data_7AP1 # _model_server_result.job_id Mc91Rb9dZIi8Ia_BJIKRgw _model_server_result.datetime_utc '2025-03-21 14:36:15' _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 7ap1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7AP1 # _exptl.entry_id 7AP1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 461.447 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate' _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 7AP1 _cell.length_a 84.67 _cell.length_b 84.67 _cell.length_c 229.865 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7AP1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A O ASP 254 A ASP 254 1_555 F CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc2 A OG SER 336 A SER 336 1_555 G CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.965 ? metalc ? metalc3 F CA CA . A CA 505 1_555 I O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc4 F CA CA . A CA 505 1_555 I O HOH . A HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc5 F CA CA . A CA 505 1_555 I O HOH . A HOH 677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc6 F CA CA . A CA 505 1_555 I O HOH . A HOH 679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc7 F CA CA . A CA 505 1_555 I O HOH . A HOH 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? # _chem_comp.formula 'C16 H23 N5 O9 S' _chem_comp.formula_weight 461.447 _chem_comp.id RUZ _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SerS7HMDDA # 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 N CA RUZ sing 286 n n CA CB RUZ sing 287 n n CA C RUZ sing 288 n n CB OG RUZ sing 289 n n C O RUZ doub 290 n n C N3S RUZ sing 291 n n N3S S RUZ sing 292 n n S O2S RUZ doub 293 n n S O1S RUZ doub 294 n n S O5' RUZ sing 295 n n C5' O5' RUZ sing 296 n n C5' C4' RUZ sing 297 n n C4' C3' RUZ sing 298 n n C4' O4' RUZ sing 299 n n O3' C3' RUZ sing 300 n n C3' C2' RUZ sing 301 n n O4' C1' RUZ sing 302 n n N6 C6 RUZ sing 303 n n C2' C1' RUZ sing 304 n n C2' O2' RUZ sing 305 n n C1' N7 RUZ sing 306 n n C6 C1 RUZ doub 307 n y C6 C5 RUZ sing 308 n y C1 C2 RUZ sing 309 n y N7 C5 RUZ sing 310 n y N7 C8 RUZ sing 311 n y C5 C4 RUZ doub 312 n y C8 N9 RUZ doub 313 n y C2 C2M RUZ sing 314 n n C2 C3 RUZ doub 315 n y C4 C3 RUZ sing 316 n y C4 N9 RUZ sing 317 n y C2M O2M RUZ sing 318 n n C1 H1 RUZ sing 319 n n C3 H2 RUZ sing 320 n n C8 H3 RUZ sing 321 n n N H4 RUZ sing 322 n n N H5 RUZ sing 323 n n CA H7 RUZ sing 324 n n CB H8 RUZ sing 325 n n CB H9 RUZ sing 326 n n OG H10 RUZ sing 327 n n N3S H11 RUZ sing 328 n n C5' H12 RUZ sing 329 n n C5' H13 RUZ sing 330 n n C4' H14 RUZ sing 331 n n C1' H15 RUZ sing 332 n n C2' H16 RUZ sing 333 n n O2' H17 RUZ sing 334 n n C3' H18 RUZ sing 335 n n O3' H19 RUZ sing 336 n n N6 H20 RUZ sing 337 n n N6 H21 RUZ sing 338 n n C2M H22 RUZ sing 339 n n C2M H23 RUZ sing 340 n n O2M H24 RUZ sing 341 n n # _atom_sites.entry_id 7AP1 _atom_sites.fract_transf_matrix[1][1] 0.011811 _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] 0.011811 _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] 0.00435 _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 RUZ A 1 501 501 RUZ SMH . C 3 EDO A 1 502 1 EDO EDO . D 3 EDO A 1 503 2 EDO EDO . E 3 EDO A 1 504 3 EDO EDO . F 4 CA A 1 505 1 CA CA . G 4 CA A 1 506 2 CA CA . H 4 CA A 1 507 3 CA CA . I 5 HOH A 1 601 1 HOH HOH . I 5 HOH A 2 602 27 HOH HOH . I 5 HOH A 3 603 11 HOH HOH . I 5 HOH A 4 604 2 HOH HOH . I 5 HOH A 5 605 16 HOH HOH . I 5 HOH A 6 606 14 HOH HOH . I 5 HOH A 7 607 65 HOH HOH . I 5 HOH A 8 608 94 HOH HOH . I 5 HOH A 9 609 84 HOH HOH . I 5 HOH A 10 610 17 HOH HOH . I 5 HOH A 11 611 13 HOH HOH . I 5 HOH A 12 612 3 HOH HOH . I 5 HOH A 13 613 9 HOH HOH . I 5 HOH A 14 614 82 HOH HOH . I 5 HOH A 15 615 26 HOH HOH . I 5 HOH A 16 616 52 HOH HOH . I 5 HOH A 17 617 22 HOH HOH . I 5 HOH A 18 618 51 HOH HOH . I 5 HOH A 19 619 91 HOH HOH . I 5 HOH A 20 620 18 HOH HOH . I 5 HOH A 21 621 72 HOH HOH . I 5 HOH A 22 622 71 HOH HOH . I 5 HOH A 23 623 43 HOH HOH . I 5 HOH A 24 624 111 HOH HOH . I 5 HOH A 25 625 24 HOH HOH . I 5 HOH A 26 626 66 HOH HOH . I 5 HOH A 27 627 10 HOH HOH . I 5 HOH A 28 628 119 HOH HOH . I 5 HOH A 29 629 104 HOH HOH . I 5 HOH A 30 630 33 HOH HOH . I 5 HOH A 31 631 80 HOH HOH . I 5 HOH A 32 632 56 HOH HOH . I 5 HOH A 33 633 37 HOH HOH . I 5 HOH A 34 634 78 HOH HOH . I 5 HOH A 35 635 34 HOH HOH . I 5 HOH A 36 636 47 HOH HOH . I 5 HOH A 37 637 109 HOH HOH . I 5 HOH A 38 638 8 HOH HOH . I 5 HOH A 39 639 15 HOH HOH . I 5 HOH A 40 640 12 HOH HOH . I 5 HOH A 41 641 4 HOH HOH . I 5 HOH A 42 642 98 HOH HOH . I 5 HOH A 43 643 38 HOH HOH . I 5 HOH A 44 644 39 HOH HOH . I 5 HOH A 45 645 96 HOH HOH . I 5 HOH A 46 646 31 HOH HOH . I 5 HOH A 47 647 28 HOH HOH . I 5 HOH A 48 648 23 HOH HOH . I 5 HOH A 49 649 55 HOH HOH . I 5 HOH A 50 650 6 HOH HOH . I 5 HOH A 51 651 62 HOH HOH . I 5 HOH A 52 652 81 HOH HOH . I 5 HOH A 53 653 106 HOH HOH . I 5 HOH A 54 654 36 HOH HOH . I 5 HOH A 55 655 46 HOH HOH . I 5 HOH A 56 656 25 HOH HOH . I 5 HOH A 57 657 57 HOH HOH . I 5 HOH A 58 658 30 HOH HOH . I 5 HOH A 59 659 85 HOH HOH . I 5 HOH A 60 660 113 HOH HOH . I 5 HOH A 61 661 102 HOH HOH . I 5 HOH A 62 662 110 HOH HOH . I 5 HOH A 63 663 64 HOH HOH . I 5 HOH A 64 664 41 HOH HOH . I 5 HOH A 65 665 5 HOH HOH . I 5 HOH A 66 666 7 HOH HOH . I 5 HOH A 67 667 86 HOH HOH . I 5 HOH A 68 668 40 HOH HOH . I 5 HOH A 69 669 21 HOH HOH . I 5 HOH A 70 670 60 HOH HOH . I 5 HOH A 71 671 58 HOH HOH . I 5 HOH A 72 672 19 HOH HOH . I 5 HOH A 73 673 53 HOH HOH . I 5 HOH A 74 674 83 HOH HOH . I 5 HOH A 75 675 44 HOH HOH . I 5 HOH A 76 676 61 HOH HOH . I 5 HOH A 77 677 93 HOH HOH . I 5 HOH A 78 678 45 HOH HOH . I 5 HOH A 79 679 95 HOH HOH . I 5 HOH A 80 680 99 HOH HOH . I 5 HOH A 81 681 20 HOH HOH . I 5 HOH A 82 682 87 HOH HOH . I 5 HOH A 83 683 90 HOH HOH . I 5 HOH A 84 684 32 HOH HOH . I 5 HOH A 85 685 101 HOH HOH . I 5 HOH A 86 686 48 HOH HOH . I 5 HOH A 87 687 114 HOH HOH . I 5 HOH A 88 688 69 HOH HOH . I 5 HOH A 89 689 42 HOH HOH . I 5 HOH A 90 690 79 HOH HOH . I 5 HOH A 91 691 35 HOH HOH . I 5 HOH A 92 692 120 HOH HOH . I 5 HOH A 93 693 100 HOH HOH . I 5 HOH A 94 694 54 HOH HOH . I 5 HOH A 95 695 105 HOH HOH . I 5 HOH A 96 696 108 HOH HOH . I 5 HOH A 97 697 88 HOH HOH . I 5 HOH A 98 698 68 HOH HOH . I 5 HOH A 99 699 73 HOH HOH . I 5 HOH A 100 700 63 HOH HOH . I 5 HOH A 101 701 67 HOH HOH . I 5 HOH A 102 702 89 HOH HOH . I 5 HOH A 103 703 116 HOH HOH . I 5 HOH A 104 704 74 HOH HOH . I 5 HOH A 105 705 118 HOH HOH . I 5 HOH A 106 706 117 HOH HOH . I 5 HOH A 107 707 122 HOH HOH . I 5 HOH A 108 708 103 HOH HOH . I 5 HOH A 109 709 49 HOH HOH . I 5 HOH A 110 710 76 HOH HOH . I 5 HOH A 111 711 75 HOH HOH . I 5 HOH A 112 712 50 HOH HOH . I 5 HOH A 113 713 29 HOH HOH . I 5 HOH A 114 714 70 HOH HOH . I 5 HOH A 115 715 77 HOH HOH . I 5 HOH A 116 716 59 HOH HOH . I 5 HOH A 117 717 97 HOH HOH . I 5 HOH A 118 718 92 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 RUZ . . . B 2 -11.324 -33.228 1.573 1 53.66 ? C1 RUZ 501 A 1 HETATM 2 C C2 RUZ . . . B 2 -11.958 -32.919 2.772 1 54.32 ? C2 RUZ 501 A 1 HETATM 3 C C3 RUZ . . . B 2 -11.557 -31.801 3.493 1 53.24 ? C3 RUZ 501 A 1 HETATM 4 C C4 RUZ . . . B 2 -10.517 -30.996 3.03 1 52.93 ? C4 RUZ 501 A 1 HETATM 5 C C5 RUZ . . . B 2 -9.853 -31.305 1.828 1 52.84 ? C5 RUZ 501 A 1 HETATM 6 C C6 RUZ . . . B 2 -10.279 -32.446 1.063 1 53.27 ? C6 RUZ 501 A 1 HETATM 7 C C8 RUZ . . . B 2 -9.046 -29.481 2.749 1 52.59 ? C8 RUZ 501 A 1 HETATM 8 N N RUZ . . . B 2 -10.065 -29.839 -7.752 1 48.21 ? N RUZ 501 A 1 HETATM 9 C CA RUZ . . . B 2 -8.981 -30.688 -7.231 1 49.18 ? CA RUZ 501 A 1 HETATM 10 C CB RUZ . . . B 2 -7.717 -29.843 -7.068 1 48.97 ? CB RUZ 501 A 1 HETATM 11 O OG RUZ . . . B 2 -7.824 -28.91 -5.99 1 48.69 ? OG RUZ 501 A 1 HETATM 12 C C RUZ . . . B 2 -9.369 -31.31 -5.905 1 50.77 ? C RUZ 501 A 1 HETATM 13 O O RUZ . . . B 2 -10.445 -31.047 -5.374 1 50.95 ? O RUZ 501 A 1 HETATM 14 N N3S RUZ . . . B 2 -8.473 -32.17 -5.342 1 52.21 ? N3S RUZ 501 A 1 HETATM 15 S S RUZ . . . B 2 -8.648 -32.888 -3.935 1 53.4 ? S RUZ 501 A 1 HETATM 16 O O1S RUZ . . . B 2 -7.458 -33.612 -3.668 1 53.25 ? O1S RUZ 501 A 1 HETATM 17 O O2S RUZ . . . B 2 -9.917 -33.523 -3.88 1 53.41 ? O2S RUZ 501 A 1 HETATM 18 O O5' RUZ . . . B 2 -8.804 -31.705 -2.869 1 53.98 ? O5' RUZ 501 A 1 HETATM 19 C C5' RUZ . . . B 2 -7.878 -30.58 -2.933 1 53.6 ? C5' RUZ 501 A 1 HETATM 20 C C4' RUZ . . . B 2 -7.354 -30.342 -1.54 1 53.75 ? C4' RUZ 501 A 1 HETATM 21 O O4' RUZ . . . B 2 -8.438 -30.101 -0.624 1 53.09 ? O4' RUZ 501 A 1 HETATM 22 C C1' RUZ . . . B 2 -7.854 -30.183 0.657 1 53.16 ? C1' RUZ 501 A 1 HETATM 23 C C2' RUZ . . . B 2 -6.809 -31.307 0.599 1 54.1 ? C2' RUZ 501 A 1 HETATM 24 O O2' RUZ . . . B 2 -5.615 -30.841 1.211 1 54.87 ? O2' RUZ 501 A 1 HETATM 25 C C3' RUZ . . . B 2 -6.601 -31.514 -0.914 1 54.57 ? C3' RUZ 501 A 1 HETATM 26 O O3' RUZ . . . B 2 -5.229 -31.498 -1.284 1 55.53 ? O3' RUZ 501 A 1 HETATM 27 N N7 RUZ . . . B 2 -8.892 -30.321 1.677 1 52.78 ? N7 RUZ 501 A 1 HETATM 28 N N9 RUZ . . . B 2 -9.988 -29.837 3.583 1 52.73 ? N9 RUZ 501 A 1 HETATM 29 N N6 RUZ . . . B 2 -9.761 -32.785 -0.177 1 53.03 ? N6 RUZ 501 A 1 HETATM 30 C C2M RUZ . . . B 2 -13.091 -33.768 3.274 1 55.63 ? C2M RUZ 501 A 1 HETATM 31 O O2M RUZ . . . B 2 -14.263 -32.988 3.389 1 56.74 ? O2M RUZ 501 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 450 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #