data_6DII # _model_server_result.job_id ewnJhZvE4YAJyaDaMm0z-w _model_server_result.datetime_utc '2024-10-19 12:40:25' _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 6dii # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":700}' # _entry.id 6DII # _exptl.entry_id 6DII _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 344.444 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description methyl-9Z,12Z,15Z-octadecatrienylphosphonofluoridate _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.98 _cell.angle_gamma 90 _cell.entry_id 6DII _cell.length_a 225.577 _cell.length_b 83.311 _cell.length_c 272.811 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DII _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 PISA dimeric 2 author_and_software_defined_assembly 5 PISA dimeric 2 author_and_software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,M,N 1 1 C,D,O,P 2 1 E,F,Q,R 3 1 G,H,S,T 4 1 I,J,U,V 5 1 K,L,W,X 6 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 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X 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 OG SER 305 A SER 305 1_555 M P1 GJY . A GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.583 ? covale ? covale2 B OG SER 305 B SER 305 1_555 N P1 GJY . B GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.575 ? covale ? covale3 C OG SER 305 C SER 305 1_555 O P1 GJY . C GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.586 ? covale ? covale4 D OG SER 305 D SER 305 1_555 P P1 GJY . D GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.573 ? covale ? covale5 E OG SER 305 E SER 305 1_555 Q P1 GJY . E GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.567 ? covale ? covale6 F OG SER 305 F SER 305 1_555 R P1 GJY . F GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.591 ? covale ? covale7 G OG SER 305 G SER 305 1_555 S P1 GJY . G GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.571 ? covale ? covale8 H OG SER 305 H SER 305 1_555 T P1 GJY . H GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.563 ? covale ? covale9 I OG SER 305 I SER 305 1_555 U P1 GJY . I GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.578 ? covale ? covale10 J OG SER 305 J SER 305 1_555 V P1 GJY . J GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.552 ? covale ? covale11 K OG SER 305 K SER 305 1_555 W P1 GJY . K GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.578 ? covale ? covale12 L OG SER 305 L SER 305 1_555 X P1 GJY . L GJY 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.557 ? # _chem_comp.formula 'C19 H34 F O2 P' _chem_comp.formula_weight 344.444 _chem_comp.id GJY _chem_comp.mon_nstd_flag . _chem_comp.name methyl-9Z,12Z,15Z-octadecatrienylphosphonofluoridate _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Methyl alpha-Linolenyl Fluorophosphonate (MLnFP)' # 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 P1 GJY sing 83 n n C1 C2 GJY sing 84 n n P1 O2 GJY sing 85 n n P1 O1 GJY doub 86 n n O2 CM GJY sing 87 n n C2 C3 GJY sing 88 n n C3 C4 GJY sing 89 n n C4 C5 GJY sing 90 n n C5 C6 GJY sing 91 n n C6 C7 GJY sing 92 n n C8 C7 GJY sing 93 n n C8 C9 GJY sing 94 n n C9 C10 GJY doub 95 z n C10 C11 GJY sing 96 n n C12 C11 GJY sing 97 n n C12 C13 GJY doub 98 z n C18 C17 GJY sing 99 n n C13 C14 GJY sing 100 n n C17 C16 GJY sing 101 n n C14 C15 GJY sing 102 n n C16 C15 GJY doub 103 z n P1 F1 GJY sing 104 n n CM H1 GJY sing 105 n n CM H2 GJY sing 106 n n CM H3 GJY sing 107 n n C1 H4 GJY sing 108 n n C1 H5 GJY sing 109 n n C2 H6 GJY sing 110 n n C2 H7 GJY sing 111 n n C3 H8 GJY sing 112 n n C3 H9 GJY sing 113 n n C4 H10 GJY sing 114 n n C4 H11 GJY sing 115 n n C5 H12 GJY sing 116 n n C5 H13 GJY sing 117 n n C6 H14 GJY sing 118 n n C6 H15 GJY sing 119 n n C7 H16 GJY sing 120 n n C7 H17 GJY sing 121 n n C8 H18 GJY sing 122 n n C8 H19 GJY sing 123 n n C9 H20 GJY sing 124 n n C10 H21 GJY sing 125 n n C11 H22 GJY sing 126 n n C11 H23 GJY sing 127 n n C12 H24 GJY sing 128 n n C13 H25 GJY sing 129 n n C14 H26 GJY sing 130 n n C14 H27 GJY sing 131 n n C15 H28 GJY sing 132 n n C16 H29 GJY sing 133 n n C17 H30 GJY sing 134 n n C17 H31 GJY sing 135 n n C18 H32 GJY sing 136 n n C18 H33 GJY sing 137 n n C18 H34 GJY sing 138 n n # _atom_sites.entry_id 6DII _atom_sites.fract_transf_matrix[1][1] 0.004433 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0017 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012003 _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] 0.003926 _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 M 2 GJY A 1 700 700 GJY MLF . N 2 GJY B 1 700 700 GJY MLF . O 2 GJY C 1 700 700 GJY MLF . P 2 GJY D 1 700 700 GJY MLF . Q 2 GJY E 1 700 700 GJY MLF . R 2 GJY F 1 700 700 GJY MLF . S 2 GJY G 1 700 700 GJY MLF . T 2 GJY H 1 700 700 GJY MLF . U 2 GJY I 1 700 700 GJY MLF . V 2 GJY J 1 700 700 GJY MLF . W 2 GJY K 1 700 700 GJY MLF . X 2 GJY L 1 700 700 GJY MLF . # 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 O O1 GJY . . . N 2 30.927 16.347 -88.464 1 57.63 ? O1 GJY 700 B 1 HETATM 2 P P1 GJY . . . N 2 29.969 17.283 -87.666 1 55.69 ? P1 GJY 700 B 1 HETATM 3 O O2 GJY . . . N 2 28.473 16.978 -88.078 1 58.04 ? O2 GJY 700 B 1 HETATM 4 C CM GJY . . . N 2 28.084 15.736 -88.704 1 59.3 ? CM GJY 700 B 1 HETATM 5 C C1 GJY . . . N 2 30.071 19.095 -87.329 1 82.83 ? C1 GJY 700 B 1 HETATM 6 C C2 GJY . . . N 2 30.645 19.869 -88.514 1 74.47 ? C2 GJY 700 B 1 HETATM 7 C C3 GJY . . . N 2 29.985 21.232 -88.698 1 73.05 ? C3 GJY 700 B 1 HETATM 8 C C4 GJY . . . N 2 28.679 21.15 -89.485 1 72.27 ? C4 GJY 700 B 1 HETATM 9 C C5 GJY . . . N 2 27.85 22.429 -89.391 1 71.64 ? C5 GJY 700 B 1 HETATM 10 C C6 GJY . . . N 2 28.669 23.686 -89.67 1 69.05 ? C6 GJY 700 B 1 HETATM 11 C C7 GJY . . . N 2 27.936 24.681 -90.566 1 69.5 ? C7 GJY 700 B 1 HETATM 12 C C8 GJY . . . N 2 28.455 26.11 -90.41 1 72.11 ? C8 GJY 700 B 1 HETATM 13 C C9 GJY . . . N 2 27.341 27.154 -90.313 1 75.25 ? C9 GJY 700 B 1 HETATM 14 C C10 GJY . . . N 2 27.264 28.122 -91.204 1 79.32 ? C10 GJY 700 B 1 HETATM 15 C C11 GJY . . . N 2 28.287 28.201 -92.336 1 78.93 ? C11 GJY 700 B 1 HETATM 16 C C12 GJY . . . N 2 29.677 28.621 -91.863 1 75.13 ? C12 GJY 700 B 1 HETATM 17 C C13 GJY . . . N 2 30.468 29.287 -92.675 1 73.5 ? C13 GJY 700 B 1 HETATM 18 C C14 GJY . . . N 2 29.989 29.636 -94.083 1 74.51 ? C14 GJY 700 B 1 HETATM 19 C C15 GJY . . . N 2 30.608 30.927 -94.612 1 75.02 ? C15 GJY 700 B 1 HETATM 20 C C16 GJY . . . N 2 30.105 32.092 -94.264 1 74.57 ? C16 GJY 700 B 1 HETATM 21 C C17 GJY . . . N 2 28.9 32.149 -93.329 1 73.69 ? C17 GJY 700 B 1 HETATM 22 C C18 GJY . . . N 2 29.04 33.211 -92.241 1 73.12 ? C18 GJY 700 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #