4 DMS DMS . F 4 DMS A 1 605 5 DMS DMS . G 5 HOH A 1 701 124 HOH HOH . G 5 HOH A 2 702 205 HOH HOH . G 5 HOH A 3 703 324 HOH HOH . G 5 HOH A 4 704 330 HOH HOH . G 5 HOH A 5 705 119 HOH HOH . G 5 HOH A 6 706 82 HOH HOH . G 5 HOH A 7 707 371 HOH HOH . G 5 HOH A 8 708 301 HOH HOH . G 5 HOH A 9 709 91 HOH HOH . G 5 HOH A 10 710 49 HOH HOH . G 5 HOH A 11 711 50 HOH HOH . G 5 HOH A 12 712 1 HOH HOH . G 5 HOH A 13 713 92 HOH HOH . G 5 HOH A 14 714 3 HOH HOH . G 5 HOH A 15 715 133 HOH HOH . G 5 HOH A 16 716 335 HOH HOH . G 5 HOH A 17 717 85 HOH HOH . G 5 HOH A 18 718 288 HOH HOH . G 5 HOH A 19 719 175 HOH HOH . G 5 HOH A 20 720 334 HOH HOH . G 5 HOH A 21 721 65 HOH HOH . G 5 HOH A 22 722 110 HOH HOH . G 5 HOH A 23 723 147 HOH HOH . G 5 HOH A 24 724 140 HOH HOH . G 5 HOH A 25 725 48 HOH HOH . G 5 HOH A 26 726 166 HOH HOH . G 5 HOH A 27 727 163 HOH HOH . G 5 HOH A 28 728 54 HOH HOH . G 5 HOH A 29 729 51 HOH HOH . G 5 HOH A 30 730 68 HOH HOH . G 5 HOH A 31 731 57 HOH HOH . G 5 HOH A 32 732 348 HOH HOH . G 5 HOH A 33 733 58 HOH HOH . G 5 HOH A 34 734 67 HOH HOH . G 5 HOH A 35 735 90 HOH HOH . G 5 HOH A 36 736 123 HOH HOH . G 5 HOH A 37 737 368 HOH HOH . G 5 HOH A 38 738 64 HOH HOH . G 5 HOH A 39 739 266 HOH HOH . G 5 HOH A 40 740 130 HOH HOH . G 5 HOH A 41 741 304 HOH HOH . G 5 HOH A 42 742 292 HOH HOH . G 5 HOH A 43 743 312 HOH HOH . G 5 HOH A 44 744 317 HOH HOH . G 5 HOH A 45 745 305 HOH HOH . G 5 HOH A 46 746 333 HOH HOH . G 5 HOH A 47 747 94 HOH HOH . G 5 HOH A 48 748 99 HOH HOH . G 5 HOH A 49 749 296 HOH HOH . G 5 HOH A 50 750 293 HOH HOH . G 5 HOH A 51 751 347 HOH HOH . G 5 HOH A 52 752 316 HOH HOH . G 5 HOH A 53 753 303 HOH HOH . G 5 HOH A 54 754 297 HOH HOH . G 5 HOH A 55 755 268 HOH HOH . G 5 HOH A 56 756 356 HOH HOH . G 5 HOH A 57 757 2 HOH HOH . G 5 HOH A 58 758 33 HOH HOH . G 5 HOH A 59 759 83 HOH HOH . G 5 HOH A 60 760 369 HOH HOH . G 5 HOH A 61 761 258 HOH HOH . G 5 HOH A 62 762 75 HOH HOH . G 5 HOH A 63 763 367 HOH HOH . G 5 HOH A 64 764 308 HOH HOH . G 5 HOH A 65 765 111 HOH HOH . G 5 HOH A 66 766 80 HOH HOH . G 5 HOH A 67 767 69 HOH HOH . G 5 HOH A 68 768 81 HOH HOH . G 5 HOH A 69 769 84 HOH HOH . G 5 HOH A 70 770 370 HOH HOH . G 5 HOH A 71 771 253 HOH HOH . G 5 HOH A 72 772 326 HOH HOH . G 5 HOH A 73 773 311 HOH HOH . G 5 HOH A 74 774 42 HOH HOH . G 5 HOH A 75 775 257 HOH HOH . G 5 HOH A 76 776 162 HOH HOH . G 5 HOH A 77 777 141 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 C1 ZH8 . . . B 2 -28.274 13.169 -61.078 1 53.34 ? C1 ZH8 601 A 1 HETATM 2 C C2 ZH8 . . . B 2 -29.233 13.694 -62.109 1 54.23 ? C2 ZH8 601 A 1 HETATM 3 O O1 ZH8 . . . B 2 -29.012 13.589 -63.304 1 57.04 ? O1 ZH8 601 A 1 HETATM 4 N N1 ZH8 . . . B 2 -30.33 14.309 -61.666 1 61.68 ? N1 ZH8 601 A 1 HETATM 5 C C3 ZH8 . . . B 2 -31.43 14.757 -62.497 1 56.93 ? C3 ZH8 601 A 1 HETATM 6 C C4 ZH8 . . . B 2 -31.549 16.267 -62.363 1 60.08 ? C4 ZH8 601 A 1 HETATM 7 O O2 ZH8 . . . B 2 -30.287 16.864 -62.608 1 61.56 ? O2 ZH8 601 A 1 HETATM 8 C C5 ZH8 . . . B 2 -32.651 16.782 -63.293 1 61.75 ? C5 ZH8 601 A 1 HETATM 9 O O3 ZH8 . . . B 2 -32.797 18.19 -63.126 1 64.07 ? O3 ZH8 601 A 1 HETATM 10 C C6 ZH8 . . . B 2 -33.967 16.071 -62.944 1 58.68 ? C6 ZH8 601 A 1 HETATM 11 C C7 ZH8 . . . B 2 -35.133 16.4 -63.849 1 57.23 ? C7 ZH8 601 A 1 HETATM 12 O O4 ZH8 . . . B 2 -36.309 15.709 -63.394 1 52.82 ? O4 ZH8 601 A 1 HETATM 13 O O5 ZH8 . . . B 2 -33.795 14.645 -63.056 1 52.4 ? O5 ZH8 601 A 1 HETATM 14 C C8 ZH8 . . . B 2 -32.8 14.14 -62.171 1 59.19 ? C8 ZH8 601 A 1 HETATM 15 O O6 ZH8 . . . B 2 -32.746 12.74 -62.312 1 58.56 ? O6 ZH8 601 A 1 HETATM 16 C C9 ZH8 . . . B 2 -33.895 12.052 -61.809 1 63.97 ? C9 ZH8 601 A 1 HETATM 17 C C10 ZH8 . . . B 2 -33.391 10.913 -60.978 1 71.56 ? C10 ZH8 601 A 1 HETATM 18 C C11 ZH8 . . . B 2 -32.035 10.844 -60.581 1 75.6 ? C11 ZH8 601 A 1 HETATM 19 C C12 ZH8 . . . B 2 -31.579 9.733 -59.825 1 76.54 ? C12 ZH8 601 A 1 HETATM 20 O O7 ZH8 . . . B 2 -30.441 9.544 -59.406 1 71.38 ? O7 ZH8 601 A 1 HETATM 21 N N2 ZH8 . . . B 2 -32.601 8.736 -59.529 1 80.33 ? N2 ZH8 601 A 1 HETATM 22 C C13 ZH8 . . . B 2 -32.252 7.621 -58.798 1 77.99 ? C13 ZH8 601 A 1 HETATM 23 C C14 ZH8 . . . B 2 -33.164 6.667 -58.511 1 80.85 ? C14 ZH8 601 A 1 HETATM 24 C C15 ZH8 . . . B 2 -34.493 6.809 -58.959 1 80.28 ? C15 ZH8 601 A 1 HETATM 25 C C16 ZH8 . . . B 2 -34.846 7.901 -59.673 1 81.32 ? C16 ZH8 601 A 1 HETATM 26 C C17 ZH8 . . . B 2 -33.896 8.912 -59.981 1 86.19 ? C17 ZH8 601 A 1 HETATM 27 N N3 ZH8 . . . B 2 -34.284 9.961 -60.677 1 79.32 ? N3 ZH8 601 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 436 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #