data_5KYM
#
_model_server_result.job_id            8dP0hfhow3ONbckChQG5nw 
_model_server_result.datetime_utc      '2024-11-05 01:02:41' 
_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          5kym 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":302}' 
#
_entry.id    5KYM 
#
_exptl.entry_id    5KYM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              706.994 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL CHOLINE' 
_entity.pdbx_number_of_molecules    6 
_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            5KYM 
_cell.length_a            173.836 
_cell.length_b            173.836 
_cell.length_c            173.836 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KYM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        197 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 2 3' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_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,C,D,E,F,L 1 1 
B,G,H,I,J,K 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 
#
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 D N N 
? 2 E N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
#
_chem_comp.formula           'C38 H77 N O8 P 1' 
_chem_comp.formula_weight    706.994 
_chem_comp.id                HGX 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL CHOLINE' 
_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
O11 C11 HGX doub 144 n n 
C11 C12 HGX sing 145 n n 
C11 O3 HGX sing 146 n n 
C12 C13 HGX sing 147 n n 
C12 H121 HGX sing 148 n n 
C12 H122 HGX sing 149 n n 
C13 C14 HGX sing 150 n n 
C13 H131 HGX sing 151 n n 
C13 H132 HGX sing 152 n n 
C14 C15 HGX sing 153 n n 
C14 H141 HGX sing 154 n n 
C14 H142 HGX sing 155 n n 
C15 C16 HGX sing 156 n n 
C15 H151 HGX sing 157 n n 
C15 H152 HGX sing 158 n n 
C16 C17 HGX sing 159 n n 
C16 H161 HGX sing 160 n n 
C16 H162 HGX sing 161 n n 
C17 C18 HGX sing 162 n n 
C17 H171 HGX sing 163 n n 
C17 H172 HGX sing 164 n n 
C18 C19 HGX sing 165 n n 
C18 H181 HGX sing 166 n n 
C18 H182 HGX sing 167 n n 
C19 C20 HGX sing 168 n n 
C19 H191 HGX sing 169 n n 
C19 H192 HGX sing 170 n n 
C20 C21 HGX sing 171 n n 
C20 H201 HGX sing 172 n n 
C20 H202 HGX sing 173 n n 
C21 C22 HGX sing 174 n n 
C21 H211 HGX sing 175 n n 
C21 H212 HGX sing 176 n n 
C22 C23 HGX sing 177 n n 
C22 H221 HGX sing 178 n n 
C22 H222 HGX sing 179 n n 
C23 H231 HGX sing 180 n n 
C23 H232 HGX sing 181 n n 
C23 H233 HGX sing 182 n n 
O3 C3 HGX sing 183 n n 
C3 C2 HGX sing 184 n n 
C3 H31 HGX sing 185 n n 
C3 H32 HGX sing 186 n n 
C2 C1 HGX sing 187 n n 
C2 O2 HGX sing 188 n n 
C2 H2 HGX sing 189 n n 
C1 O3P HGX sing 190 n n 
C1 H11 HGX sing 191 n n 
C1 H12 HGX sing 192 n n 
O3P P1 HGX sing 193 n n 
O2 C31 HGX sing 194 n n 
C31 O31 HGX doub 195 n n 
C31 C32 HGX sing 196 n n 
C32 C33 HGX sing 197 n n 
C32 H321 HGX sing 198 n n 
C32 H322 HGX sing 199 n n 
C33 C34 HGX sing 200 n n 
C33 H331 HGX sing 201 n n 
C33 H332 HGX sing 202 n n 
C34 C35 HGX sing 203 n n 
C34 H341 HGX sing 204 n n 
C34 H342 HGX sing 205 n n 
C35 C36 HGX sing 206 n n 
C35 H351 HGX sing 207 n n 
C35 H352 HGX sing 208 n n 
C36 C37 HGX sing 209 n n 
C36 H361 HGX sing 210 n n 
C36 H362 HGX sing 211 n n 
C37 C38 HGX sing 212 n n 
C37 H371 HGX sing 213 n n 
C37 H372 HGX sing 214 n n 
C38 C39 HGX sing 215 n n 
C38 H381 HGX sing 216 n n 
C38 H382 HGX sing 217 n n 
C39 C40 HGX sing 218 n n 
C39 H391 HGX sing 219 n n 
C39 H392 HGX sing 220 n n 
C40 C42 HGX sing 221 n n 
C40 H401 HGX sing 222 n n 
C40 H402 HGX sing 223 n n 
C42 C43 HGX sing 224 n n 
C42 H421 HGX sing 225 n n 
C42 H422 HGX sing 226 n n 
C43 C44 HGX sing 227 n n 
C43 H431 HGX sing 228 n n 
C43 H432 HGX sing 229 n n 
C44 C45 HGX sing 230 n n 
C44 H441 HGX sing 231 n n 
C44 H442 HGX sing 232 n n 
C45 C46 HGX sing 233 n n 
C45 H451 HGX sing 234 n n 
C45 H452 HGX sing 235 n n 
C46 C47 HGX sing 236 n n 
C46 H461 HGX sing 237 n n 
C46 H462 HGX sing 238 n n 
C47 C48 HGX sing 239 n n 
C47 H471 HGX sing 240 n n 
C47 H472 HGX sing 241 n n 
C48 H481 HGX sing 242 n n 
C48 H482 HGX sing 243 n n 
C48 H483 HGX sing 244 n n 
O1 P1 HGX sing 245 n n 
O1 HO1 HGX sing 246 n n 
P1 O4 HGX doub 247 n n 
P1 O5 HGX sing 248 n n 
O5 C4 HGX sing 249 n n 
C4 C5 HGX sing 250 n n 
C4 H41 HGX sing 251 n n 
C4 H42 HGX sing 252 n n 
C5 N1 HGX sing 253 n n 
C5 H51 HGX sing 254 n n 
C5 H52 HGX sing 255 n n 
N1 C6 HGX sing 256 n n 
N1 C7 HGX sing 257 n n 
N1 C8 HGX sing 258 n n 
C6 H61 HGX sing 259 n n 
C6 H62 HGX sing 260 n n 
C6 H63 HGX sing 261 n n 
C7 H71 HGX sing 262 n n 
C7 H72 HGX sing 263 n n 
C7 H73 HGX sing 264 n n 
C8 H81 HGX sing 265 n n 
C8 H82 HGX sing 266 n n 
C8 H83 HGX sing 267 n n 
#
_atom_sites.entry_id                     5KYM 
_atom_sites.fract_transf_matrix[1][1]    0.005753 
_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]    0.005753 
_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]    0.005753 
_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 HGX A 1 301 1 HGX HGX . 
D 2 HGX A 1 302 2 HGX HGX . 
E 2 HGX A 1 303 3 HGX HGX . 
F 3 DD9 A 1 304 1 DD9 GK2 . 
G 2 HGX B 1 301 4 HGX HGX . 
H 2 HGX B 1 302 5 HGX HGX . 
I 2 HGX B 1 303 6 HGX HGX . 
J 4 LMT B 1 304 1 LMT LMT . 
K 3 DD9 B 1 305 2 DD9 GK2 . 
L 5 HOH A 1 401 1 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 O11 HGX . . . H 2 47.372 54.323 39.096 1 117.55 ? O11 HGX 302 B 1 
HETATM 2 C C11 HGX . . . H 2 47.713 53.315 39.683 1 107.88 ? C11 HGX 302 B 1 
HETATM 3 C C12 HGX . . . H 2 48.562 53.406 40.953 1 101.35 ? C12 HGX 302 B 1 
HETATM 4 C C13 HGX . . . H 2 49.438 54.67 41.031 1 96.24 ? C13 HGX 302 B 1 
HETATM 5 C C14 HGX . . . H 2 50.366 54.727 42.251 1 92.43 ? C14 HGX 302 B 1 
HETATM 6 C C15 HGX . . . H 2 50.263 56.045 43.027 1 98.63 ? C15 HGX 302 B 1 
HETATM 7 C C16 HGX . . . H 2 51.383 56.238 44.064 1 107.77 ? C16 HGX 302 B 1 
HETATM 8 C C17 HGX . . . H 2 50.945 56.903 45.387 1 117.28 ? C17 HGX 302 B 1 
HETATM 9 C C18 HGX . . . H 2 51.982 56.897 46.54 1 121.98 ? C18 HGX 302 B 1 
HETATM 10 C C19 HGX . . . H 2 53.386 57.373 46.122 1 131.28 ? C19 HGX 302 B 1 
HETATM 11 C C20 HGX . . . H 2 54.212 58.139 47.172 1 126.22 ? C20 HGX 302 B 1 
HETATM 12 C C21 HGX . . . H 2 55.656 58.418 46.713 1 111.55 ? C21 HGX 302 B 1 
HETATM 13 O O3 HGX . . . H 2 47.247 52.051 39.11 1 119.05 ? O3 HGX 302 B 1 
HETATM 14 C C3 HGX . . . H 2 46.052 51.987 38.31 1 132.55 ? C3 HGX 302 B 1 
HETATM 15 C C2 HGX . . . H 2 45.403 50.604 38.419 1 147.55 ? C2 HGX 302 B 1 
HETATM 16 C C1 HGX . . . H 2 44.465 50.355 37.239 1 157.05 ? C1 HGX 302 B 1 
HETATM 17 O O3P HGX . . . H 2 43.969 49.01 37.307 1 180.37 ? O3P HGX 302 B 1 
HETATM 18 O O2 HGX . . . H 2 44.635 50.506 39.634 1 150.44 ? O2 HGX 302 B 1 
HETATM 19 C C31 HGX . . . H 2 44.906 49.359 40.51 1 129.23 ? C31 HGX 302 B 1 
HETATM 20 O O31 HGX . . . H 2 44.966 48.222 40.058 1 137.05 ? O31 HGX 302 B 1 
HETATM 21 C C32 HGX . . . H 2 45.088 49.581 41.993 1 108.52 ? C32 HGX 302 B 1 
HETATM 22 C C33 HGX . . . H 2 46.398 50.312 42.272 1 100.49 ? C33 HGX 302 B 1 
HETATM 23 C C34 HGX . . . H 2 46.522 50.666 43.75 1 96.52 ? C34 HGX 302 B 1 
HETATM 24 C C35 HGX . . . H 2 47.421 51.869 44.04 1 94.12 ? C35 HGX 302 B 1 
HETATM 25 C C36 HGX . . . H 2 47.394 52.211 45.536 1 97.56 ? C36 HGX 302 B 1 
HETATM 26 C C37 HGX . . . H 2 48.397 53.291 45.965 1 94.32 ? C37 HGX 302 B 1 
HETATM 27 C C38 HGX . . . H 2 47.848 54.225 47.051 1 93.79 ? C38 HGX 302 B 1 
HETATM 28 C C39 HGX . . . H 2 48.893 54.526 48.128 1 100 ? C39 HGX 302 B 1 
HETATM 29 C C40 HGX . . . H 2 48.357 55.435 49.245 1 100.44 ? C40 HGX 302 B 1 
HETATM 30 C C42 HGX . . . H 2 49.453 55.844 50.243 1 100.95 ? C42 HGX 302 B 1 
HETATM 31 C C43 HGX . . . H 2 49.114 57.099 51.06 1 97.95 ? C43 HGX 302 B 1 
HETATM 32 C C44 HGX . . . H 2 49.738 57.051 52.458 1 96.31 ? C44 HGX 302 B 1 
HETATM 33 C C45 HGX . . . H 2 49.904 58.438 53.074 1 89.52 ? C45 HGX 302 B 1 
HETATM 34 O O1 HGX . . . H 2 45.067 47.379 35.697 1 231.76 ? O1 HGX 302 B 1 
HETATM 35 P P1 HGX . . . H 2 43.771 48.094 35.987 1 208.84 ? P1 HGX 302 B 1 
HETATM 36 O O4 HGX . . . H 2 43.185 48.98 34.909 1 204.15 ? O4 HGX 302 B 1 
HETATM 37 O O5 HGX . . . H 2 42.696 46.945 36.401 1 204.7 ? O5 HGX 302 B 1 
HETATM 38 C C4 HGX . . . H 2 42.935 45.933 37.391 1 182.88 ? C4 HGX 302 B 1 
HETATM 39 C C5 HGX . . . H 2 42.993 44.5 36.825 1 177.58 ? C5 HGX 302 B 1 
HETATM 40 N N1 HGX . . . H 2 41.83 43.984 36.036 1 172.28 ? N1 HGX 302 B 1 
HETATM 41 C C6 HGX . . . H 2 41.896 44.389 34.616 1 161.7 ? C6 HGX 302 B 1 
HETATM 42 C C7 HGX . . . H 2 41.861 42.509 36.078 1 165.45 ? C7 HGX 302 B 1 
HETATM 43 C C8 HGX . . . H 2 40.526 44.409 36.582 1 171.1 ? C8 HGX 302 B 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           43 
#