data_1Y5N # _model_server_result.job_id ibACJtojCi5R56ONdRdeGA _model_server_result.datetime_utc '2024-11-24 00:33:26' _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 1y5n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":309}' # _entry.id 1Y5N # _exptl.entry_id 1Y5N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 455.457 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE' _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 1Y5N _cell.length_a 154.258 _cell.length_b 241.957 _cell.length_c 140.121 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y5N _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 2 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' 3_354 -x-2,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -308.516 0 -70.0605 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id O _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 C C FME 1 C FME 1 1_555 C N GLN 2 C GLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? metalc ? metalc1 A ND1 HIS 49 A HIS 49 1_555 G FE3 SF4 . A SF4 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc2 A SG CYS 53 A CYS 53 1_555 G FE4 SF4 . A SF4 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc3 A SG CYS 57 A CYS 57 1_555 G FE1 SF4 . A SF4 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc4 A SG CYS 92 A CYS 92 1_555 G FE2 SF4 . A SF4 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc5 A OD1 ASP 222 A ASP 222 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc6 D S12 MD1 . A MD1 1800 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc7 D S13 MD1 . A MD1 1800 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc8 E S12 MD1 . A MD1 2800 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc9 E S13 MD1 . A MD1 2800 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc10 B SG CYS 16 B CYS 16 1_555 H FE4 SF4 . B SF4 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc11 B SG CYS 19 B CYS 19 1_555 H FE3 SF4 . B SF4 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc12 B SG CYS 22 B CYS 22 1_555 H FE2 SF4 . B SF4 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc13 B SG CYS 26 B CYS 26 1_555 I FE4 SF4 . B SF4 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc14 B SG CYS 184 B CYS 184 1_555 J FE1 SF4 . B SF4 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc15 B SG CYS 187 B CYS 187 1_555 J FE2 SF4 . B SF4 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc16 B SG CYS 192 B CYS 192 1_555 J FE3 SF4 . B SF4 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc17 B SG CYS 196 B CYS 196 1_555 K FE1 F3S . B F3S 1805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc18 B SG CYS 217 B CYS 217 1_555 K FE4 F3S . B F3S 1805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc19 B SG CYS 223 B CYS 223 1_555 K FE3 F3S . B F3S 1805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc20 B SG CYS 227 B CYS 227 1_555 J FE4 SF4 . B SF4 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc21 B SG CYS 244 B CYS 244 1_555 I FE2 SF4 . B SF4 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc22 B SG CYS 247 B CYS 247 1_555 I FE1 SF4 . B SF4 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc23 B SG CYS 259 B CYS 259 1_555 I FE3 SF4 . B SF4 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc24 B SG CYS 263 B CYS 263 1_555 H FE1 SF4 . B SF4 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc25 C NE2 HIS 56 C HIS 56 1_555 M FE HEM . C HEM 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc26 C NE2 HIS 66 C HIS 66 1_555 N FE HEM . C HEM 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc27 C NE2 HIS 187 C HIS 187 1_555 N FE HEM . C HEM 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc28 C NE2 HIS 205 C HIS 205 1_555 M FE HEM . C HEM 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? # _chem_comp.formula 'C19 H36 O10 P -1' _chem_comp.formula_weight 455.457 _chem_comp.id AGA _chem_comp.mon_nstd_flag . _chem_comp.name '(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PHOSPHATIDYL GLYCEROL' # 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 AGA sing 125 n n O1 HO1 AGA sing 126 n n C1 C2 AGA sing 127 n n C1 H11 AGA sing 128 n n C1 H12 AGA sing 129 n n C2 O2 AGA sing 130 n n C2 C3 AGA sing 131 n n C2 H2 AGA sing 132 n n O2 HO2 AGA sing 133 n n C3 O5 AGA sing 134 n n C3 H31 AGA sing 135 n n C3 H32 AGA sing 136 n n P1 O3 AGA sing 137 n n P1 O4 AGA doub 138 n n P1 O5 AGA sing 139 n n P1 O6 AGA sing 140 n n O6 C4 AGA sing 141 n n C4 C5 AGA sing 142 n n C4 H41 AGA sing 143 n n C4 H42 AGA sing 144 n n C5 C6 AGA sing 145 n n C5 O9 AGA sing 146 n n C5 H5 AGA sing 147 n n C6 O7 AGA sing 148 n n C6 H61 AGA sing 149 n n C6 H62 AGA sing 150 n n O7 C7 AGA sing 151 n n C7 O8 AGA doub 152 n n C7 C8 AGA sing 153 n n C8 C9 AGA sing 154 n n C8 H81 AGA sing 155 n n C8 H82 AGA sing 156 n n C9 C10 AGA sing 157 n n C9 H91 AGA sing 158 n n C9 H92 AGA sing 159 n n C10 C11 AGA sing 160 n n C10 H101 AGA sing 161 n n C10 H102 AGA sing 162 n n C11 H111 AGA sing 163 n n C11 H112 AGA sing 164 n n C11 H113 AGA sing 165 n n O9 C12 AGA sing 166 n n C12 O10 AGA doub 167 n n C12 C13 AGA sing 168 n n C13 C14 AGA sing 169 n n C13 H131 AGA sing 170 n n C13 H132 AGA sing 171 n n C14 C15 AGA sing 172 n n C14 H141 AGA sing 173 n n C14 H142 AGA sing 174 n n C15 C16 AGA sing 175 n n C15 H151 AGA sing 176 n n C15 H152 AGA sing 177 n n C16 C17 AGA sing 178 n n C16 H161 AGA sing 179 n n C16 H162 AGA sing 180 n n C17 C18 AGA sing 181 n n C17 H171 AGA sing 182 n n C17 H172 AGA sing 183 n n C18 C19 AGA sing 184 n n C18 H181 AGA sing 185 n n C18 H182 AGA sing 186 n n C19 H191 AGA sing 187 n n C19 H192 AGA sing 188 n n C19 H193 AGA sing 189 n n # _atom_sites.entry_id 1Y5N _atom_sites.fract_transf_matrix[1][1] 0.006483 _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] 0.004133 _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] 0.007137 _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 D 4 MD1 A 1 1800 1800 MD1 MD1 . E 4 MD1 A 1 2800 2800 MD1 MD1 . F 5 6MO A 1 3800 3800 6MO 6MO . G 6 SF4 A 1 1801 1801 SF4 SF4 . H 6 SF4 B 1 1802 1802 SF4 SF4 . I 6 SF4 B 1 1803 1803 SF4 SF4 . J 6 SF4 B 1 1804 1804 SF4 SF4 . K 7 F3S B 1 1805 1805 F3S F3S . L 8 3PH B 1 1806 310 3PH 3PH . M 9 HEM C 1 806 806 HEM HEM . N 9 HEM C 1 807 807 HEM HEM . O 10 AGA C 1 309 309 AGA AGA . P 11 PCI C 1 808 808 PCI PCI . Q 12 HOH A 1 3801 1 HOH HOH . Q 12 HOH A 2 3802 2 HOH HOH . Q 12 HOH A 3 3803 4 HOH HOH . Q 12 HOH A 4 3804 8 HOH HOH . Q 12 HOH A 5 3805 12 HOH HOH . Q 12 HOH A 6 3806 15 HOH HOH . Q 12 HOH A 7 3807 16 HOH HOH . Q 12 HOH A 8 3808 17 HOH HOH . Q 12 HOH A 9 3809 20 HOH HOH . Q 12 HOH A 10 3810 24 HOH HOH . Q 12 HOH A 11 3811 28 HOH HOH . Q 12 HOH A 12 3812 29 HOH HOH . Q 12 HOH A 13 3813 31 HOH HOH . Q 12 HOH A 14 3814 37 HOH HOH . Q 12 HOH A 15 3815 41 HOH HOH . Q 12 HOH A 16 3816 42 HOH HOH . Q 12 HOH A 17 3817 43 HOH HOH . Q 12 HOH A 18 3818 44 HOH HOH . Q 12 HOH A 19 3819 46 HOH HOH . Q 12 HOH A 20 3820 49 HOH HOH . Q 12 HOH A 21 3821 50 HOH HOH . Q 12 HOH A 22 3822 52 HOH HOH . Q 12 HOH A 23 3823 54 HOH HOH . R 12 HOH B 1 1807 3 HOH HOH . R 12 HOH B 2 1808 5 HOH HOH . R 12 HOH B 3 1809 6 HOH HOH . R 12 HOH B 4 1810 7 HOH HOH . R 12 HOH B 5 1811 9 HOH HOH . R 12 HOH B 6 1812 10 HOH HOH . R 12 HOH B 7 1813 11 HOH HOH . R 12 HOH B 8 1814 13 HOH HOH . R 12 HOH B 9 1815 14 HOH HOH . R 12 HOH B 10 1816 18 HOH HOH . R 12 HOH B 11 1817 19 HOH HOH . R 12 HOH B 12 1818 21 HOH HOH . R 12 HOH B 13 1819 22 HOH HOH . R 12 HOH B 14 1820 25 HOH HOH . R 12 HOH B 15 1821 26 HOH HOH . R 12 HOH B 16 1822 27 HOH HOH . R 12 HOH B 17 1823 30 HOH HOH . R 12 HOH B 18 1824 32 HOH HOH . R 12 HOH B 19 1825 33 HOH HOH . R 12 HOH B 20 1826 34 HOH HOH . R 12 HOH B 21 1827 36 HOH HOH . R 12 HOH B 22 1828 38 HOH HOH . R 12 HOH B 23 1829 39 HOH HOH . R 12 HOH B 24 1830 40 HOH HOH . R 12 HOH B 25 1831 45 HOH HOH . R 12 HOH B 26 1832 47 HOH HOH . R 12 HOH B 27 1833 48 HOH HOH . R 12 HOH B 28 1834 51 HOH HOH . R 12 HOH B 29 1835 53 HOH HOH . S 12 HOH C 1 809 23 HOH HOH . S 12 HOH C 2 810 35 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 O O1 AGA . . . O 10 -162.051 -17.353 -14.25 1 95.75 ? O1 AGA 309 C 1 HETATM 2 C C1 AGA . . . O 10 -160.864 -18.033 -14.63 1 93.03 ? C1 AGA 309 C 1 HETATM 3 C C2 AGA . . . O 10 -161.179 -19.226 -15.607 1 84.22 ? C2 AGA 309 C 1 HETATM 4 O O2 AGA . . . O 10 -161.124 -20.473 -14.935 1 85.73 ? O2 AGA 309 C 1 HETATM 5 C C3 AGA . . . O 10 -160.197 -19.258 -16.803 1 73.41 ? C3 AGA 309 C 1 HETATM 6 P P1 AGA . . . O 10 -159.871 -18.666 -19.36 1 45.48 ? P1 AGA 309 C 1 HETATM 7 O O3 AGA . . . O 10 -160.162 -19.85 -20.28 1 54.88 ? O3 AGA 309 C 1 HETATM 8 O O4 AGA . . . O 10 -158.363 -18.55 -18.957 1 30.2 ? O4 AGA 309 C 1 HETATM 9 O O5 AGA . . . O 10 -160.717 -18.737 -18.056 1 54.3 ? O5 AGA 309 C 1 HETATM 10 O O6 AGA . . . O 10 -160.259 -17.257 -20.054 1 45.88 ? O6 AGA 309 C 1 HETATM 11 C C4 AGA . . . O 10 -160.062 -16.011 -19.374 1 41.4 ? C4 AGA 309 C 1 HETATM 12 C C5 AGA . . . O 10 -160.554 -14.887 -20.238 1 47.13 ? C5 AGA 309 C 1 HETATM 13 C C6 AGA . . . O 10 -160.973 -13.64 -19.528 1 47.99 ? C6 AGA 309 C 1 HETATM 14 O O7 AGA . . . O 10 -161.375 -12.703 -20.543 1 60.41 ? O7 AGA 309 C 1 HETATM 15 C C7 AGA . . . O 10 -162.675 -12.414 -20.775 1 71.53 ? C7 AGA 309 C 1 HETATM 16 O O8 AGA . . . O 10 -163.593 -13.217 -20.753 1 76.06 ? O8 AGA 309 C 1 HETATM 17 C C8 AGA . . . O 10 -162.849 -10.886 -21.094 1 67.44 ? C8 AGA 309 C 1 HETATM 18 C C9 AGA . . . O 10 -163.325 -10.155 -22.364 1 64.85 ? C9 AGA 309 C 1 HETATM 19 C C10 AGA . . . O 10 -162.992 -8.666 -22.383 1 70.94 ? C10 AGA 309 C 1 HETATM 20 C C11 AGA . . . O 10 -163.734 -7.872 -23.457 1 65.23 ? C11 AGA 309 C 1 HETATM 21 O O9 AGA . . . O 10 -159.633 -14.615 -21.344 1 53.77 ? O9 AGA 309 C 1 HETATM 22 C C12 AGA . . . O 10 -159.997 -14.629 -22.667 1 48.33 ? C12 AGA 309 C 1 HETATM 23 O O10 AGA . . . O 10 -161.101 -14.902 -23.096 1 52.08 ? O10 AGA 309 C 1 HETATM 24 C C13 AGA . . . O 10 -158.901 -14.087 -23.578 1 40.68 ? C13 AGA 309 C 1 HETATM 25 C C14 AGA . . . O 10 -158.797 -13.722 -25.062 1 45.35 ? C14 AGA 309 C 1 HETATM 26 C C15 AGA . . . O 10 -159.068 -12.228 -25.313 1 56.89 ? C15 AGA 309 C 1 HETATM 27 C C16 AGA . . . O 10 -160.177 -11.964 -26.335 1 56.61 ? C16 AGA 309 C 1 HETATM 28 C C17 AGA . . . O 10 -160.441 -10.452 -26.587 1 55.25 ? C17 AGA 309 C 1 HETATM 29 C C18 AGA . . . O 10 -161.551 -10.107 -27.621 1 54.01 ? C18 AGA 309 C 1 HETATM 30 C C19 AGA . . . O 10 -161.717 -8.59 -27.8 1 49.93 ? C19 AGA 309 C 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #