data_3NYM # _model_server_result.job_id 0XEsqORU7aUnroPt9FyzCQ _model_server_result.datetime_utc '2025-02-05 14:10:05' _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 3nym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":126}' # _entry.id 3NYM # _exptl.entry_id 3NYM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 106.12 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DI(HYDROXYETHYL)ETHER _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.79 _cell.angle_gamma 90 _cell.entry_id 3NYM _cell.length_a 43.646 _cell.length_b 35.741 _cell.length_c 101.565 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NYM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 F N 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 C ALA 3 A ALA 0 1_555 A N MSE 4 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 4 A MSE 1 1_555 A N GLU 5 A GLU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C ILE 10 A ILE 7 1_555 A N MLY 11 A MLY 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C MLY 11 A MLY 8 1_555 A N LYS 12 A LYS 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C ASN 40 A ASN 37 1_555 A N MSE 41 A MSE 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C MSE 41 A MSE 38 1_555 A N MLY 42 A MLY 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C MLY 42 A MLY 39 1_555 A N TRP 43 A TRP 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C ILE 44 A ILE 41 1_555 A N MLY 45 A MLY 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale9 A C MLY 45 A MLY 42 1_555 A N ASP 46 A ASP 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale10 A C LEU 61 A LEU 58 1_555 A N MLY 62 A MLY 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 A C MLY 62 A MLY 59 1_555 A N ASN 63 A ASN 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale12 A C TYR 67 A TYR 64 1_555 A N MSE 68 A MSE 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 A C MSE 68 A MSE 65 1_555 A N GLU 69 A GLU 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale14 A C ASP 77 A ASP 74 1_555 A N MLY 78 A MLY 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 A C MLY 78 A MLY 75 1_555 A N ASN 79 A ASN 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale16 A C PHE 80 A PHE 77 1_555 A N MLY 81 A MLY 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 A C MLY 81 A MLY 78 1_555 A N ILE 82 A ILE 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale18 A C PHE 88 A PHE 85 1_555 A N MSE 89 A MSE 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale19 A C MSE 89 A MSE 86 1_555 A N ALA 90 A ALA 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale20 A C ALA 90 A ALA 87 1_555 A N MSE 91 A MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale21 A C MSE 91 A MSE 88 1_555 A N ILE 92 A ILE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale22 B C ILE 10 B ILE 7 1_555 B N MLY 11 B MLY 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale23 B C MLY 11 B MLY 8 1_555 B N LYS 12 B LYS 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale24 B C ASN 40 B ASN 37 1_555 B N MSE 41 B MSE 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale25 B C MSE 41 B MSE 38 1_555 B N MLY 42 B MLY 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale26 B C MLY 42 B MLY 39 1_555 B N TRP 43 B TRP 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale27 B C ILE 44 B ILE 41 1_555 B N MLY 45 B MLY 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale28 B C MLY 45 B MLY 42 1_555 B N ASP 46 B ASP 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale29 B C LEU 61 B LEU 58 1_555 B N MLY 62 B MLY 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale30 B C MLY 62 B MLY 59 1_555 B N ASN 63 B ASN 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale31 B C TYR 67 B TYR 64 1_555 B N MSE 68 B MSE 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale32 B C MSE 68 B MSE 65 1_555 B N GLU 69 B GLU 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale33 B C ASP 77 B ASP 74 1_555 B N MLY 78 B MLY 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale34 B C MLY 78 B MLY 75 1_555 B N ASN 79 B ASN 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale35 B C PHE 80 B PHE 77 1_555 B N MLY 81 B MLY 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale36 B C MLY 81 B MLY 78 1_555 B N ILE 82 B ILE 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale37 B C PHE 88 B PHE 85 1_555 B N MSE 89 B MSE 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale38 B C MSE 89 B MSE 86 1_555 B N ALA 90 B ALA 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale39 B C ALA 90 B ALA 87 1_555 B N MSE 91 B MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale40 B C MSE 91 B MSE 88 1_555 B N ILE 92 B ILE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? # _chem_comp.formula 'C4 H10 O3' _chem_comp.formula_weight 106.12 _chem_comp.id PEG _chem_comp.mon_nstd_flag . _chem_comp.name DI(HYDROXYETHYL)ETHER _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3NYM _atom_sites.fract_transf_matrix[1][1] 0.022912 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002322 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.027979 _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] 0.009896 _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 PEG A 1 126 1 PEG PEG . D 2 PEG A 1 127 2 PEG PEG . E 3 SO4 A 1 128 2 SO4 SO4 . F 2 PEG B 1 126 3 PEG PEG . G 3 SO4 B 1 127 1 SO4 SO4 . H 4 ACT B 1 128 1 ACT ACT . I 5 HOH A 1 129 129 HOH HOH . I 5 HOH A 2 130 130 HOH HOH . I 5 HOH A 3 131 131 HOH HOH . I 5 HOH A 4 132 132 HOH HOH . I 5 HOH A 5 133 133 HOH HOH . I 5 HOH A 6 134 2 HOH HOH . I 5 HOH A 7 135 135 HOH HOH . I 5 HOH A 8 136 136 HOH HOH . I 5 HOH A 9 137 137 HOH HOH . I 5 HOH A 10 138 138 HOH HOH . I 5 HOH A 11 139 5 HOH HOH . I 5 HOH A 12 140 7 HOH HOH . I 5 HOH A 13 141 141 HOH HOH . I 5 HOH A 14 142 142 HOH HOH . I 5 HOH A 15 143 13 HOH HOH . I 5 HOH A 16 144 144 HOH HOH . I 5 HOH A 17 145 17 HOH HOH . I 5 HOH A 18 146 19 HOH HOH . I 5 HOH A 19 147 147 HOH HOH . I 5 HOH A 20 148 24 HOH HOH . I 5 HOH A 21 149 149 HOH HOH . I 5 HOH A 22 150 150 HOH HOH . I 5 HOH A 23 151 34 HOH HOH . I 5 HOH A 24 152 152 HOH HOH . I 5 HOH A 25 153 36 HOH HOH . I 5 HOH A 26 154 38 HOH HOH . I 5 HOH A 27 155 42 HOH HOH . I 5 HOH A 28 156 156 HOH HOH . I 5 HOH A 29 157 157 HOH HOH . I 5 HOH A 30 158 50 HOH HOH . I 5 HOH A 31 159 52 HOH HOH . I 5 HOH A 32 160 53 HOH HOH . I 5 HOH A 33 161 58 HOH HOH . I 5 HOH A 34 162 60 HOH HOH . I 5 HOH A 35 163 63 HOH HOH . I 5 HOH A 36 164 64 HOH HOH . I 5 HOH A 37 165 66 HOH HOH . I 5 HOH A 38 166 68 HOH HOH . I 5 HOH A 39 167 69 HOH HOH . I 5 HOH A 40 168 73 HOH HOH . I 5 HOH A 41 169 80 HOH HOH . I 5 HOH A 42 170 81 HOH HOH . I 5 HOH A 43 171 83 HOH HOH . I 5 HOH A 44 172 85 HOH HOH . I 5 HOH A 45 173 87 HOH HOH . I 5 HOH A 46 174 90 HOH HOH . I 5 HOH A 47 175 92 HOH HOH . I 5 HOH A 48 176 93 HOH HOH . I 5 HOH A 49 177 96 HOH HOH . I 5 HOH A 50 178 97 HOH HOH . I 5 HOH A 51 179 99 HOH HOH . I 5 HOH A 52 180 100 HOH HOH . I 5 HOH A 53 181 104 HOH HOH . I 5 HOH A 54 182 106 HOH HOH . I 5 HOH A 55 183 112 HOH HOH . I 5 HOH A 56 184 113 HOH HOH . I 5 HOH A 57 185 115 HOH HOH . I 5 HOH A 58 186 116 HOH HOH . I 5 HOH A 59 187 120 HOH HOH . I 5 HOH A 60 188 126 HOH HOH . I 5 HOH A 61 189 128 HOH HOH . J 5 HOH B 1 129 1 HOH HOH . J 5 HOH B 2 130 3 HOH HOH . J 5 HOH B 3 131 4 HOH HOH . J 5 HOH B 4 132 6 HOH HOH . J 5 HOH B 5 133 8 HOH HOH . J 5 HOH B 6 134 134 HOH HOH . J 5 HOH B 7 135 9 HOH HOH . J 5 HOH B 8 136 10 HOH HOH . J 5 HOH B 9 137 11 HOH HOH . J 5 HOH B 10 138 12 HOH HOH . J 5 HOH B 11 139 139 HOH HOH . J 5 HOH B 12 140 140 HOH HOH . J 5 HOH B 13 141 14 HOH HOH . J 5 HOH B 14 142 15 HOH HOH . J 5 HOH B 15 143 143 HOH HOH . J 5 HOH B 16 144 16 HOH HOH . J 5 HOH B 17 145 145 HOH HOH . J 5 HOH B 18 146 146 HOH HOH . J 5 HOH B 19 147 18 HOH HOH . J 5 HOH B 20 148 148 HOH HOH . J 5 HOH B 21 149 20 HOH HOH . J 5 HOH B 22 150 21 HOH HOH . J 5 HOH B 23 151 151 HOH HOH . J 5 HOH B 24 152 22 HOH HOH . J 5 HOH B 25 153 153 HOH HOH . J 5 HOH B 26 154 154 HOH HOH . J 5 HOH B 27 155 155 HOH HOH . J 5 HOH B 28 156 23 HOH HOH . J 5 HOH B 29 157 25 HOH HOH . J 5 HOH B 30 158 26 HOH HOH . J 5 HOH B 31 159 27 HOH HOH . J 5 HOH B 32 160 28 HOH HOH . J 5 HOH B 33 161 29 HOH HOH . J 5 HOH B 34 162 30 HOH HOH . J 5 HOH B 35 163 31 HOH HOH . J 5 HOH B 36 164 32 HOH HOH . J 5 HOH B 37 165 33 HOH HOH . J 5 HOH B 38 166 35 HOH HOH . J 5 HOH B 39 167 37 HOH HOH . J 5 HOH B 40 168 39 HOH HOH . J 5 HOH B 41 169 40 HOH HOH . J 5 HOH B 42 170 41 HOH HOH . J 5 HOH B 43 171 43 HOH HOH . J 5 HOH B 44 172 44 HOH HOH . J 5 HOH B 45 173 45 HOH HOH . J 5 HOH B 46 174 46 HOH HOH . J 5 HOH B 47 175 47 HOH HOH . J 5 HOH B 48 176 48 HOH HOH . J 5 HOH B 49 177 49 HOH HOH . J 5 HOH B 50 178 51 HOH HOH . J 5 HOH B 51 179 54 HOH HOH . J 5 HOH B 52 180 55 HOH HOH . J 5 HOH B 53 181 56 HOH HOH . J 5 HOH B 54 182 57 HOH HOH . J 5 HOH B 55 183 59 HOH HOH . J 5 HOH B 56 184 61 HOH HOH . J 5 HOH B 57 185 62 HOH HOH . J 5 HOH B 58 186 65 HOH HOH . J 5 HOH B 59 187 67 HOH HOH . J 5 HOH B 60 188 70 HOH HOH . J 5 HOH B 61 189 71 HOH HOH . J 5 HOH B 62 190 72 HOH HOH . J 5 HOH B 63 191 74 HOH HOH . J 5 HOH B 64 192 75 HOH HOH . J 5 HOH B 65 193 76 HOH HOH . J 5 HOH B 66 194 77 HOH HOH . J 5 HOH B 67 195 78 HOH HOH . J 5 HOH B 68 196 79 HOH HOH . J 5 HOH B 69 197 82 HOH HOH . J 5 HOH B 70 198 84 HOH HOH . J 5 HOH B 71 199 86 HOH HOH . J 5 HOH B 72 200 88 HOH HOH . J 5 HOH B 73 201 89 HOH HOH . J 5 HOH B 74 202 91 HOH HOH . J 5 HOH B 75 203 94 HOH HOH . J 5 HOH B 76 204 95 HOH HOH . J 5 HOH B 77 205 98 HOH HOH . J 5 HOH B 78 206 101 HOH HOH . J 5 HOH B 79 207 102 HOH HOH . J 5 HOH B 80 208 103 HOH HOH . J 5 HOH B 81 209 105 HOH HOH . J 5 HOH B 82 210 107 HOH HOH . J 5 HOH B 83 211 108 HOH HOH . J 5 HOH B 84 212 109 HOH HOH . J 5 HOH B 85 213 110 HOH HOH . J 5 HOH B 86 214 111 HOH HOH . J 5 HOH B 87 215 114 HOH HOH . J 5 HOH B 88 216 117 HOH HOH . J 5 HOH B 89 217 118 HOH HOH . J 5 HOH B 90 218 119 HOH HOH . J 5 HOH B 91 219 121 HOH HOH . J 5 HOH B 92 220 122 HOH HOH . J 5 HOH B 93 221 123 HOH HOH . J 5 HOH B 94 222 124 HOH HOH . J 5 HOH B 95 223 125 HOH HOH . J 5 HOH B 96 224 127 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 PEG . . . F 2 37.78 15.192 39.14 1 69.82 ? C1 PEG 126 B 1 HETATM 2 O O1 PEG . . . F 2 39.13 15.462 38.835 1 75.34 ? O1 PEG 126 B 1 HETATM 3 C C2 PEG . . . F 2 37.656 14.546 40.535 1 71.47 ? C2 PEG 126 B 1 HETATM 4 O O2 PEG . . . F 2 38.277 15.358 41.517 1 71.92 ? O2 PEG 126 B 1 HETATM 5 C C3 PEG . . . F 2 38.683 14.777 42.741 1 74.54 ? C3 PEG 126 B 1 HETATM 6 C C4 PEG . . . F 2 37.447 14.58 43.635 1 74.33 ? C4 PEG 126 B 1 HETATM 7 O O4 PEG . . . F 2 37.431 13.267 44.147 1 73.44 ? O4 PEG 126 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 7 #