data_7OCQ # _model_server_result.job_id dBtIQsgfOBbcCkiS_ROGkg _model_server_result.datetime_utc '2024-12-27 02:34:06' _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 7ocq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":801}' # _entry.id 7OCQ # _exptl.entry_id 7OCQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 548.33 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-4~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(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 90 _cell.angle_gamma 90 _cell.entry_id 7OCQ _cell.length_a 99.301 _cell.length_b 157.337 _cell.length_c 219.02 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OCQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 # 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 OD2 ASP 16 A ASP 16 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc2 A O ASP 18 A ASP 18 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc3 A OD1 ASP 176 A ASP 176 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc4 B OD2 ASP 16 B ASP 16 1_555 P MG MG . B MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc5 B O ASP 18 B ASP 18 1_555 P MG MG . B MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc6 B OD1 ASP 176 B ASP 176 1_555 P MG MG . B MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? # _chem_comp.formula 'C16 H26 N2 O15 P2' _chem_comp.formula_weight 548.33 _chem_comp.id V8H _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-4~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(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 C5N C6N V8H doub 494 n n C5N C4N V8H sing 495 n n C6N N1N V8H sing 496 n n C4N C3N V8H sing 497 n n N1N C1D V8H sing 498 n n N1N C2N V8H sing 499 n n C1D O4D V8H sing 500 n n C1D C2D V8H sing 501 n n C3N C2N V8H doub 502 n n C3N C7N V8H sing 503 n n O4D C4D V8H sing 504 n n C7N N7N V8H sing 505 n n C7N O7N V8H doub 506 n n C4D C5D V8H sing 507 n n C4D C3D V8H sing 508 n n O2D C2D V8H sing 509 n n C2D C3D V8H sing 510 n n C5D O5D V8H sing 511 n n C3D O3D V8H sing 512 n n O5D PN V8H sing 513 n n O2N PN V8H doub 514 n n PN O1N V8H sing 515 n n PN O3 V8H sing 516 n n O3 PA V8H sing 517 n n O4B C4B V8H sing 518 n n O4B C1B V8H sing 519 n n O5B C5B V8H sing 520 n n O5B PA V8H sing 521 n n C4B C5B V8H sing 522 n n C4B C3B V8H sing 523 n n PA O2A V8H doub 524 n n PA O1A V8H sing 525 n n O3B C3B V8H sing 526 n n C1B O1 V8H sing 527 n n C1B C2B V8H sing 528 n n C3B C2B V8H sing 529 n n C2B O2B V8H sing 530 n n N7N H1 V8H sing 531 n n N7N H2 V8H sing 532 n n C2N H3 V8H sing 533 n n C4N H4 V8H sing 534 n n C5N H5 V8H sing 535 n n C6N H6 V8H sing 536 n n C1D H7 V8H sing 537 n n C2D H8 V8H sing 538 n n O2D H9 V8H sing 539 n n C3D H10 V8H sing 540 n n O3D H11 V8H sing 541 n n C4D H12 V8H sing 542 n n C5D H13 V8H sing 543 n n C5D H14 V8H sing 544 n n O1N H15 V8H sing 545 n n O1A H16 V8H sing 546 n n C5B H17 V8H sing 547 n n C5B H18 V8H sing 548 n n C4B H19 V8H sing 549 n n C3B H20 V8H sing 550 n n O3B H21 V8H sing 551 n n C2B H22 V8H sing 552 n n O2B H23 V8H sing 553 n n C1B H24 V8H sing 554 n n O1 H25 V8H sing 555 n n C4N H26 V8H sing 556 n n # _atom_sites.entry_id 7OCQ _atom_sites.fract_transf_matrix[1][1] 0.01007 _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] 0.006356 _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] 0.004566 _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 V8H A 1 801 701 V8H 883 . D 3 MG A 1 802 702 MG MG . E 4 SO4 A 1 803 703 SO4 SO4 . F 5 EDO A 1 804 1001 EDO EDO . G 5 EDO A 1 805 1101 EDO EDO . H 6 GOL A 1 806 901 GOL GOL . I 7 CL A 1 807 1 CL CL . J 7 CL A 1 808 2 CL CL . K 7 CL A 1 809 4 CL CL . L 7 CL A 1 810 7 CL CL . M 8 EPE B 1 801 801 EPE EPE . N 8 EPE B 1 802 901 EPE EPE . O 9 NAI B 1 803 701 NAI NAI . P 3 MG B 1 804 702 MG MG . Q 4 SO4 B 1 805 703 SO4 SO4 . R 4 SO4 B 1 806 704 SO4 SO4 . S 6 GOL B 1 807 801 GOL GOL . T 7 CL B 1 808 3 CL CL . U 7 CL B 1 809 5 CL CL . V 7 CL B 1 810 6 CL CL . W 10 HOH A 1 901 10 HOH HOH . W 10 HOH A 2 902 33 HOH HOH . W 10 HOH A 3 903 1 HOH HOH . W 10 HOH A 4 904 15 HOH HOH . W 10 HOH A 5 905 25 HOH HOH . W 10 HOH A 6 906 3 HOH HOH . W 10 HOH A 7 907 11 HOH HOH . W 10 HOH A 8 908 39 HOH HOH . W 10 HOH A 9 909 32 HOH HOH . W 10 HOH A 10 910 17 HOH HOH . W 10 HOH A 11 911 21 HOH HOH . W 10 HOH A 12 912 35 HOH HOH . W 10 HOH A 13 913 22 HOH HOH . W 10 HOH A 14 914 40 HOH HOH . W 10 HOH A 15 915 26 HOH HOH . W 10 HOH A 16 916 23 HOH HOH . W 10 HOH A 17 917 37 HOH HOH . W 10 HOH A 18 918 27 HOH HOH . W 10 HOH A 19 919 16 HOH HOH . W 10 HOH A 20 920 9 HOH HOH . W 10 HOH A 21 921 45 HOH HOH . W 10 HOH A 22 922 24 HOH HOH . W 10 HOH A 23 923 19 HOH HOH . W 10 HOH A 24 924 20 HOH HOH . W 10 HOH A 25 925 2 HOH HOH . W 10 HOH A 26 926 18 HOH HOH . W 10 HOH A 27 927 38 HOH HOH . X 10 HOH B 1 901 28 HOH HOH . X 10 HOH B 2 902 44 HOH HOH . X 10 HOH B 3 903 30 HOH HOH . X 10 HOH B 4 904 14 HOH HOH . X 10 HOH B 5 905 5 HOH HOH . X 10 HOH B 6 906 41 HOH HOH . X 10 HOH B 7 907 29 HOH HOH . X 10 HOH B 8 908 706 HOH HOH . X 10 HOH B 9 909 42 HOH HOH . X 10 HOH B 10 910 705 HOH HOH . X 10 HOH B 11 911 13 HOH HOH . X 10 HOH B 12 912 46 HOH HOH . X 10 HOH B 13 913 12 HOH HOH . X 10 HOH B 14 914 4 HOH HOH . X 10 HOH B 15 915 43 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 O7N V8H . . . C 2 59.282 13.586 -16.175 0.7 97.39 ? O7N V8H 801 A 1 HETATM 2 C C7N V8H . . . C 2 58.451 12.789 -16.577 0.7 96.52 ? C7N V8H 801 A 1 HETATM 3 N N7N V8H . . . C 2 57.165 12.887 -16.239 0.7 96.24 ? N7N V8H 801 A 1 HETATM 4 C C3N V8H . . . C 2 58.884 11.665 -17.47 0.7 95.79 ? C3N V8H 801 A 1 HETATM 5 C C2N V8H . . . C 2 58.526 10.365 -17.138 0.7 96.52 ? C2N V8H 801 A 1 HETATM 6 C C4N V8H . . . C 2 59.692 11.955 -18.716 0.7 94.29 ? C4N V8H 801 A 1 HETATM 7 C C5N V8H . . . C 2 60.019 10.741 -19.455 0.7 93.63 ? C5N V8H 801 A 1 HETATM 8 C C6N V8H . . . C 2 59.604 9.485 -19.022 0.7 94.38 ? C6N V8H 801 A 1 HETATM 9 N N1N V8H . . . C 2 58.886 9.321 -17.899 0.7 95.91 ? N1N V8H 801 A 1 HETATM 10 C C1D V8H . . . C 2 58.488 7.965 -17.498 0.7 97.25 ? C1D V8H 801 A 1 HETATM 11 O O4D V8H . . . C 2 57.067 7.85 -17.401 0.7 96.77 ? O4D V8H 801 A 1 HETATM 12 C C2D V8H . . . C 2 59.053 7.593 -16.129 0.7 100.25 ? C2D V8H 801 A 1 HETATM 13 O O2D V8H . . . C 2 60.179 6.719 -16.26 0.7 101.27 ? O2D V8H 801 A 1 HETATM 14 C C3D V8H . . . C 2 57.903 6.936 -15.384 0.7 101.16 ? C3D V8H 801 A 1 HETATM 15 O O3D V8H . . . C 2 58.234 5.608 -14.968 0.7 102.92 ? O3D V8H 801 A 1 HETATM 16 C C4D V8H . . . C 2 56.736 6.922 -16.364 0.7 98.77 ? C4D V8H 801 A 1 HETATM 17 C C5D V8H . . . C 2 55.407 7.287 -15.71 0.7 99.21 ? C5D V8H 801 A 1 HETATM 18 O O5D V8H . . . C 2 55.461 8.608 -15.176 0.7 99.75 ? O5D V8H 801 A 1 HETATM 19 P PN V8H . . . C 2 54.284 9.158 -14.224 0.7 100.99 ? PN V8H 801 A 1 HETATM 20 O O1N V8H . . . C 2 54.829 10.297 -13.395 0.7 102.46 ? O1N V8H 801 A 1 HETATM 21 O O2N V8H . . . C 2 53.14 9.627 -15.09 0.7 99 ? O2N V8H 801 A 1 HETATM 22 O O3 V8H . . . C 2 53.766 7.984 -13.244 0.7 103.11 ? O3 V8H 801 A 1 HETATM 23 P PA V8H . . . C 2 52.662 8.241 -12.094 0.7 104.92 ? PA V8H 801 A 1 HETATM 24 O O1A V8H . . . C 2 53.132 7.603 -10.81 0.7 107.75 ? O1A V8H 801 A 1 HETATM 25 O O2A V8H . . . C 2 52.458 9.724 -11.884 0.7 104.78 ? O2A V8H 801 A 1 HETATM 26 O O5B V8H . . . C 2 51.255 7.587 -12.528 0.7 104 ? O5B V8H 801 A 1 HETATM 27 C C5B V8H . . . C 2 51.021 6.182 -12.45 0.7 104.71 ? C5B V8H 801 A 1 HETATM 28 C C4B V8H . . . C 2 49.521 5.914 -12.515 0.7 104.51 ? C4B V8H 801 A 1 HETATM 29 C C3B V8H . . . C 2 48.807 6.372 -11.251 0.7 106.71 ? C3B V8H 801 A 1 HETATM 30 O O3B V8H . . . C 2 47.696 7.211 -11.586 0.7 105.46 ? O3B V8H 801 A 1 HETATM 31 C C2B V8H . . . C 2 48.363 5.103 -10.542 0.7 108.77 ? C2B V8H 801 A 1 HETATM 32 O O2B V8H . . . C 2 46.961 5.122 -10.251 0.7 109.33 ? O2B V8H 801 A 1 HETATM 33 C C1B V8H . . . C 2 48.702 3.951 -11.479 0.7 107.59 ? C1B V8H 801 A 1 HETATM 34 O O4B V8H . . . C 2 49.283 4.511 -12.66 0.7 105.02 ? O4B V8H 801 A 1 HETATM 35 O O1 V8H . . . C 2 49.629 3.055 -10.855 0.7 109.53 ? O1 V8H 801 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 35 #