data_5ZM6
#
_model_server_result.job_id            czQ1qMOSL9SKXf1k0PCvLw 
_model_server_result.datetime_utc      '2024-11-05 06:48:41' 
_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          5zm6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1001}' 
#
_entry.id    5ZM6 
#
_exptl.entry_id    5ZM6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              1047.088 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] icosa-5,8,11,14-tetraenoate' 
_entity.pdbx_number_of_molecules    2 
_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            5ZM6 
_cell.length_a            188.661 
_cell.length_b            188.661 
_cell.length_c            64.585 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZM6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_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,G,H 
_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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -32.2925 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N N 
#
_chem_comp.formula           'C47 H85 O19 P3' 
_chem_comp.formula_weight    1047.088 
_chem_comp.id                IEP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] icosa-5,8,11,14-tetraenoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C63 C64 IEP doub 158 z n 
C63 C62 IEP sing 159 n n 
C62 C61 IEP sing 160 n n 
C61 C60 IEP doub 161 e n 
C60 C59 IEP sing 162 n n 
C59 C58 IEP sing 163 n n 
C58 C57 IEP doub 164 e n 
O40 P37 IEP doub 165 n n 
O39 P37 IEP sing 166 n n 
C57 C56 IEP sing 167 n n 
O45 P42 IEP doub 168 n n 
O38 P37 IEP sing 169 n n 
P37 O36 IEP sing 170 n n 
C56 C55 IEP sing 171 n n 
P42 O41 IEP sing 172 n n 
P42 O44 IEP sing 173 n n 
P42 O43 IEP sing 174 n n 
C54 C55 IEP doub 175 e n 
C54 C53 IEP sing 176 n n 
O41 C32 IEP sing 177 n n 
O36 C33 IEP sing 178 n n 
C52 C51 IEP sing 179 n n 
C52 C53 IEP sing 180 n n 
C51 C49 IEP sing 181 n n 
C32 C33 IEP sing 182 n n 
C32 C31 IEP sing 183 n n 
C33 C34 IEP sing 184 n n 
O35 C34 IEP sing 185 n n 
C49 O50 IEP doub 186 n n 
C49 O48 IEP sing 187 n n 
O46 C31 IEP sing 188 n n 
C31 C30 IEP sing 189 n n 
C34 C29 IEP sing 190 n n 
O48 C22 IEP sing 191 n n 
C16 C15 IEP sing 192 n n 
C16 C17 IEP sing 193 n n 
O19 C18 IEP doub 194 n n 
C15 C14 IEP sing 195 n n 
C18 C17 IEP sing 196 n n 
C18 O20 IEP sing 197 n n 
C30 C29 IEP sing 198 n n 
C30 O47 IEP sing 199 n n 
C29 O28 IEP sing 200 n n 
C14 C13 IEP sing 201 n n 
C22 C21 IEP sing 202 n n 
C22 C23 IEP sing 203 n n 
C21 O20 IEP sing 204 n n 
O28 P25 IEP sing 205 n n 
C13 C12 IEP sing 206 n n 
C23 O24 IEP sing 207 n n 
P25 O24 IEP sing 208 n n 
P25 O26 IEP doub 209 n n 
P25 O27 IEP sing 210 n n 
C12 C11 IEP sing 211 n n 
C11 C10 IEP sing 212 n n 
C10 C09 IEP sing 213 n n 
C09 C08 IEP sing 214 n n 
C08 C07 IEP sing 215 n n 
C06 C07 IEP sing 216 n n 
C06 C05 IEP sing 217 n n 
C01 C02 IEP sing 218 n n 
C02 C03 IEP sing 219 n n 
C05 C04 IEP sing 220 n n 
C04 C03 IEP sing 221 n n 
C01 H1 IEP sing 222 n n 
C01 H2 IEP sing 223 n n 
C01 H3 IEP sing 224 n n 
C02 H4 IEP sing 225 n n 
C02 H5 IEP sing 226 n n 
C03 H6 IEP sing 227 n n 
C03 H7 IEP sing 228 n n 
C04 H8 IEP sing 229 n n 
C04 H9 IEP sing 230 n n 
C05 H10 IEP sing 231 n n 
C05 H11 IEP sing 232 n n 
C06 H12 IEP sing 233 n n 
C07 H13 IEP sing 234 n n 
C08 H14 IEP sing 235 n n 
C09 H15 IEP sing 236 n n 
C10 H16 IEP sing 237 n n 
C11 H17 IEP sing 238 n n 
C12 H18 IEP sing 239 n n 
C13 H19 IEP sing 240 n n 
C14 H20 IEP sing 241 n n 
C14 H21 IEP sing 242 n n 
C15 H22 IEP sing 243 n n 
C15 H23 IEP sing 244 n n 
C16 H24 IEP sing 245 n n 
C17 H25 IEP sing 246 n n 
C21 H27 IEP sing 247 n n 
C21 H28 IEP sing 248 n n 
C22 H29 IEP sing 249 n n 
C23 H30 IEP sing 250 n n 
C23 H31 IEP sing 251 n n 
C29 H32 IEP sing 252 n n 
C30 H33 IEP sing 253 n n 
C31 H34 IEP sing 254 n n 
C32 H35 IEP sing 255 n n 
C33 H36 IEP sing 256 n n 
C34 H37 IEP sing 257 n n 
C51 H39 IEP sing 258 n n 
C51 H40 IEP sing 259 n n 
C52 H41 IEP sing 260 n n 
C52 H42 IEP sing 261 n n 
C53 H43 IEP sing 262 n n 
C53 H44 IEP sing 263 n n 
C54 H46 IEP sing 264 n n 
C55 H47 IEP sing 265 n n 
C56 H49 IEP sing 266 n n 
C56 H50 IEP sing 267 n n 
C57 H51 IEP sing 268 n n 
C58 H53 IEP sing 269 n n 
C59 H55 IEP sing 270 n n 
C59 H56 IEP sing 271 n n 
C60 H57 IEP sing 272 n n 
C61 H59 IEP sing 273 n n 
C62 H60 IEP sing 274 n n 
C63 H61 IEP sing 275 n n 
C64 H63 IEP sing 276 n n 
O27 H67 IEP sing 277 n n 
O35 H68 IEP sing 278 n n 
O38 H69 IEP sing 279 n n 
O39 H70 IEP sing 280 n n 
O43 H71 IEP sing 281 n n 
O44 H72 IEP sing 282 n n 
O46 H73 IEP sing 283 n n 
O47 H74 IEP sing 284 n n 
C64 C1 IEP sing 285 n n 
C1 C2 IEP sing 286 n n 
C2 C3 IEP sing 287 n n 
C3 C4 IEP sing 288 n n 
C4 C5 IEP sing 289 n n 
C1 H85 IEP sing 290 n n 
C1 H86 IEP sing 291 n n 
C2 H84 IEP sing 292 n n 
C2 H83 IEP sing 293 n n 
C3 H82 IEP sing 294 n n 
C3 H81 IEP sing 295 n n 
C4 H80 IEP sing 296 n n 
C4 H79 IEP sing 297 n n 
C5 H78 IEP sing 298 n n 
C5 H76 IEP sing 299 n n 
C5 H77 IEP sing 300 n n 
C62 H38 IEP sing 301 n n 
C07 H54 IEP sing 302 n n 
C09 H58 IEP sing 303 n n 
C11 H65 IEP sing 304 n n 
C12 H75 IEP sing 305 n n 
C13 H87 IEP sing 306 n n 
C06 H52 IEP sing 307 n n 
C08 H62 IEP sing 308 n n 
C10 H64 IEP sing 309 n n 
C16 H88 IEP sing 310 n n 
C17 H89 IEP sing 311 n n 
#
_atom_sites.entry_id                     5ZM6 
_atom_sites.fract_transf_matrix[1][1]    0.005301 
_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]    0.005301 
_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]    0.015483 
_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 IEP A 1 1001 1 IEP IEP . 
D 3 ACT A 1 1002 1 ACT ACT . 
E 2 IEP B 1 1001 2 IEP IEP . 
F 3 ACT B 1 1002 2 ACT ACT . 
G 4 HOH A 1 1101 13 HOH HOH . 
G 4 HOH A 2 1102 8 HOH HOH . 
G 4 HOH A 3 1103 9 HOH HOH . 
G 4 HOH A 4 1104 5 HOH HOH . 
G 4 HOH A 5 1105 12 HOH HOH . 
G 4 HOH A 6 1106 6 HOH HOH . 
G 4 HOH A 7 1107 4 HOH HOH . 
G 4 HOH A 8 1108 10 HOH HOH . 
G 4 HOH A 9 1109 19 HOH HOH . 
G 4 HOH A 10 1110 11 HOH HOH . 
H 4 HOH B 1 1101 24 HOH HOH . 
H 4 HOH B 2 1102 16 HOH HOH . 
H 4 HOH B 3 1103 15 HOH HOH . 
H 4 HOH B 4 1104 18 HOH HOH . 
H 4 HOH B 5 1105 29 HOH HOH . 
H 4 HOH B 6 1106 32 HOH HOH . 
H 4 HOH B 7 1107 30 HOH HOH . 
H 4 HOH B 8 1108 31 HOH HOH . 
H 4 HOH B 9 1109 34 HOH HOH . 
H 4 HOH B 10 1110 1 HOH HOH . 
H 4 HOH B 11 1111 25 HOH HOH . 
H 4 HOH B 12 1112 3 HOH HOH . 
H 4 HOH B 13 1113 2 HOH HOH . 
H 4 HOH B 14 1114 28 HOH HOH . 
H 4 HOH B 15 1115 22 HOH HOH . 
H 4 HOH B 16 1116 26 HOH HOH . 
H 4 HOH B 17 1117 27 HOH HOH . 
H 4 HOH B 18 1118 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 C C01 IEP . . . C 2 -35.133 64.099 -2.221 1 53.87 ? C01 IEP 1001 A 1 
HETATM 2 C C02 IEP . . . C 2 -35.379 62.622 -2.116 1 59.28 ? C02 IEP 1001 A 1 
HETATM 3 C C03 IEP . . . C 2 -34.714 61.805 -1.043 1 56.31 ? C03 IEP 1001 A 1 
HETATM 4 C C04 IEP . . . C 2 -34.526 60.336 -1.314 1 59.85 ? C04 IEP 1001 A 1 
HETATM 5 C C05 IEP . . . C 2 -35.762 59.459 -1.478 1 67.64 ? C05 IEP 1001 A 1 
HETATM 6 C C06 IEP . . . C 2 -35.76 58.261 -2.421 1 64.93 ? C06 IEP 1001 A 1 
HETATM 7 C C07 IEP . . . C 2 -36.655 57.079 -2.062 1 71.44 ? C07 IEP 1001 A 1 
HETATM 8 C C08 IEP . . . C 2 -36.732 55.908 -3.031 1 68.83 ? C08 IEP 1001 A 1 
HETATM 9 C C09 IEP . . . C 2 -37.661 56.049 -4.228 1 66.59 ? C09 IEP 1001 A 1 
HETATM 10 C C10 IEP . . . C 2 -37.944 54.777 -5.015 1 69.96 ? C10 IEP 1001 A 1 
HETATM 11 C C11 IEP . . . C 2 -37.818 54.814 -6.53 1 75.26 ? C11 IEP 1001 A 1 
HETATM 12 C C12 IEP . . . C 2 -38.212 53.58 -7.328 1 75.09 ? C12 IEP 1001 A 1 
HETATM 13 C C13 IEP . . . C 2 -37.655 53.437 -8.73 1 86.85 ? C13 IEP 1001 A 1 
HETATM 14 C C14 IEP . . . C 2 -38.237 52.403 -9.676 1 103.29 ? C14 IEP 1001 A 1 
HETATM 15 C C15 IEP . . . C 2 -39.642 52.568 -10.258 1 111.03 ? C15 IEP 1001 A 1 
HETATM 16 C C16 IEP . . . C 2 -40.214 53.956 -10.627 1 108 ? C16 IEP 1001 A 1 
HETATM 17 C C17 IEP . . . C 2 -40.301 55.114 -9.608 1 101.97 ? C17 IEP 1001 A 1 
HETATM 18 C C18 IEP . . . C 2 -41.075 56.358 -9.973 1 102.39 ? C18 IEP 1001 A 1 
HETATM 19 C C21 IEP . . . C 2 -40.606 58.578 -9.014 1 101.57 ? C21 IEP 1001 A 1 
HETATM 20 C C22 IEP . . . C 2 -41.678 59.747 -9.245 1 101.69 ? C22 IEP 1001 A 1 
HETATM 21 C C23 IEP . . . C 2 -41.729 60.976 -8.21 1 94.98 ? C23 IEP 1001 A 1 
HETATM 22 C C29 IEP . . . C 2 -44.351 62.484 -9.84 1 94.36 ? C29 IEP 1001 A 1 
HETATM 23 C C30 IEP . . . C 2 -45.548 63.398 -9.939 1 94.36 ? C30 IEP 1001 A 1 
HETATM 24 C C31 IEP . . . C 2 -46.404 63.369 -11.207 1 88.9 ? C31 IEP 1001 A 1 
HETATM 25 C C32 IEP . . . C 2 -45.54 63.347 -12.435 1 94.9 ? C32 IEP 1001 A 1 
HETATM 26 C C33 IEP . . . C 2 -44.709 62.145 -12.35 1 99.49 ? C33 IEP 1001 A 1 
HETATM 27 C C34 IEP . . . C 2 -43.822 61.956 -11.154 1 100.89 ? C34 IEP 1001 A 1 
HETATM 28 C C49 IEP . . . C 2 -42.056 58.903 -11.452 1 102.6 ? C49 IEP 1001 A 1 
HETATM 29 C C51 IEP . . . C 2 -41.608 58.934 -12.934 1 101.05 ? C51 IEP 1001 A 1 
HETATM 30 C C52 IEP . . . C 2 -40.2 59.429 -13.243 1 91.24 ? C52 IEP 1001 A 1 
HETATM 31 C C53 IEP . . . C 2 -39.804 60.834 -12.829 1 93.18 ? C53 IEP 1001 A 1 
HETATM 32 C C54 IEP . . . C 2 -39.708 61.941 -13.878 1 94.56 ? C54 IEP 1001 A 1 
HETATM 33 C C55 IEP . . . C 2 -40.122 63.326 -13.441 1 88.84 ? C55 IEP 1001 A 1 
HETATM 34 C C56 IEP . . . C 2 -39.421 64.496 -14.086 1 91.94 ? C56 IEP 1001 A 1 
HETATM 35 C C57 IEP . . . C 2 -39.695 64.796 -15.542 1 92.49 ? C57 IEP 1001 A 1 
HETATM 36 C C58 IEP . . . C 2 -38.544 65.222 -16.41 1 87.96 ? C58 IEP 1001 A 1 
HETATM 37 C C59 IEP . . . C 2 -38.562 64.834 -17.867 1 80.81 ? C59 IEP 1001 A 1 
HETATM 38 C C60 IEP . . . C 2 -39.913 64.787 -18.552 1 83.31 ? C60 IEP 1001 A 1 
HETATM 39 C C61 IEP . . . C 2 -40.116 65.608 -19.817 1 86.67 ? C61 IEP 1001 A 1 
HETATM 40 C C62 IEP . . . C 2 -41.293 66.582 -19.823 1 84.28 ? C62 IEP 1001 A 1 
HETATM 41 C C63 IEP . . . C 2 -41.641 67.256 -21.151 1 87.54 ? C63 IEP 1001 A 1 
HETATM 42 C C64 IEP . . . C 2 -42.883 68.156 -21.147 1 84.16 ? C64 IEP 1001 A 1 
HETATM 43 O O19 IEP . . . C 2 -42.336 55.999 -10.365 1 104.78 ? O19 IEP 1001 A 1 
HETATM 44 O O20 IEP . . . C 2 -41.187 57.324 -8.963 1 104.09 ? O20 IEP 1001 A 1 
HETATM 45 O O24 IEP . . . C 2 -42.67 60.765 -7.22 1 97.32 ? O24 IEP 1001 A 1 
HETATM 46 O O26 IEP . . . C 2 -44.992 60.203 -6.814 1 96.41 -1 O26 IEP 1001 A 1 
HETATM 47 O O27 IEP . . . C 2 -44.532 62.362 -6.645 1 92.25 ? O27 IEP 1001 A 1 
HETATM 48 O O28 IEP . . . C 2 -44.611 61.383 -9.004 1 102.3 ? O28 IEP 1001 A 1 
HETATM 49 O O35 IEP . . . C 2 -42.564 62.437 -11.463 1 104.04 ? O35 IEP 1001 A 1 
HETATM 50 O O36 IEP . . . C 2 -44.261 61.658 -13.456 1 104.23 ? O36 IEP 1001 A 1 
HETATM 51 O O38 IEP . . . C 2 -43.393 63.3 -15.158 1 105.85 ? O38 IEP 1001 A 1 
HETATM 52 O O39 IEP . . . C 2 -45.66 62.26 -15.547 1 95.94 -1 O39 IEP 1001 A 1 
HETATM 53 O O40 IEP . . . C 2 -43.451 61.107 -15.684 1 104.36 ? O40 IEP 1001 A 1 
HETATM 54 O O41 IEP . . . C 2 -46.046 63.877 -13.617 1 93.97 ? O41 IEP 1001 A 1 
HETATM 55 O O43 IEP . . . C 2 -48.273 65.059 -13.546 1 88.12 ? O43 IEP 1001 A 1 
HETATM 56 O O44 IEP . . . C 2 -48.15 62.565 -13.585 1 85.1 -1 O44 IEP 1001 A 1 
HETATM 57 O O45 IEP . . . C 2 -47.631 64.06 -15.494 1 95.88 ? O45 IEP 1001 A 1 
HETATM 58 O O46 IEP . . . C 2 -47.15 62.207 -11.233 1 83.24 ? O46 IEP 1001 A 1 
HETATM 59 O O47 IEP . . . C 2 -46.281 63.291 -8.78 1 91.47 ? O47 IEP 1001 A 1 
HETATM 60 O O48 IEP . . . C 2 -41.739 60.022 -10.711 1 95.67 ? O48 IEP 1001 A 1 
HETATM 61 O O50 IEP . . . C 2 -43.425 58.76 -11.316 1 105.74 ? O50 IEP 1001 A 1 
HETATM 62 P P25 IEP . . . C 2 -44.137 61.216 -7.492 1 115.01 ? P25 IEP 1001 A 1 
HETATM 63 P P37 IEP . . . C 2 -44.245 62.105 -14.945 1 110.82 ? P37 IEP 1001 A 1 
HETATM 64 P P42 IEP . . . C 2 -47.534 63.888 -14.04 1 95.45 ? P42 IEP 1001 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           64 
#