data_1O9M # _model_server_result.job_id CQUUM6PW2UIn1X1VMfwa5w _model_server_result.datetime_utc '2024-10-18 14:37:14' _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 1o9m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2500}' # _entry.id 1O9M # _exptl.entry_id 1O9M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PAROMOMYCIN (RING 2)' _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 1O9M _cell.length_a 32.8 _cell.length_b 46.55 _cell.length_c 88.81 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1O9M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PQS _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 _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 D _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 C O1 BDG . B BDG 2499 1_555 D C4 PA2 . B PA2 2500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 D O2 PA2 . B PA2 2500 1_555 E C2 P24 . B P24 2501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 D N1 PA2 . B PA2 2500 1_555 F C3 42B . B 42B 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.774 ? hydrog WATSON-CRICK hydrog1 A N1 G 2 A G 1403 1_555 B N3 C 22 B C 1498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 2 A G 1403 1_555 B O2 C 22 B C 1498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 2 A G 1403 1_555 B N4 C 22 B C 1498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 C 3 A C 1404 1_555 B N1 G 21 B G 1497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 C 3 A C 1404 1_555 B O6 G 21 B G 1497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 C 3 A C 1404 1_555 B N2 G 21 B G 1497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 G 4 A G 1405 1_555 B N3 C 20 B C 1496 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 G 4 A G 1405 1_555 B O2 C 20 B C 1496 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 G 4 A G 1405 1_555 B N4 C 20 B C 1496 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 C 6 A C 1407 1_555 B N1 G 18 B G 1494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N4 C 6 A C 1407 1_555 B O6 G 18 B G 1494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O2 C 6 A C 1407 1_555 B N2 G 18 B G 1494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 C 8 A C 1409 1_555 B N1 G 15 B G 1491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 C 8 A C 1409 1_555 B O6 G 15 B G 1491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 C 8 A C 1409 1_555 B N2 G 15 B G 1491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 A 9 A A 1410 1_555 B N3 U 14 B U 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N6 A 9 A A 1410 1_555 B O4 U 14 B U 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 C 10 A C 1411 1_555 B N1 G 13 B G 1489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N4 C 10 A C 1411 1_555 B O6 G 13 B G 1489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O2 C 10 A C 1411 1_555 B N2 G 13 B G 1489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 C 11 A C 1412 1_555 B N1 G 12 B G 1488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 C 11 A C 1412 1_555 B O6 G 12 B G 1488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 C 11 A C 1412 1_555 B N2 G 12 B G 1488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 G 12 A G 1488 1_555 B N3 C 11 B C 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 G 12 A G 1488 1_555 B O2 C 11 B C 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 G 12 A G 1488 1_555 B N4 C 11 B C 1412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N1 G 13 A G 1489 1_555 B N3 C 10 B C 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N2 G 13 A G 1489 1_555 B O2 C 10 B C 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O6 G 13 A G 1489 1_555 B N4 C 10 B C 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N3 U 14 A U 1490 1_555 B N1 A 9 B A 1410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A O4 U 14 A U 1490 1_555 B N6 A 9 B A 1410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N1 G 15 A G 1491 1_555 B N3 C 8 B C 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N2 G 15 A G 1491 1_555 B O2 C 8 B C 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A O6 G 15 A G 1491 1_555 B N4 C 8 B C 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog35 A N6 A 17 A A 1493 1_555 B N1 A 7 B A 1408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-C MISPAIR' hydrog36 A N6 A 17 A A 1493 1_555 B O2 C 8 B C 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A N1 G 18 A G 1494 1_555 B N3 C 6 B C 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 A N2 G 18 A G 1494 1_555 B O2 C 6 B C 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 A O6 G 18 A G 1494 1_555 B N4 C 6 B C 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog40 A N3 U 19 A U 1495 1_555 B O2 U 5 B U 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog41 A O4 U 19 A U 1495 1_555 B N3 U 5 B U 1406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 A N3 C 20 A C 1496 1_555 B N1 G 4 B G 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 A N4 C 20 A C 1496 1_555 B O6 G 4 B G 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 A O2 C 20 A C 1496 1_555 B N2 G 4 B G 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 A N1 G 21 A G 1497 1_555 B N3 C 3 B C 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 A N2 G 21 A G 1497 1_555 B O2 C 3 B C 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 A O6 G 21 A G 1497 1_555 B N4 C 3 B C 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 A N3 C 22 A C 1498 1_555 B N1 G 2 B G 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog49 A N4 C 22 A C 1498 1_555 B O6 G 2 B G 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog50 A O2 C 22 A C 1498 1_555 B N2 G 2 B G 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C6 H14 N2 O2' _chem_comp.formula_weight 146.188 _chem_comp.id PA2 _chem_comp.mon_nstd_flag . _chem_comp.name 'PAROMOMYCIN (RING 2)' _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 C1 N1 PA2 sing 185 n n C1 C2 PA2 sing 186 n n C1 C6 PA2 sing 187 n n C1 H1 PA2 sing 188 n n N1 HN11 PA2 sing 189 n n N1 HN12 PA2 sing 190 n n C2 O2 PA2 sing 191 n n C2 C3 PA2 sing 192 n n C2 H2 PA2 sing 193 n n O2 HO2 PA2 sing 194 n n C3 O3 PA2 sing 195 n n C3 C4 PA2 sing 196 n n C3 H3 PA2 sing 197 n n O3 HO3 PA2 sing 198 n n C4 C5 PA2 sing 199 n n C4 H41 PA2 sing 200 n n C4 H42 PA2 sing 201 n n C5 N5 PA2 sing 202 n n C5 C6 PA2 sing 203 n n C5 H5 PA2 sing 204 n n N5 HN51 PA2 sing 205 n n N5 HN52 PA2 sing 206 n n C6 H61 PA2 sing 207 n n C6 H62 PA2 sing 208 n n # _atom_sites.entry_id 1O9M _atom_sites.fract_transf_matrix[1][1] 0.030488 _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] 0.021482 _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] 0.01126 _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 BDG B 1 2499 2499 BDG BDG . D 3 PA2 B 1 2500 2500 PA2 PA2 . E 4 P24 B 1 2501 2501 P24 P24 . F 5 42B B 1 2502 2502 42B 42B . G 6 HOH A 1 2001 2001 HOH HOH . G 6 HOH A 2 2002 2002 HOH HOH . G 6 HOH A 3 2003 2003 HOH HOH . G 6 HOH A 4 2004 2004 HOH HOH . G 6 HOH A 5 2005 2005 HOH HOH . G 6 HOH A 6 2006 2006 HOH HOH . G 6 HOH A 7 2007 2007 HOH HOH . G 6 HOH A 8 2008 2008 HOH HOH . G 6 HOH A 9 2009 2009 HOH HOH . G 6 HOH A 10 2010 2010 HOH HOH . G 6 HOH A 11 2011 2011 HOH HOH . G 6 HOH A 12 2012 2012 HOH HOH . G 6 HOH A 13 2013 2013 HOH HOH . G 6 HOH A 14 2014 2014 HOH HOH . G 6 HOH A 15 2015 2015 HOH HOH . G 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH A 17 2017 2017 HOH HOH . G 6 HOH A 18 2018 2018 HOH HOH . G 6 HOH A 19 2019 2019 HOH HOH . G 6 HOH A 20 2020 2020 HOH HOH . G 6 HOH A 21 2021 2021 HOH HOH . G 6 HOH A 22 2022 2022 HOH HOH . G 6 HOH A 23 2023 2023 HOH HOH . G 6 HOH A 24 2024 2024 HOH HOH . G 6 HOH A 25 2025 2025 HOH HOH . G 6 HOH A 26 2026 2026 HOH HOH . G 6 HOH A 27 2027 2027 HOH HOH . G 6 HOH A 28 2028 2028 HOH HOH . G 6 HOH A 29 2029 2029 HOH HOH . G 6 HOH A 30 2030 2030 HOH HOH . H 6 HOH B 1 2001 2001 HOH HOH . H 6 HOH B 2 2002 2002 HOH HOH . H 6 HOH B 3 2003 2003 HOH HOH . H 6 HOH B 4 2004 2004 HOH HOH . H 6 HOH B 5 2005 2005 HOH HOH . H 6 HOH B 6 2006 2006 HOH HOH . H 6 HOH B 7 2007 2007 HOH HOH . H 6 HOH B 8 2008 2008 HOH HOH . H 6 HOH B 9 2009 2009 HOH HOH . H 6 HOH B 10 2010 2010 HOH HOH . H 6 HOH B 11 2011 2011 HOH HOH . H 6 HOH B 12 2012 2012 HOH HOH . H 6 HOH B 13 2013 2013 HOH HOH . H 6 HOH B 14 2014 2014 HOH HOH . H 6 HOH B 15 2015 2015 HOH HOH . H 6 HOH B 16 2016 2016 HOH HOH . H 6 HOH B 17 2017 2017 HOH HOH . H 6 HOH B 18 2018 2018 HOH HOH . H 6 HOH B 19 2019 2019 HOH HOH . H 6 HOH B 20 2020 2020 HOH HOH . H 6 HOH B 21 2021 2021 HOH HOH . H 6 HOH B 22 2022 2022 HOH HOH . H 6 HOH B 23 2023 2023 HOH HOH . H 6 HOH B 24 2024 2024 HOH HOH . H 6 HOH B 25 2025 2025 HOH HOH . H 6 HOH B 26 2026 2026 HOH HOH . H 6 HOH B 27 2027 2027 HOH HOH . H 6 HOH B 28 2028 2028 HOH HOH . H 6 HOH B 29 2029 2029 HOH HOH . H 6 HOH B 30 2030 2030 HOH HOH . H 6 HOH B 31 2031 2031 HOH HOH . H 6 HOH B 32 2032 2032 HOH HOH . H 6 HOH B 33 2033 2033 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 PA2 . . . D 3 -8.907 17.643 6.092 1 29.51 ? C1 PA2 2500 B 1 HETATM 2 N N1 PA2 . . . D 3 -10.201 18.018 6.728 1 29.49 ? N1 PA2 2500 B 1 HETATM 3 C C2 PA2 . . . D 3 -7.983 17.07 7.158 1 30.68 ? C2 PA2 2500 B 1 HETATM 4 O O2 PA2 . . . D 3 -7.832 18.033 8.158 1 35.52 ? O2 PA2 2500 B 1 HETATM 5 C C3 PA2 . . . D 3 -6.604 16.679 6.539 1 29.87 ? C3 PA2 2500 B 1 HETATM 6 O O3 PA2 . . . D 3 -5.735 16.111 7.566 1 30.36 ? O3 PA2 2500 B 1 HETATM 7 C C4 PA2 . . . D 3 -6.82 15.599 5.402 1 27.48 ? C4 PA2 2500 B 1 HETATM 8 C C5 PA2 . . . D 3 -7.727 16.167 4.321 1 27.04 ? C5 PA2 2500 B 1 HETATM 9 N N5 PA2 . . . D 3 -7.9 15.165 3.28 1 26.83 ? N5 PA2 2500 B 1 HETATM 10 C C6 PA2 . . . D 3 -9.091 16.574 4.94 1 28.14 ? C6 PA2 2500 B 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #