data_9CKO # _model_server_result.job_id JAe0TfTtidTpG1tllUZTmg _model_server_result.datetime_utc '2025-07-20 07:25:37' _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 9cko # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":602}' # _entry.id 9CKO # _exptl.entry_id 9CKO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.278 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SANGIVAMYCIN _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 9CKO _cell.length_a 140.259 _cell.length_b 140.259 _cell.length_c 78.766 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CKO _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 3 _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 covale ? covale1 A N MET 1 A MET 1 1_555 B C ACE . A ACE 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? metalc ? metalc1 A O HIS 274 A HIS 274 1_555 D K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc2 A O ILE 275 A ILE 275 1_555 D K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.354 ? metalc ? metalc3 A O MET 278 A MET 278 1_555 D K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.039 ? metalc ? metalc4 A O ASN 280 A ASN 280 1_555 D K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc5 A O GLY 282 A GLY 282 1_555 D K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc6 D K K . A K 603 1_555 E O HOH . A HOH 735 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc7 D K K . A K 603 1_555 E O HOH . A HOH 759 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? # _chem_comp.formula 'C12 H15 N5 O5' _chem_comp.formula_weight 309.278 _chem_comp.id SGV _chem_comp.mon_nstd_flag . _chem_comp.name SANGIVAMYCIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide # 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 N1 C2 SGV doub 296 n y N1 C6 SGV sing 297 n y C2 N3 SGV sing 298 n y N3 C4 SGV doub 299 n y C4 C5 SGV sing 300 n y C4 N9 SGV sing 301 n y C5 C6 SGV doub 302 n y C5 C7 SGV sing 303 n y C6 N6 SGV sing 304 n n C7 C8 SGV doub 305 n y C7 C10 SGV sing 306 n n C8 N9 SGV sing 307 n y N9 C1' SGV sing 308 n n C1' C2' SGV sing 309 n n C1' O4' SGV sing 310 n n C10 N11 SGV sing 311 n n C10 O12 SGV doub 312 n n C2' O2' SGV sing 313 n n C2' C3' SGV sing 314 n n C3' O3' SGV sing 315 n n C3' C4' SGV sing 316 n n C4' O4' SGV sing 317 n n C4' C5' SGV sing 318 n n C5' O5' SGV sing 319 n n C2 H2 SGV sing 320 n n N6 HN6 SGV sing 321 n n N6 HN6A SGV sing 322 n n C8 H8 SGV sing 323 n n C1' H1' SGV sing 324 n n N11 HN11 SGV sing 325 n n N11 HN1A SGV sing 326 n n C2' H2' SGV sing 327 n n O2' HO2' SGV sing 328 n n C3' H3' SGV sing 329 n n O3' HO3' SGV sing 330 n n C4' H4' SGV sing 331 n n C5' H5' SGV sing 332 n n C5' "H5'A" SGV sing 333 n n O5' HO5' SGV sing 334 n n # _atom_sites.entry_id 9CKO _atom_sites.fract_transf_matrix[1][1] 0.00713 _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] 0.00713 _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] 0.012696 _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 ACE A 1 601 0 ACE ACE . C 3 SGV A 1 602 601 SGV SGV . D 4 K A 1 603 1 K K . E 5 HOH A 1 701 73 HOH HOH . E 5 HOH A 2 702 72 HOH HOH . E 5 HOH A 3 703 4 HOH HOH . E 5 HOH A 4 704 37 HOH HOH . E 5 HOH A 5 705 94 HOH HOH . E 5 HOH A 6 706 104 HOH HOH . E 5 HOH A 7 707 116 HOH HOH . E 5 HOH A 8 708 1 HOH HOH . E 5 HOH A 9 709 122 HOH HOH . E 5 HOH A 10 710 90 HOH HOH . E 5 HOH A 11 711 31 HOH HOH . E 5 HOH A 12 712 76 HOH HOH . E 5 HOH A 13 713 33 HOH HOH . E 5 HOH A 14 714 13 HOH HOH . E 5 HOH A 15 715 61 HOH HOH . E 5 HOH A 16 716 32 HOH HOH . E 5 HOH A 17 717 127 HOH HOH . E 5 HOH A 18 718 124 HOH HOH . E 5 HOH A 19 719 46 HOH HOH . E 5 HOH A 20 720 47 HOH HOH . E 5 HOH A 21 721 86 HOH HOH . E 5 HOH A 22 722 63 HOH HOH . E 5 HOH A 23 723 69 HOH HOH . E 5 HOH A 24 724 6 HOH HOH . E 5 HOH A 25 725 30 HOH HOH . E 5 HOH A 26 726 87 HOH HOH . E 5 HOH A 27 727 51 HOH HOH . E 5 HOH A 28 728 77 HOH HOH . E 5 HOH A 29 729 12 HOH HOH . E 5 HOH A 30 730 114 HOH HOH . E 5 HOH A 31 731 45 HOH HOH . E 5 HOH A 32 732 21 HOH HOH . E 5 HOH A 33 733 8 HOH HOH . E 5 HOH A 34 734 100 HOH HOH . E 5 HOH A 35 735 126 HOH HOH . E 5 HOH A 36 736 44 HOH HOH . E 5 HOH A 37 737 55 HOH HOH . E 5 HOH A 38 738 83 HOH HOH . E 5 HOH A 39 739 121 HOH HOH . E 5 HOH A 40 740 23 HOH HOH . E 5 HOH A 41 741 68 HOH HOH . E 5 HOH A 42 742 2 HOH HOH . E 5 HOH A 43 743 18 HOH HOH . E 5 HOH A 44 744 3 HOH HOH . E 5 HOH A 45 745 102 HOH HOH . E 5 HOH A 46 746 11 HOH HOH . E 5 HOH A 47 747 74 HOH HOH . E 5 HOH A 48 748 123 HOH HOH . E 5 HOH A 49 749 52 HOH HOH . E 5 HOH A 50 750 54 HOH HOH . E 5 HOH A 51 751 120 HOH HOH . E 5 HOH A 52 752 56 HOH HOH . E 5 HOH A 53 753 15 HOH HOH . E 5 HOH A 54 754 66 HOH HOH . E 5 HOH A 55 755 22 HOH HOH . E 5 HOH A 56 756 20 HOH HOH . E 5 HOH A 57 757 125 HOH HOH . E 5 HOH A 58 758 50 HOH HOH . E 5 HOH A 59 759 115 HOH HOH . E 5 HOH A 60 760 113 HOH HOH . E 5 HOH A 61 761 119 HOH HOH . E 5 HOH A 62 762 92 HOH HOH . E 5 HOH A 63 763 49 HOH HOH . E 5 HOH A 64 764 117 HOH HOH . E 5 HOH A 65 765 60 HOH HOH . E 5 HOH A 66 766 10 HOH HOH . E 5 HOH A 67 767 82 HOH HOH . E 5 HOH A 68 768 89 HOH HOH . E 5 HOH A 69 769 84 HOH HOH . E 5 HOH A 70 770 41 HOH HOH . E 5 HOH A 71 771 14 HOH HOH . E 5 HOH A 72 772 105 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 N N1 SGV . . . C 3 -40.75 -3.525 16.298 1 66.32 ? N1 SGV 602 A 1 HETATM 2 C C2 SGV . . . C 3 -41.205 -4.763 16.136 1 62.7 ? C2 SGV 602 A 1 HETATM 3 N N3 SGV . . . C 3 -41.089 -5.783 16.96 1 61.97 ? N3 SGV 602 A 1 HETATM 4 C C4 SGV . . . C 3 -40.425 -5.468 18.07 1 66.08 ? C4 SGV 602 A 1 HETATM 5 C C5 SGV . . . C 3 -39.881 -4.22 18.393 1 67.7 ? C5 SGV 602 A 1 HETATM 6 C C6 SGV . . . C 3 -40.082 -3.215 17.416 1 68.34 ? C6 SGV 602 A 1 HETATM 7 N N6 SGV . . . C 3 -39.633 -1.967 17.557 1 69.47 ? N6 SGV 602 A 1 HETATM 8 C C7 SGV . . . C 3 -39.261 -4.359 19.683 1 70.98 ? C7 SGV 602 A 1 HETATM 9 C C8 SGV . . . C 3 -39.462 -5.662 20.053 1 73 ? C8 SGV 602 A 1 HETATM 10 N N9 SGV . . . C 3 -40.161 -6.326 19.094 1 67.58 ? N9 SGV 602 A 1 HETATM 11 C C1' SGV . . . C 3 -40.539 -7.75 19.181 1 70.19 ? C1' SGV 602 A 1 HETATM 12 C C10 SGV . . . C 3 -38.544 -3.359 20.487 1 78.07 ? C10 SGV 602 A 1 HETATM 13 N N11 SGV . . . C 3 -37.813 -2.449 19.826 1 89.07 ? N11 SGV 602 A 1 HETATM 14 O O12 SGV . . . C 3 -38.614 -3.36 21.716 1 75.55 ? O12 SGV 602 A 1 HETATM 15 C C2' SGV . . . C 3 -39.502 -8.643 18.506 1 70.66 ? C2' SGV 602 A 1 HETATM 16 O O2' SGV . . . C 3 -40.148 -9.772 17.935 1 68.02 ? O2' SGV 602 A 1 HETATM 17 C C3' SGV . . . C 3 -38.613 -9.038 19.677 1 67.21 ? C3' SGV 602 A 1 HETATM 18 O O3' SGV . . . C 3 -37.955 -10.278 19.478 1 64.94 ? O3' SGV 602 A 1 HETATM 19 C C4' SGV . . . C 3 -39.585 -9.099 20.841 1 69.51 ? C4' SGV 602 A 1 HETATM 20 O O4' SGV . . . C 3 -40.593 -8.102 20.54 1 73.3 ? O4' SGV 602 A 1 HETATM 21 C C5' SGV . . . C 3 -39.009 -8.807 22.198 1 74.9 ? C5' SGV 602 A 1 HETATM 22 O O5' SGV . . . C 3 -37.751 -9.444 22.387 1 79.01 ? O5' SGV 602 A 1 HETATM 23 H H2 SGV . . . C 3 -41.66 -4.923 15.342 1 75.93 ? H2 SGV 602 A 1 HETATM 24 H HN6 SGV . . . C 3 -38.995 -1.68 17.056 1 84.06 ? HN6 SGV 602 A 1 HETATM 25 H HN6A SGV . . . C 3 -39.985 -1.454 18.15 1 84.06 ? HN6A SGV 602 A 1 HETATM 26 H H8 SGV . . . C 3 -39.194 -6.105 20.826 1 88.29 ? H8 SGV 602 A 1 HETATM 27 H H1' SGV . . . C 3 -41.403 -7.848 18.752 1 84.92 ? H1' SGV 602 A 1 HETATM 28 H HN11 SGV . . . C 3 -37.746 -2.429 18.97 1 107.57 ? HN11 SGV 602 A 1 HETATM 29 H HN1A SGV . . . C 3 -37.378 -1.85 20.265 1 107.57 ? HN1A SGV 602 A 1 HETATM 30 H H2' SGV . . . C 3 -38.985 -8.13 17.865 1 85.49 ? H2' SGV 602 A 1 HETATM 31 H HO2' SGV . . . C 3 -39.58 -10.205 17.474 1 82.32 ? HO2' SGV 602 A 1 HETATM 32 H H3' SGV . . . C 3 -37.969 -8.33 19.837 1 81.35 ? H3' SGV 602 A 1 HETATM 33 H HO3' SGV . . . C 3 -37.46 -10.212 18.79 1 78.62 ? HO3' SGV 602 A 1 HETATM 34 H H4' SGV . . . C 3 -40.033 -9.959 20.859 1 84.11 ? H4' SGV 602 A 1 HETATM 35 H H5' SGV . . . C 3 -38.943 -7.842 22.279 1 90.57 ? H5' SGV 602 A 1 HETATM 36 H "H5'A" SGV . . . C 3 -39.663 -9.093 22.854 1 90.57 ? "H5'A" SGV 602 A 1 HETATM 37 H HO5' SGV . . . C 3 -37.314 -8.997 22.963 1 95.5 ? HO5' SGV 602 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 37 #