data_1OD9 # _model_server_result.job_id 5PyZ5JHMIX0bqkCnGeZi7Q _model_server_result.datetime_utc '2024-11-07 10:44:27' _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 1od9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 1OD9 # _exptl.entry_id 1OD9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 426.418 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' _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 1OD9 _cell.length_a 67.86 _cell.length_b 67.86 _cell.length_c 69.247 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1OD9 _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 PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 22 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 22 _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 79 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 79 _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 2.042 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C19 H26 N2 O9' _chem_comp.formula_weight 426.418 _chem_comp.id BND _chem_comp.mon_nstd_flag . _chem_comp.name 'methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC;methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulosidonic acid;methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-D-galacto-non-2-ulosidonic acid;methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-galacto-non-2-ulosidonic acid' # 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 CY1 O2 BND sing 70 n n CY1 HY11 BND sing 71 n n CY1 HY12 BND sing 72 n n CY1 HY13 BND sing 73 n n C1 O1A BND doub 74 n n C1 O1B BND sing 75 n n C1 C2 BND sing 76 n n O1B HO1B BND sing 77 n n C2 O2 BND sing 78 n n C2 C3 BND sing 79 n n C2 O6 BND sing 80 n n C3 C4 BND sing 81 n n C3 H32 BND sing 82 n n C3 H31 BND sing 83 n n C4 O4 BND sing 84 n n C4 C5 BND sing 85 n n C4 H4 BND sing 86 n n O4 HO4 BND sing 87 n n C5 N5 BND sing 88 n n C5 C6 BND sing 89 n n C5 H5 BND sing 90 n n N5 C10 BND sing 91 n n N5 HN5 BND sing 92 n n C10 O10 BND doub 93 n n C10 C11 BND sing 94 n n C11 H111 BND sing 95 n n C11 H113 BND sing 96 n n C11 H112 BND sing 97 n n C6 O6 BND sing 98 n n C6 C7 BND sing 99 n n C6 H6 BND sing 100 n n C7 O7 BND sing 101 n n C7 C8 BND sing 102 n n C7 H7 BND sing 103 n n O7 HO7 BND sing 104 n n C8 O8 BND sing 105 n n C8 C9 BND sing 106 n n C8 H8 BND sing 107 n n O8 HO8 BND sing 108 n n C9 NX6 BND sing 109 n n C9 H92 BND sing 110 n n C9 H91 BND sing 111 n n NX6 C12 BND sing 112 n n NX6 HE BND sing 113 n n C12 O12 BND doub 114 n n C12 C1G BND sing 115 n n C1G CD1 BND doub 116 n y C1G CD2 BND sing 117 n y CD1 CE1 BND sing 118 n y CD1 HD1 BND sing 119 n n CE1 C1Z BND doub 120 n y CE1 HE1 BND sing 121 n n CD2 CE2 BND doub 122 n y CD2 HD2 BND sing 123 n n CE2 C1Z BND sing 124 n y CE2 HE2 BND sing 125 n n C1Z H1Z BND sing 126 n n # _atom_sites.entry_id 1OD9 _atom_sites.fract_transf_matrix[1][1] 0.014736 _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] 0.014736 _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] 0.014441 _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 BND A 1 201 201 BND BND . C 3 SO4 A 1 202 202 SO4 SO4 . D 4 HOH A 1 2001 2001 HOH HOH . D 4 HOH A 2 2002 2002 HOH HOH . D 4 HOH A 3 2003 2003 HOH HOH . D 4 HOH A 4 2004 2004 HOH HOH . D 4 HOH A 5 2005 2005 HOH HOH . D 4 HOH A 6 2006 2006 HOH HOH . D 4 HOH A 7 2007 2007 HOH HOH . D 4 HOH A 8 2008 2008 HOH HOH . D 4 HOH A 9 2009 2009 HOH HOH . D 4 HOH A 10 2010 2010 HOH HOH . D 4 HOH A 11 2011 2011 HOH HOH . D 4 HOH A 12 2012 2012 HOH HOH . D 4 HOH A 13 2013 2013 HOH HOH . D 4 HOH A 14 2014 2014 HOH HOH . D 4 HOH A 15 2015 2015 HOH HOH . D 4 HOH A 16 2016 2016 HOH HOH . D 4 HOH A 17 2017 2017 HOH HOH . D 4 HOH A 18 2018 2018 HOH HOH . D 4 HOH A 19 2019 2019 HOH HOH . D 4 HOH A 20 2020 2020 HOH HOH . D 4 HOH A 21 2021 2021 HOH HOH . D 4 HOH A 22 2022 2022 HOH HOH . D 4 HOH A 23 2023 2023 HOH HOH . D 4 HOH A 24 2024 2024 HOH HOH . D 4 HOH A 25 2025 2025 HOH HOH . D 4 HOH A 26 2026 2026 HOH HOH . D 4 HOH A 27 2027 2027 HOH HOH . D 4 HOH A 28 2028 2028 HOH HOH . D 4 HOH A 29 2029 2029 HOH HOH . D 4 HOH A 30 2030 2030 HOH HOH . D 4 HOH A 31 2031 2031 HOH HOH . D 4 HOH A 32 2032 2032 HOH HOH . D 4 HOH A 33 2033 2033 HOH HOH . D 4 HOH A 34 2034 2034 HOH HOH . D 4 HOH A 35 2035 2035 HOH HOH . D 4 HOH A 36 2036 2036 HOH HOH . D 4 HOH A 37 2037 2037 HOH HOH . D 4 HOH A 38 2038 2038 HOH HOH . D 4 HOH A 39 2039 2039 HOH HOH . D 4 HOH A 40 2040 2040 HOH HOH . D 4 HOH A 41 2041 2041 HOH HOH . D 4 HOH A 42 2042 2042 HOH HOH . D 4 HOH A 43 2043 2043 HOH HOH . D 4 HOH A 44 2044 2044 HOH HOH . D 4 HOH A 45 2045 2045 HOH HOH . D 4 HOH A 46 2046 2046 HOH HOH . D 4 HOH A 47 2047 2047 HOH HOH . D 4 HOH A 48 2048 2048 HOH HOH . D 4 HOH A 49 2049 2049 HOH HOH . D 4 HOH A 50 2050 2050 HOH HOH . D 4 HOH A 51 2051 2051 HOH HOH . D 4 HOH A 52 2052 2052 HOH HOH . D 4 HOH A 53 2053 2053 HOH HOH . D 4 HOH A 54 2054 2054 HOH HOH . D 4 HOH A 55 2055 2055 HOH HOH . D 4 HOH A 56 2056 2056 HOH HOH . D 4 HOH A 57 2057 2057 HOH HOH . D 4 HOH A 58 2058 2058 HOH HOH . D 4 HOH A 59 2059 2059 HOH HOH . D 4 HOH A 60 2060 2060 HOH HOH . D 4 HOH A 61 2061 2061 HOH HOH . D 4 HOH A 62 2062 2062 HOH HOH . D 4 HOH A 63 2063 2063 HOH HOH . D 4 HOH A 64 2064 2064 HOH HOH . D 4 HOH A 65 2065 2065 HOH HOH . D 4 HOH A 66 2066 2066 HOH HOH . D 4 HOH A 67 2067 2067 HOH HOH . D 4 HOH A 68 2068 2068 HOH HOH . D 4 HOH A 69 2069 2069 HOH HOH . D 4 HOH A 70 2070 2070 HOH HOH . D 4 HOH A 71 2071 2071 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 CY1 BND . . . B 2 66.117 39.999 35.798 1 38.17 ? CY1 BND 201 A 1 HETATM 2 C C1 BND . . . B 2 63.387 39.15 34.815 1 34.44 ? C1 BND 201 A 1 HETATM 3 O O1A BND . . . B 2 62.477 39.701 35.476 1 33.95 ? O1A BND 201 A 1 HETATM 4 O O1B BND . . . B 2 63.561 39.332 33.572 1 37.66 ? O1B BND 201 A 1 HETATM 5 C C2 BND . . . B 2 64.357 38.218 35.587 1 33.92 ? C2 BND 201 A 1 HETATM 6 O O2 BND . . . B 2 65.131 39.029 36.424 1 36.77 ? O2 BND 201 A 1 HETATM 7 C C3 BND . . . B 2 63.629 37.21 36.493 1 39.82 ? C3 BND 201 A 1 HETATM 8 C C4 BND . . . B 2 62.943 36.101 35.644 1 37.36 ? C4 BND 201 A 1 HETATM 9 O O4 BND . . . B 2 62.499 35.06 36.486 1 39.32 ? O4 BND 201 A 1 HETATM 10 C C5 BND . . . B 2 63.857 35.467 34.578 1 34.57 ? C5 BND 201 A 1 HETATM 11 N N5 BND . . . B 2 63.007 34.579 33.78 1 40.42 ? N5 BND 201 A 1 HETATM 12 C C10 BND . . . B 2 63.327 33.281 33.649 1 41.15 ? C10 BND 201 A 1 HETATM 13 O O10 BND . . . B 2 64.346 32.762 34.157 1 34.66 ? O10 BND 201 A 1 HETATM 14 C C11 BND . . . B 2 62.393 32.404 32.845 1 39.71 ? C11 BND 201 A 1 HETATM 15 C C6 BND . . . B 2 64.487 36.601 33.741 1 33.45 ? C6 BND 201 A 1 HETATM 16 O O6 BND . . . B 2 65.202 37.53 34.625 1 31.64 ? O6 BND 201 A 1 HETATM 17 C C7 BND . . . B 2 65.415 36.171 32.616 1 35.45 ? C7 BND 201 A 1 HETATM 18 O O7 BND . . . B 2 66.484 35.434 33.17 1 37.35 ? O7 BND 201 A 1 HETATM 19 C C8 BND . . . B 2 66.038 37.376 31.888 1 27.15 ? C8 BND 201 A 1 HETATM 20 O O8 BND . . . B 2 65.072 38.309 31.454 1 29.88 ? O8 BND 201 A 1 HETATM 21 C C9 BND . . . B 2 66.872 36.852 30.701 1 35.05 ? C9 BND 201 A 1 HETATM 22 N NX6 BND . . . B 2 67.583 37.943 30.034 1 29.88 ? NX6 BND 201 A 1 HETATM 23 C C12 BND . . . B 2 68.812 38.318 30.384 1 35.44 ? C12 BND 201 A 1 HETATM 24 O O12 BND . . . B 2 69.525 37.552 31.004 1 38.87 ? O12 BND 201 A 1 HETATM 25 C C1G BND . . . B 2 69.411 39.656 30.072 1 24.98 ? C1G BND 201 A 1 HETATM 26 C CD1 BND . . . B 2 68.78 40.542 29.199 1 24.54 ? CD1 BND 201 A 1 HETATM 27 C CE1 BND . . . B 2 69.339 41.777 28.901 1 38.72 ? CE1 BND 201 A 1 HETATM 28 C CD2 BND . . . B 2 70.62 40.03 30.647 1 30.24 ? CD2 BND 201 A 1 HETATM 29 C CE2 BND . . . B 2 71.202 41.275 30.362 1 24.03 ? CE2 BND 201 A 1 HETATM 30 C C1Z BND . . . B 2 70.553 42.144 29.487 1 35.17 ? C1Z BND 201 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 30 #