data_6FJD # _model_server_result.job_id dBsxQQlyuJY7avSg5UlBcg _model_server_result.datetime_utc '2024-11-29 06:54:29' _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 6fjd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":809}' # _entry.id 6FJD # _exptl.entry_id 6FJD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 634.354 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYL DIBUTANOATE' _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 120 _cell.entry_id 6FJD _cell.length_a 83.404 _cell.length_b 83.404 _cell.length_c 208.254 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FJD _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,P 1 1 B,L,M,N,O,Q 2 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 4 _struct_asym.id K _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 A SG CYS 60 A CYS 705 1_555 A SG CYS 66 A CYS 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 104 A CYS 749 1_555 A SG CYS 114 A CYS 759 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 B SG CYS 60 B CYS 705 1_555 B SG CYS 66 B CYS 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 104 B CYS 749 1_555 B SG CYS 114 B CYS 759 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? # _chem_comp.formula 'C17 H33 O19 P3' _chem_comp.formula_weight 634.354 _chem_comp.id PBU _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1 ,2-DIYL DIBUTANOATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'di-butanoyl L-alpha-phosphatidyl-D-myo-inositol 4,5-bisphosphate;di-C4-PIP2' # 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 P1 O1 PBU sing 250 n n P1 OP1 PBU sing 251 n n P1 OP2 PBU doub 252 n n P1 OP3 PBU sing 253 n n P4 O4 PBU sing 254 n n P4 O41 PBU doub 255 n n P4 O42 PBU sing 256 n n P4 O43 PBU sing 257 n n P5 O5 PBU sing 258 n n P5 O51 PBU doub 259 n n P5 O52 PBU sing 260 n n P5 O53 PBU sing 261 n n C3' C2' PBU sing 262 n n C3' OP1 PBU sing 263 n n C3' "H3'1" PBU sing 264 n n C3' "H3'2" PBU sing 265 n n C2' O2' PBU sing 266 n n C2' C1' PBU sing 267 n n C2' H2' PBU sing 268 n n O2' C7 PBU sing 269 n n C1' O1' PBU sing 270 n n C1' "H1'1" PBU sing 271 n n C1' "H1'2" PBU sing 272 n n O1' C11 PBU sing 273 n n C1 O1 PBU sing 274 n n C1 C2 PBU sing 275 n n C1 C6 PBU sing 276 n n C1 H1 PBU sing 277 n n C2 O2 PBU sing 278 n n C2 C3 PBU sing 279 n n C2 H2 PBU sing 280 n n O2 H02 PBU sing 281 n n C3 O3 PBU sing 282 n n C3 C4 PBU sing 283 n n C3 H3 PBU sing 284 n n O3 H03 PBU sing 285 n n C4 O4 PBU sing 286 n n C4 C5 PBU sing 287 n n C4 H4 PBU sing 288 n n C5 O5 PBU sing 289 n n C5 C6 PBU sing 290 n n C5 H5 PBU sing 291 n n C6 O6 PBU sing 292 n n C6 H6 PBU sing 293 n n O6 H06 PBU sing 294 n n C7 O7 PBU doub 295 n n C7 C8 PBU sing 296 n n C8 C9 PBU sing 297 n n C8 H81 PBU sing 298 n n C8 H82 PBU sing 299 n n C9 C10 PBU sing 300 n n C9 H91 PBU sing 301 n n C9 H92 PBU sing 302 n n C10 H11 PBU sing 303 n n C10 H12 PBU sing 304 n n C10 H13 PBU sing 305 n n C11 O11 PBU doub 306 n n C11 C12 PBU sing 307 n n C12 C13 PBU sing 308 n n C12 H121 PBU sing 309 n n C12 H122 PBU sing 310 n n C13 C14 PBU sing 311 n n C13 H131 PBU sing 312 n n C13 H132 PBU sing 313 n n C14 H141 PBU sing 314 n n C14 H142 PBU sing 315 n n C14 H143 PBU sing 316 n n O42 H42 PBU sing 317 n n O43 H43 PBU sing 318 n n O52 H52 PBU sing 319 n n O53 H53 PBU sing 320 n n OP3 HP3 PBU sing 321 n n # _atom_sites.entry_id 6FJD _atom_sites.fract_transf_matrix[1][1] 0.01199 _atom_sites.fract_transf_matrix[1][2] 0.006922 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013845 _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] 0.004802 _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 GOL A 1 801 3 GOL GOL . D 2 GOL A 1 802 4 GOL GOL . E 2 GOL A 1 803 5 GOL GOL . F 2 GOL A 1 804 6 GOL GOL . G 2 GOL A 1 805 8 GOL GOL . H 2 GOL A 1 806 10 GOL GOL . I 3 SO4 A 1 807 2 SO4 SO4 . J 3 SO4 A 1 808 4 SO4 SO4 . K 4 PBU A 1 809 1 PBU PBU . L 2 GOL B 1 801 7 GOL GOL . M 2 GOL B 1 802 9 GOL GOL . N 3 SO4 B 1 803 1 SO4 SO4 . O 3 SO4 B 1 804 3 SO4 SO4 . P 5 HOH A 1 901 35 HOH HOH . P 5 HOH A 2 902 14 HOH HOH . P 5 HOH A 3 903 38 HOH HOH . P 5 HOH A 4 904 37 HOH HOH . P 5 HOH A 5 905 53 HOH HOH . P 5 HOH A 6 906 24 HOH HOH . P 5 HOH A 7 907 18 HOH HOH . P 5 HOH A 8 908 39 HOH HOH . P 5 HOH A 9 909 44 HOH HOH . P 5 HOH A 10 910 7 HOH HOH . P 5 HOH A 11 911 3 HOH HOH . P 5 HOH A 12 912 43 HOH HOH . P 5 HOH A 13 913 21 HOH HOH . P 5 HOH A 14 914 20 HOH HOH . P 5 HOH A 15 915 19 HOH HOH . P 5 HOH A 16 916 17 HOH HOH . P 5 HOH A 17 917 2 HOH HOH . P 5 HOH A 18 918 6 HOH HOH . P 5 HOH A 19 919 41 HOH HOH . P 5 HOH A 20 920 26 HOH HOH . P 5 HOH A 21 921 22 HOH HOH . P 5 HOH A 22 922 45 HOH HOH . P 5 HOH A 23 923 16 HOH HOH . P 5 HOH A 24 924 15 HOH HOH . P 5 HOH A 25 925 25 HOH HOH . P 5 HOH A 26 926 33 HOH HOH . P 5 HOH A 27 927 48 HOH HOH . P 5 HOH A 28 928 30 HOH HOH . P 5 HOH A 29 929 27 HOH HOH . P 5 HOH A 30 930 34 HOH HOH . P 5 HOH A 31 931 50 HOH HOH . Q 5 HOH B 1 901 28 HOH HOH . Q 5 HOH B 2 902 54 HOH HOH . Q 5 HOH B 3 903 32 HOH HOH . Q 5 HOH B 4 904 46 HOH HOH . Q 5 HOH B 5 905 29 HOH HOH . Q 5 HOH B 6 906 8 HOH HOH . Q 5 HOH B 7 907 51 HOH HOH . Q 5 HOH B 8 908 5 HOH HOH . Q 5 HOH B 9 909 36 HOH HOH . Q 5 HOH B 10 910 1 HOH HOH . Q 5 HOH B 11 911 23 HOH HOH . Q 5 HOH B 12 912 9 HOH HOH . Q 5 HOH B 13 913 40 HOH HOH . Q 5 HOH B 14 914 31 HOH HOH . Q 5 HOH B 15 915 10 HOH HOH . Q 5 HOH B 16 916 42 HOH HOH . Q 5 HOH B 17 917 52 HOH HOH . Q 5 HOH B 18 918 4 HOH HOH . Q 5 HOH B 19 919 13 HOH HOH . Q 5 HOH B 20 920 12 HOH HOH . Q 5 HOH B 21 921 47 HOH HOH . Q 5 HOH B 22 922 55 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 P P1 PBU . . . K 4 -16.608 -4.801 -24.015 1 106.98 ? P1 PBU 809 A 1 HETATM 2 P P4 PBU . . . K 4 -8.512 -6.277 -23.591 1 149.87 ? P4 PBU 809 A 1 HETATM 3 P P5 PBU . . . K 4 -10.439 -2.234 -21.478 1 141.03 ? P5 PBU 809 A 1 HETATM 4 C C3' PBU . . . K 4 -19.086 -4.196 -23.579 1 74.45 ? C3' PBU 809 A 1 HETATM 5 C C2' PBU . . . K 4 -20.418 -4.702 -23.016 1 71.23 ? C2' PBU 809 A 1 HETATM 6 O O2' PBU . . . K 4 -20.315 -4.667 -21.613 1 70.99 ? O2' PBU 809 A 1 HETATM 7 C C1' PBU . . . K 4 -20.749 -6.11 -23.55 1 38.47 ? C1' PBU 809 A 1 HETATM 8 O O1' PBU . . . K 4 -19.873 -6.474 -24.6 1 62.55 ? O1' PBU 809 A 1 HETATM 9 C C1 PBU . . . K 4 -14.057 -5.054 -23.488 1 100.67 ? C1 PBU 809 A 1 HETATM 10 O O1 PBU . . . K 4 -15.375 -5.328 -23.06 1 101.7 ? O1 PBU 809 A 1 HETATM 11 C C2 PBU . . . K 4 -13.492 -6.309 -24.199 1 94.65 ? C2 PBU 809 A 1 HETATM 12 O O2 PBU . . . K 4 -14.089 -7.466 -23.657 1 112.96 ? O2 PBU 809 A 1 HETATM 13 C C3 PBU . . . K 4 -11.957 -6.504 -24.162 1 104.68 ? C3 PBU 809 A 1 HETATM 14 O O3 PBU . . . K 4 -11.732 -7.877 -23.887 1 91.51 ? O3 PBU 809 A 1 HETATM 15 C C4 PBU . . . K 4 -11.121 -5.646 -23.164 1 114.98 ? C4 PBU 809 A 1 HETATM 16 O O4 PBU . . . K 4 -9.88 -5.348 -23.795 1 128.21 ? O4 PBU 809 A 1 HETATM 17 C C5 PBU . . . K 4 -11.773 -4.321 -22.67 1 109.6 ? C5 PBU 809 A 1 HETATM 18 O O5 PBU . . . K 4 -11.054 -3.787 -21.557 1 117.18 ? O5 PBU 809 A 1 HETATM 19 C C6 PBU . . . K 4 -13.243 -4.558 -22.276 1 108.63 ? C6 PBU 809 A 1 HETATM 20 O O6 PBU . . . K 4 -13.832 -3.367 -21.786 1 94.82 ? O6 PBU 809 A 1 HETATM 21 C C7 PBU . . . K 4 -21.531 -4.755 -20.926 1 57.28 ? C7 PBU 809 A 1 HETATM 22 O O7 PBU . . . K 4 -22.474 -5.142 -21.528 1 54.13 ? O7 PBU 809 A 1 HETATM 23 C C8 PBU . . . K 4 -21.655 -4.376 -19.437 1 51.96 ? C8 PBU 809 A 1 HETATM 24 C C9 PBU . . . K 4 -22.382 -5.495 -18.679 1 54.57 ? C9 PBU 809 A 1 HETATM 25 C C10 PBU . . . K 4 -21.732 -5.77 -17.321 1 38.36 ? C10 PBU 809 A 1 HETATM 26 C C11 PBU . . . K 4 -20.435 -7.07 -25.755 1 57.25 ? C11 PBU 809 A 1 HETATM 27 O O11 PBU . . . K 4 -21.41 -7.731 -25.645 1 45.27 ? O11 PBU 809 A 1 HETATM 28 C C12 PBU . . . K 4 -19.791 -6.883 -27.145 1 56.54 ? C12 PBU 809 A 1 HETATM 29 C C13 PBU . . . K 4 -20.684 -7.397 -28.284 1 47.41 ? C13 PBU 809 A 1 HETATM 30 C C14 PBU . . . K 4 -20.847 -6.317 -29.361 1 44.75 ? C14 PBU 809 A 1 HETATM 31 O O41 PBU . . . K 4 -7.337 -5.323 -23.541 1 110.1 ? O41 PBU 809 A 1 HETATM 32 O O42 PBU . . . K 4 -8.587 -7.034 -22.281 1 96.89 ? O42 PBU 809 A 1 HETATM 33 O O43 PBU . . . K 4 -8.316 -7.281 -24.721 1 76.46 ? O43 PBU 809 A 1 HETATM 34 O O51 PBU . . . K 4 -11.026 -1.363 -22.574 1 93.92 ? O51 PBU 809 A 1 HETATM 35 O O52 PBU . . . K 4 -10.75 -1.628 -20.124 1 99.97 ? O52 PBU 809 A 1 HETATM 36 O O53 PBU . . . K 4 -8.928 -2.259 -21.617 1 91.76 ? O53 PBU 809 A 1 HETATM 37 O OP1 PBU . . . K 4 -18.063 -5.107 -23.308 1 81.21 ? OP1 PBU 809 A 1 HETATM 38 O OP2 PBU . . . K 4 -16.494 -3.298 -24.169 1 90.6 ? OP2 PBU 809 A 1 HETATM 39 O OP3 PBU . . . K 4 -16.51 -5.532 -25.343 1 89.52 ? OP3 PBU 809 A 1 HETATM 40 H "H3'1" PBU . . . K 4 -19.167 -4.081 -24.539 1 89.34 ? "H3'1" PBU 809 A 1 HETATM 41 H "H3'2" PBU . . . K 4 -18.87 -3.342 -23.172 1 89.34 ? "H3'2" PBU 809 A 1 HETATM 42 H H2' PBU . . . K 4 -21.122 -4.093 -23.291 1 85.47 ? H2' PBU 809 A 1 HETATM 43 H "H1'1" PBU . . . K 4 -21.663 -6.134 -23.871 1 46.17 ? "H1'1" PBU 809 A 1 HETATM 44 H "H1'2" PBU . . . K 4 -20.654 -6.75 -22.827 1 46.17 ? "H1'2" PBU 809 A 1 HETATM 45 H H1 PBU . . . K 4 -14.091 -4.335 -24.138 1 120.81 ? H1 PBU 809 A 1 HETATM 46 H H2 PBU . . . K 4 -13.752 -6.251 -25.131 1 113.58 ? H2 PBU 809 A 1 HETATM 47 H H02 PBU . . . K 4 -13.704 -7.668 -22.926 1 135.55 ? H02 PBU 809 A 1 HETATM 48 H H3 PBU . . . K 4 -11.621 -6.32 -25.053 1 125.61 ? H3 PBU 809 A 1 HETATM 49 H H03 PBU . . . K 4 -10.897 -8.035 -23.898 1 109.81 ? H03 PBU 809 A 1 HETATM 50 H H4 PBU . . . K 4 -10.939 -6.194 -22.384 1 137.98 ? H4 PBU 809 A 1 HETATM 51 H H5 PBU . . . K 4 -11.749 -3.678 -23.396 1 131.52 ? H5 PBU 809 A 1 HETATM 52 H H6 PBU . . . K 4 -13.274 -5.236 -21.582 1 130.35 ? H6 PBU 809 A 1 HETATM 53 H H06 PBU . . . K 4 -14.481 -3.562 -21.273 1 113.78 ? H06 PBU 809 A 1 HETATM 54 H H81 PBU . . . K 4 -22.159 -3.551 -19.355 1 62.35 ? H81 PBU 809 A 1 HETATM 55 H H82 PBU . . . K 4 -20.77 -4.253 -19.06 1 62.35 ? H82 PBU 809 A 1 HETATM 56 H H91 PBU . . . K 4 -22.357 -6.306 -19.211 1 65.48 ? H91 PBU 809 A 1 HETATM 57 H H92 PBU . . . K 4 -23.306 -5.235 -18.54 1 65.48 ? H92 PBU 809 A 1 HETATM 58 H H11 PBU . . . K 4 -20.815 -6.057 -17.454 1 46.03 ? H11 PBU 809 A 1 HETATM 59 H H12 PBU . . . K 4 -22.226 -6.467 -16.862 1 46.03 ? H12 PBU 809 A 1 HETATM 60 H H13 PBU . . . K 4 -21.744 -4.96 -16.787 1 46.03 ? H13 PBU 809 A 1 HETATM 61 H H121 PBU . . . K 4 -18.949 -7.364 -27.167 1 67.85 ? H121 PBU 809 A 1 HETATM 62 H H122 PBU . . . K 4 -19.617 -5.939 -27.286 1 67.85 ? H122 PBU 809 A 1 HETATM 63 H H131 PBU . . . K 4 -21.556 -7.629 -27.927 1 56.9 ? H131 PBU 809 A 1 HETATM 64 H H132 PBU . . . K 4 -20.279 -8.185 -28.678 1 56.9 ? H132 PBU 809 A 1 HETATM 65 H H141 PBU . . . K 4 -19.974 -5.982 -29.618 1 53.69 ? H141 PBU 809 A 1 HETATM 66 H H142 PBU . . . K 4 -21.382 -5.588 -29.009 1 53.69 ? H142 PBU 809 A 1 HETATM 67 H H143 PBU . . . K 4 -21.289 -6.697 -30.136 1 53.69 ? H143 PBU 809 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 67 #