data_3SMK # _model_server_result.job_id skalv1FLZ9TsxUnR9dcP1Q _model_server_result.datetime_utc '2024-12-14 17:27:52' _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 3smk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":232}' # _entry.id 3SMK # _exptl.entry_id 3SMK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 622.743 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Cotylenin A' _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 3SMK _cell.length_a 81.29 _cell.length_b 111.78 _cell.length_c 63.11 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SMK _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 B C LYS 4 P LYS 372 1_555 B N SEP 5 P SEP 373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 B C SEP 5 P SEP 373 1_555 B N VAL 6 P VAL 374 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? metalc ? metalc1 D MG MG . A MG 233 1_555 E O HOH . A HOH 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? # _chem_comp.formula 'C33 H50 O11' _chem_comp.formula_weight 622.743 _chem_comp.id CW7 _chem_comp.mon_nstd_flag . _chem_comp.name 'Cotylenin A' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (1R,3aR,5R,6R,9aR,10aS)-6-({(1S,2R,4S,5S,6R,8S,9S)-5-hydroxy-2-(methoxymethyl)-9-methyl-9-[(2S)-oxiran-2-yl]-3,7,10,11-tetraoxatricyclo[6.2.1.0~1,6~]undec-4-yl}oxy)-1-(methoxymethyl)-9a-methyl-4-methylidene-7-(propan-2-yl)-1,2,3,3a,4,5,6,8,9,9a,10,10a-dodecahydrodicyclopenta[a,d][8]annulene-1,5-diol # 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 O1 C1 CW7 sing 70 n n CAA CAB CW7 doub 71 n n CAB CAC CW7 sing 72 n n CAC CAG CW7 sing 73 n n CAC CAD CW7 sing 74 n n CAD CAE CW7 sing 75 n n CAF CAE CW7 sing 76 n n CAF OBR CW7 sing 77 n n CAG CAF CW7 sing 78 n n CAH CAG CW7 sing 79 n n CAI CAH CW7 sing 80 n n CAI CAJ CW7 sing 81 n n CAJ CAK CW7 sing 82 n n CAL CAK CW7 sing 83 n n CAM CAI CW7 sing 84 n n CAM CAL CW7 doub 85 n n CAN CAM CW7 sing 86 n n CAN CAO CW7 sing 87 n n CAO CAB CW7 sing 88 n n OAP CAO CW7 sing 89 n n OAQ CAN CW7 sing 90 n n CAR OAQ CW7 sing 91 n n CAS CAR CW7 sing 92 n n CAT CAS CW7 sing 93 n n CAU CAT CW7 sing 94 n n CAU OBE CW7 sing 95 n n CAU CAV CW7 sing 96 n n CAV OAW CW7 sing 97 n n OAW CAR CW7 sing 98 n n CAX CAV CW7 sing 99 n n OAY CAX CW7 sing 100 n n CAZ OAY CW7 sing 101 n n OBA CAU CW7 sing 102 n n CBB OBA CW7 sing 103 n n CBB OBC CW7 sing 104 n n CBB CBD CW7 sing 105 n n OBC CAT CW7 sing 106 n n CBD CBG CW7 sing 107 n n CBD OBE CW7 sing 108 n n CBF CBD CW7 sing 109 n n CBG C1 CW7 sing 110 n n CBG O1 CW7 sing 111 n n OBJ CAS CW7 sing 112 n n CBK CAL CW7 sing 113 n n CBK CBL CW7 sing 114 n n CBM CBK CW7 sing 115 n n CBN CAI CW7 sing 116 n n CBO CAF CW7 sing 117 n n CBO OBP CW7 sing 118 n n CBQ OBP CW7 sing 119 n n C1 H1 CW7 sing 120 n n C1 H1A CW7 sing 121 n n CAA HAA CW7 sing 122 n n CAA HAAA CW7 sing 123 n n CAC HAC CW7 sing 124 n n CAD HAD CW7 sing 125 n n CAD HADA CW7 sing 126 n n CAE HAE CW7 sing 127 n n CAE HAEA CW7 sing 128 n n CAG HAG CW7 sing 129 n n CAH HAH CW7 sing 130 n n CAH HAHA CW7 sing 131 n n CAJ HAJ CW7 sing 132 n n CAJ HAJA CW7 sing 133 n n CAK HAK CW7 sing 134 n n CAK HAKA CW7 sing 135 n n CAN HAN CW7 sing 136 n n CAO HAO CW7 sing 137 n n OAP HOAP CW7 sing 138 n n CAR HAR CW7 sing 139 n n CAS H21 CW7 sing 140 n n CAT HAT CW7 sing 141 n n CAV HAV CW7 sing 142 n n CAX HAX CW7 sing 143 n n CAX HAXA CW7 sing 144 n n CAZ HAZ CW7 sing 145 n n CAZ HAZA CW7 sing 146 n n CAZ HAZB CW7 sing 147 n n CBB HBB CW7 sing 148 n n CBF HBF CW7 sing 149 n n CBF HBFA CW7 sing 150 n n CBF HBFB CW7 sing 151 n n CBG HBG CW7 sing 152 n n OBJ H34 CW7 sing 153 n n CBK HBK CW7 sing 154 n n CBL HBL CW7 sing 155 n n CBL HBLA CW7 sing 156 n n CBL HBLB CW7 sing 157 n n CBM HBM CW7 sing 158 n n CBM HBMA CW7 sing 159 n n CBM HBMB CW7 sing 160 n n CBN HBN CW7 sing 161 n n CBN HBNA CW7 sing 162 n n CBN HBNB CW7 sing 163 n n CBO HBO CW7 sing 164 n n CBO HBOA CW7 sing 165 n n CBQ HBQ CW7 sing 166 n n CBQ HBQA CW7 sing 167 n n CBQ HBQB CW7 sing 168 n n OBR HOBR CW7 sing 169 n n # _atom_sites.entry_id 3SMK _atom_sites.fract_transf_matrix[1][1] 0.012302 _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] 0.008946 _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] 0.015845 _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 3 CW7 A 1 232 232 CW7 CW7 . D 4 MG A 1 233 233 MG MG . E 5 HOH A 1 234 234 HOH HOH . E 5 HOH A 2 235 235 HOH HOH . E 5 HOH A 3 236 236 HOH HOH . E 5 HOH A 4 237 237 HOH HOH . E 5 HOH A 5 238 238 HOH HOH . E 5 HOH A 6 239 239 HOH HOH . E 5 HOH A 7 240 240 HOH HOH . E 5 HOH A 8 241 241 HOH HOH . E 5 HOH A 9 242 242 HOH HOH . E 5 HOH A 10 243 243 HOH HOH . E 5 HOH A 11 244 244 HOH HOH . E 5 HOH A 12 245 245 HOH HOH . E 5 HOH A 13 246 246 HOH HOH . E 5 HOH A 14 247 247 HOH HOH . E 5 HOH A 15 248 248 HOH HOH . E 5 HOH A 16 249 249 HOH HOH . E 5 HOH A 17 250 250 HOH HOH . E 5 HOH A 18 251 251 HOH HOH . E 5 HOH A 19 252 252 HOH HOH . E 5 HOH A 20 253 253 HOH HOH . E 5 HOH A 21 254 254 HOH HOH . E 5 HOH A 22 255 255 HOH HOH . E 5 HOH A 23 256 256 HOH HOH . E 5 HOH A 24 257 257 HOH HOH . E 5 HOH A 25 258 258 HOH HOH . E 5 HOH A 26 259 259 HOH HOH . E 5 HOH A 27 260 260 HOH HOH . E 5 HOH A 28 261 261 HOH HOH . E 5 HOH A 29 262 262 HOH HOH . E 5 HOH A 30 263 263 HOH HOH . E 5 HOH A 31 264 264 HOH HOH . E 5 HOH A 32 265 265 HOH HOH . E 5 HOH A 33 266 266 HOH HOH . E 5 HOH A 34 267 267 HOH HOH . E 5 HOH A 35 268 268 HOH HOH . E 5 HOH A 36 269 269 HOH HOH . E 5 HOH A 37 270 270 HOH HOH . E 5 HOH A 38 271 271 HOH HOH . E 5 HOH A 39 272 272 HOH HOH . E 5 HOH A 40 273 273 HOH HOH . E 5 HOH A 41 274 274 HOH HOH . E 5 HOH A 42 275 275 HOH HOH . E 5 HOH A 43 276 276 HOH HOH . E 5 HOH A 44 277 277 HOH HOH . E 5 HOH A 45 278 278 HOH HOH . E 5 HOH A 46 279 279 HOH HOH . E 5 HOH A 47 280 280 HOH HOH . E 5 HOH A 48 281 281 HOH HOH . E 5 HOH A 49 282 282 HOH HOH . E 5 HOH A 50 283 283 HOH HOH . E 5 HOH A 51 284 284 HOH HOH . E 5 HOH A 52 285 285 HOH HOH . E 5 HOH A 53 286 286 HOH HOH . E 5 HOH A 54 287 287 HOH HOH . E 5 HOH A 55 288 288 HOH HOH . E 5 HOH A 56 289 289 HOH HOH . E 5 HOH A 57 290 290 HOH HOH . E 5 HOH A 58 291 291 HOH HOH . E 5 HOH A 59 292 292 HOH HOH . E 5 HOH A 60 293 293 HOH HOH . E 5 HOH A 61 294 294 HOH HOH . E 5 HOH A 62 295 295 HOH HOH . E 5 HOH A 63 296 296 HOH HOH . E 5 HOH A 64 297 297 HOH HOH . E 5 HOH A 65 298 298 HOH HOH . E 5 HOH A 66 299 299 HOH HOH . E 5 HOH A 67 300 300 HOH HOH . E 5 HOH A 68 301 301 HOH HOH . E 5 HOH A 69 302 302 HOH HOH . E 5 HOH A 70 303 303 HOH HOH . E 5 HOH A 71 304 304 HOH HOH . E 5 HOH A 72 305 305 HOH HOH . E 5 HOH A 73 306 306 HOH HOH . E 5 HOH A 74 307 307 HOH HOH . E 5 HOH A 75 308 308 HOH HOH . E 5 HOH A 76 309 309 HOH HOH . E 5 HOH A 77 310 310 HOH HOH . E 5 HOH A 78 311 311 HOH HOH . E 5 HOH A 79 312 312 HOH HOH . E 5 HOH A 80 313 313 HOH HOH . E 5 HOH A 81 314 314 HOH HOH . E 5 HOH A 82 315 315 HOH HOH . E 5 HOH A 83 316 316 HOH HOH . E 5 HOH A 84 317 71 HOH HOH . E 5 HOH A 85 318 72 HOH HOH . E 5 HOH A 86 319 73 HOH HOH . F 5 HOH P 1 17 17 HOH HOH . F 5 HOH P 2 45 45 HOH HOH . F 5 HOH P 3 68 68 HOH HOH . F 5 HOH P 4 74 74 HOH HOH . F 5 HOH P 5 80 80 HOH HOH . F 5 HOH P 6 89 89 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 CW7 . . . C 3 27.976 -17.967 -4.737 1 41.04 ? C1 CW7 232 A 1 HETATM 2 O O1 CW7 . . . C 3 27.994 -16.59 -5.164 1 43.78 ? O1 CW7 232 A 1 HETATM 3 C CAA CW7 . . . C 3 21.587 -22.818 0.484 1 19.14 ? CAA CW7 232 A 1 HETATM 4 C CAB CW7 . . . C 3 22.802 -22.145 0.824 1 18.35 ? CAB CW7 232 A 1 HETATM 5 C CAC CW7 . . . C 3 22.906 -21.3 2.038 1 14.26 ? CAC CW7 232 A 1 HETATM 6 C CAD CW7 . . . C 3 22.919 -22.097 3.392 1 14.21 ? CAD CW7 232 A 1 HETATM 7 C CAE CW7 . . . C 3 21.416 -22.092 3.905 1 12.65 ? CAE CW7 232 A 1 HETATM 8 C CAF CW7 . . . C 3 20.878 -20.744 3.434 1 13.74 ? CAF CW7 232 A 1 HETATM 9 C CAG CW7 . . . C 3 21.505 -20.563 2.043 1 15.03 ? CAG CW7 232 A 1 HETATM 10 C CAH CW7 . . . C 3 21.393 -19.176 1.501 1 17.01 ? CAH CW7 232 A 1 HETATM 11 C CAI CW7 . . . C 3 21.822 -18.777 0.114 1 18.88 ? CAI CW7 232 A 1 HETATM 12 C CAJ CW7 . . . C 3 22.197 -17.31 0.246 1 16.85 ? CAJ CW7 232 A 1 HETATM 13 C CAK CW7 . . . C 3 23.705 -17.44 0.725 1 16.89 ? CAK CW7 232 A 1 HETATM 14 C CAL CW7 . . . C 3 24.137 -18.606 -0.027 1 18.15 ? CAL CW7 232 A 1 HETATM 15 C CAM CW7 . . . C 3 23.083 -19.403 -0.347 1 19.22 ? CAM CW7 232 A 1 HETATM 16 C CAN CW7 . . . C 3 23.057 -20.675 -1.066 1 23.39 ? CAN CW7 232 A 1 HETATM 17 C CAO CW7 . . . C 3 23.664 -21.862 -0.266 1 19.95 ? CAO CW7 232 A 1 HETATM 18 O OAP CW7 . . . C 3 23.798 -22.919 -1.261 1 20.15 ? OAP CW7 232 A 1 HETATM 19 O OAQ CW7 . . . C 3 23.817 -20.518 -2.263 1 24.15 ? OAQ CW7 232 A 1 HETATM 20 C CAR CW7 . . . C 3 23.24 -20.764 -3.497 1 29.95 ? CAR CW7 232 A 1 HETATM 21 C CAS CW7 . . . C 3 24.57 -20.951 -4.194 1 32.48 ? CAS CW7 232 A 1 HETATM 22 C CAT CW7 . . . C 3 25.164 -19.675 -4.863 1 34.11 ? CAT CW7 232 A 1 HETATM 23 C CAU CW7 . . . C 3 24.247 -18.408 -4.897 1 35.07 ? CAU CW7 232 A 1 HETATM 24 C CAV CW7 . . . C 3 23.061 -18.354 -3.948 1 33.02 ? CAV CW7 232 A 1 HETATM 25 O OAW CW7 . . . C 3 22.454 -19.647 -3.946 1 32.3 ? OAW CW7 232 A 1 HETATM 26 C CAX CW7 . . . C 3 22.068 -17.243 -4.415 1 31.06 ? CAX CW7 232 A 1 HETATM 27 O OAY CW7 . . . C 3 21.089 -17.774 -5.336 1 33.62 ? OAY CW7 232 A 1 HETATM 28 C CAZ CW7 . . . C 3 19.923 -16.93 -5.492 1 30.5 ? CAZ CW7 232 A 1 HETATM 29 O OBA CW7 . . . C 3 23.802 -18.41 -6.264 1 34.85 ? OBA CW7 232 A 1 HETATM 30 C CBB CW7 . . . C 3 25.119 -18.457 -6.835 1 37.77 ? CBB CW7 232 A 1 HETATM 31 O OBC CW7 . . . C 3 25.587 -19.74 -6.28 1 37.3 ? OBC CW7 232 A 1 HETATM 32 C CBD CW7 . . . C 3 25.774 -17.264 -6.115 1 39.78 ? CBD CW7 232 A 1 HETATM 33 O OBE CW7 . . . C 3 25.109 -17.234 -4.783 1 36.62 ? OBE CW7 232 A 1 HETATM 34 C CBF CW7 . . . C 3 25.43 -15.919 -6.83 1 40.84 ? CBF CW7 232 A 1 HETATM 35 C CBG CW7 . . . C 3 27.317 -17.52 -6.055 1 40.11 ? CBG CW7 232 A 1 HETATM 36 O OBJ CW7 . . . C 3 24.63 -22.168 -4.815 1 29.73 ? OBJ CW7 232 A 1 HETATM 37 C CBK CW7 . . . C 3 25.629 -18.979 -0.364 1 18.56 ? CBK CW7 232 A 1 HETATM 38 C CBL CW7 . . . C 3 26.404 -19.34 0.917 1 19.68 ? CBL CW7 232 A 1 HETATM 39 C CBM CW7 . . . C 3 26.375 -17.87 -1.124 1 20.19 ? CBM CW7 232 A 1 HETATM 40 C CBN CW7 . . . C 3 20.607 -18.864 -0.838 1 15.37 ? CBN CW7 232 A 1 HETATM 41 C CBO CW7 . . . C 3 19.331 -20.831 3.271 1 14.21 ? CBO CW7 232 A 1 HETATM 42 O OBP CW7 . . . C 3 18.611 -21.003 4.536 1 16.89 ? OBP CW7 232 A 1 HETATM 43 C CBQ CW7 . . . C 3 17.278 -21.295 4.26 1 13.76 ? CBQ CW7 232 A 1 HETATM 44 O OBR CW7 . . . C 3 21.353 -19.82 4.391 1 12.71 ? OBR CW7 232 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #