data_8GDB # _model_server_result.job_id H4ggPxIukkyoASrahpZ-Dg _model_server_result.datetime_utc '2024-11-21 14:27:07' _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 8gdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 8GDB # _exptl.entry_id 8GDB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 352.465 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic 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 8GDB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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 # _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 ? _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 6 _struct_asym.id F _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 disulf ? disulf1 D SG CYS 22 N CYS 22 1_555 D SG CYS 96 N CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 D SG CYS 99 N CYS 99 1_555 D SG CYS 107 N CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? # _chem_comp.formula 'C20 H32 O5' _chem_comp.formula_weight 352.465 _chem_comp.id P2E _chem_comp.mon_nstd_flag . _chem_comp.name '(Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Prostaglandin E2' # 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 C2 C3 P2E sing 235 n n C2 C1 P2E sing 236 n n C3 C4 P2E sing 237 n n C4 C5 P2E sing 238 n n C5 C6 P2E doub 239 n n C6 C7 P2E sing 240 n n C7 C8 P2E sing 241 n n C8 C9 P2E sing 242 n n C8 C12 P2E sing 243 n n C9 O3 P2E doub 244 n n C9 C10 P2E sing 245 z n C12 C11 P2E sing 246 n n C12 C13 P2E sing 247 n n C11 O4 P2E sing 248 n n C11 C10 P2E sing 249 n n C13 C14 P2E doub 250 n n C14 C15 P2E sing 251 n n C15 O5 P2E sing 252 n n C15 C16 P2E sing 253 n n C16 C17 P2E sing 254 n n C17 C18 P2E sing 255 n n C18 C19 P2E sing 256 n n C19 C20 P2E sing 257 n n O1 C1 P2E doub 258 n n C1 O2 P2E sing 259 n n C2 H2 P2E sing 260 n n C2 H2A P2E sing 261 n n C3 H3 P2E sing 262 n n C3 H3A P2E sing 263 n n C4 H4 P2E sing 264 n n C4 H4A P2E sing 265 n n C5 H5 P2E sing 266 e n C6 H6 P2E sing 267 n n C7 H7 P2E sing 268 n n C7 H7A P2E sing 269 n n C8 H8 P2E sing 270 n n C12 H12 P2E sing 271 n n C11 H11 P2E sing 272 n n O4 HO4 P2E sing 273 n n C10 H10 P2E sing 274 n n C10 H10A P2E sing 275 n n C13 H13 P2E sing 276 n n C14 H14 P2E sing 277 n n C15 H15 P2E sing 278 n n O5 HO5 P2E sing 279 n n C16 H16 P2E sing 280 n n C16 H16A P2E sing 281 n n C17 H17 P2E sing 282 n n C17 H17A P2E sing 283 n n C18 H18 P2E sing 284 n n C18 H18A P2E sing 285 n n C19 H19 P2E sing 286 n n C19 H19A P2E sing 287 n n C20 H20 P2E sing 288 n n C20 H20A P2E sing 289 n n C20 H20B P2E sing 290 n n O2 HO2 P2E sing 291 n n # _atom_sites.entry_id 8GDB _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id P2E _pdbx_nonpoly_scheme.pdb_strand_id R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 501 _pdbx_nonpoly_scheme.auth_seq_num 505 _pdbx_nonpoly_scheme.pdb_mon_id P2E _pdbx_nonpoly_scheme.auth_mon_id P2E _pdbx_nonpoly_scheme.pdb_ins_code . # 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 C2 P2E . . . F 6 107.147 126.658 109.91 1 76.3 0 C2 P2E 501 R 1 HETATM 2 C C3 P2E . . . F 6 107.63 126.641 111.339 1 76.3 0 C3 P2E 501 R 1 HETATM 3 C C4 P2E . . . F 6 109.035 126.071 111.483 1 76.3 0 C4 P2E 501 R 1 HETATM 4 C C5 P2E . . . F 6 110.139 126.847 110.829 1 76.3 0 C5 P2E 501 R 1 HETATM 5 C C6 P2E . . . F 6 110.555 128.095 111.027 1 76.3 0 C6 P2E 501 R 1 HETATM 6 C C7 P2E . . . F 6 109.931 129.087 111.955 1 76.3 0 C7 P2E 501 R 1 HETATM 7 C C8 P2E . . . F 6 110.9 129.767 112.92 1 76.3 0 C8 P2E 501 R 1 HETATM 8 C C9 P2E . . . F 6 110.175 130.802 113.755 1 76.3 0 C9 P2E 501 R 1 HETATM 9 O O3 P2E . . . F 6 109.548 131.732 113.313 1 76.3 0 O3 P2E 501 R 1 HETATM 10 C C12 P2E . . . F 6 111.508 128.867 114.024 1 76.3 0 C12 P2E 501 R 1 HETATM 11 C C11 P2E . . . F 6 110.478 128.945 115.158 1 76.3 0 C11 P2E 501 R 1 HETATM 12 O O4 P2E . . . F 6 109.222 128.316 114.895 1 76.3 0 O4 P2E 501 R 1 HETATM 13 C C10 P2E . . . F 6 110.339 130.457 115.2 1 76.3 0 C10 P2E 501 R 1 HETATM 14 C C13 P2E . . . F 6 112.842 129.381 114.513 1 76.3 0 C13 P2E 501 R 1 HETATM 15 C C14 P2E . . . F 6 113.897 128.601 114.625 1 76.3 0 C14 P2E 501 R 1 HETATM 16 C C15 P2E . . . F 6 115.251 129.004 115.123 1 76.3 0 C15 P2E 501 R 1 HETATM 17 O O5 P2E . . . F 6 115.511 128.4 116.394 1 76.3 0 O5 P2E 501 R 1 HETATM 18 C C16 P2E . . . F 6 116.344 128.657 114.124 1 76.3 0 C16 P2E 501 R 1 HETATM 19 C C17 P2E . . . F 6 116.3 127.222 113.595 1 76.3 0 C17 P2E 501 R 1 HETATM 20 C C18 P2E . . . F 6 116.674 126.108 114.546 1 76.3 0 C18 P2E 501 R 1 HETATM 21 C C19 P2E . . . F 6 116.629 124.741 113.948 1 76.3 0 C19 P2E 501 R 1 HETATM 22 C C20 P2E . . . F 6 115.268 124.131 113.91 1 76.3 0 C20 P2E 501 R 1 HETATM 23 O O1 P2E . . . F 6 105.394 128.196 110.449 1 76.3 0 O1 P2E 501 R 1 HETATM 24 C C1 P2E . . . F 6 105.823 127.334 109.715 1 76.3 0 C1 P2E 501 R 1 HETATM 25 O O2 P2E . . . F 6 105.17 126.898 108.672 1 76.3 0 O2 P2E 501 R 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 25 #