data_8YHQ
#
_model_server_result.job_id            Tx3Ko-9l8a9QAxyLdNr2tA 
_model_server_result.datetime_utc      '2024-12-26 12:58:02' 
_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          8yhq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"NA","auth_seq_id":101}' 
#
_entry.id    8YHQ 
#
_exptl.entry_id    8YHQ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              691.959 
_entity.id                          14 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate' 
_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            8YHQ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YHQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    eicosameric 
_pdbx_struct_assembly.oligomeric_count      20 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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
? 14 Y N N 
? 14 NA 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
disulf ? disulf1 E SG CYS 129 E CYS 159 1_555 E SG CYS 134 E CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? 
disulf ? disulf2 E SG CYS 148 E CYS 178 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? 
disulf ? disulf3 F SG CYS 29 F CYS 101 1_555 F SG CYS 51 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? 
disulf ? disulf4 N SG CYS 134 N CYS 164 1_555 N SG CYS 150 N CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? 
disulf ? disulf5 P SG CYS 29 O CYS 101 1_555 P SG CYS 51 O CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? 
metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc6 G NE2 HIS 82 L HIS 82 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc7 G NE2 HIS 96 L HIS 96 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? 
metalc ? metalc8 G NE2 HIS 183 L HIS 183 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc9 G NE2 HIS 197 L HIS 197 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? 
metalc ? metalc10 M NE2 HIS 44 M HIS 105 1_555 KA FE HEM . M HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
#
_chem_comp.formula           'C37 H74 N O8 P' 
_chem_comp.formula_weight    691.959 
_chem_comp.id                8PE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     3-SN-PHOSPHATIDYLETHANOLAMINE 
#
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
O12 P 8PE doub 195 n n 
O11 P 8PE sing 196 n n 
P O14 8PE sing 197 n n 
P O13 8PE sing 198 n n 
C12 N 8PE sing 199 n n 
N HN 8PE sing 200 n n 
N HNA 8PE sing 201 n n 
O11 C1 8PE sing 202 n n 
O13 C11 8PE sing 203 n n 
O14 HO14 8PE sing 204 n n 
C12 C11 8PE sing 205 n n 
C11 H11 8PE sing 206 n n 
C11 H11A 8PE sing 207 n n 
C12 H12 8PE sing 208 n n 
C12 H12A 8PE sing 209 n n 
C2 C1 8PE sing 210 n n 
C1 H1 8PE sing 211 n n 
C1 H1A 8PE sing 212 n n 
C3 C2 8PE sing 213 n n 
C2 O21 8PE sing 214 n n 
C2 H2 8PE sing 215 n n 
O31 C3 8PE sing 216 n n 
C3 H3 8PE sing 217 n n 
C3 H3A 8PE sing 218 n n 
C31 O31 8PE sing 219 n n 
O32 C31 8PE doub 220 n n 
C32 C31 8PE sing 221 n n 
C32 C33 8PE sing 222 n n 
C32 H32 8PE sing 223 n n 
C32 H32A 8PE sing 224 n n 
C33 C34 8PE sing 225 n n 
C33 H33 8PE sing 226 n n 
C33 H33A 8PE sing 227 n n 
C35 C34 8PE sing 228 n n 
C34 H34 8PE sing 229 n n 
C34 H34A 8PE sing 230 n n 
C35 C36 8PE sing 231 n n 
C35 H35 8PE sing 232 n n 
C35 H35A 8PE sing 233 n n 
C37 C36 8PE sing 234 n n 
C36 H36 8PE sing 235 n n 
C36 H36A 8PE sing 236 n n 
C38 C37 8PE sing 237 n n 
C37 H37 8PE sing 238 n n 
C37 H37A 8PE sing 239 n n 
C39 C38 8PE sing 240 n n 
C38 H38 8PE sing 241 n n 
C38 H38A 8PE sing 242 n n 
C39 C3A 8PE sing 243 n n 
C39 H39 8PE sing 244 n n 
C39 H39A 8PE sing 245 n n 
C3B C3A 8PE sing 246 n n 
C3A H3AA 8PE sing 247 n n 
C3A H3AB 8PE sing 248 n n 
C3C C3B 8PE sing 249 n n 
C3B H3B 8PE sing 250 n n 
C3B H3BA 8PE sing 251 n n 
C3C C3D 8PE sing 252 n n 
C3C H3C 8PE sing 253 n n 
C3C H3CA 8PE sing 254 n n 
C3E C3D 8PE sing 255 n n 
C3D H3D 8PE sing 256 n n 
C3D H3DA 8PE sing 257 n n 
C3F C3E 8PE sing 258 n n 
C3E H3E 8PE sing 259 n n 
C3E H3EA 8PE sing 260 n n 
C3G C3F 8PE sing 261 n n 
C3F H3F 8PE sing 262 n n 
C3F H3FA 8PE sing 263 n n 
C3G C3H 8PE sing 264 n n 
C3G H3G 8PE sing 265 n n 
C3G H3GA 8PE sing 266 n n 
C3I C3H 8PE sing 267 n n 
C3H H3H 8PE sing 268 n n 
C3H H3HA 8PE sing 269 n n 
C3I H3I 8PE sing 270 n n 
C3I H3IA 8PE sing 271 n n 
C3I H3IB 8PE sing 272 n n 
O21 C21 8PE sing 273 n n 
C21 O22 8PE doub 274 n n 
C21 C22 8PE sing 275 n n 
C23 C22 8PE sing 276 n n 
C22 H22 8PE sing 277 n n 
C22 H22A 8PE sing 278 n n 
C23 C24 8PE sing 279 n n 
C23 H23 8PE sing 280 n n 
C23 H23A 8PE sing 281 n n 
C25 C24 8PE sing 282 n n 
C24 H24 8PE sing 283 n n 
C24 H24A 8PE sing 284 n n 
C25 C26 8PE sing 285 n n 
C25 H25 8PE sing 286 n n 
C25 H25A 8PE sing 287 n n 
C27 C26 8PE sing 288 n n 
C26 H26 8PE sing 289 n n 
C26 H26A 8PE sing 290 n n 
C27 C28 8PE sing 291 n n 
C27 H27 8PE sing 292 n n 
C27 H27A 8PE sing 293 n n 
C29 C28 8PE sing 294 n n 
C28 H28 8PE sing 295 n n 
C28 H28A 8PE sing 296 n n 
C29 C2A 8PE sing 297 n n 
C29 H29 8PE sing 298 n n 
C29 H29A 8PE sing 299 n n 
C2B C2A 8PE sing 300 n n 
C2A H2A 8PE sing 301 n n 
C2A H2AA 8PE sing 302 n n 
C2C C2B 8PE sing 303 n n 
C2B H2B 8PE sing 304 n n 
C2B H2BA 8PE sing 305 n n 
C2C C2D 8PE sing 306 n n 
C2C H2C 8PE sing 307 n n 
C2C H2CA 8PE sing 308 n n 
C2E C2D 8PE sing 309 n n 
C2D H2D 8PE sing 310 n n 
C2D H2DA 8PE sing 311 n n 
C2E H2E 8PE sing 312 n n 
C2E H2EA 8PE sing 313 n n 
C2E H2EB 8PE sing 314 n n 
#
_atom_sites.entry_id                     8YHQ 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
U 11 6PH C 1 401 402 6PH 6PH . 
V 12 9PE C 1 402 403 9PE 9PE . 
W 13 HEM C 1 403 404 HEM HEM . 
X 13 HEM C 1 404 405 HEM HEM . 
Y 14 8PE C 1 405 406 8PE 8PE . 
Z 15 CN5 C 1 406 407 CN5 CN5 . 
AA 16 UQ6 C 1 407 408 UQ6 UQ6 . 
BA 17 A1D6K C 1 408 401 A1D6K A1D . 
CA 13 HEM D 1 401 402 HEM HEM . 
DA 18 7PH D 1 402 401 7PH 7PH . 
EA 16 UQ6 L 1 401 402 UQ6 UQ6 . 
FA 12 9PE L 1 402 403 9PE 9PE . 
GA 13 HEM L 1 403 404 HEM HEM . 
HA 19 CN3 L 1 404 405 CN3 CN3 . 
IA 13 HEM L 1 405 406 HEM HEM . 
JA 17 A1D6K L 1 406 401 A1D6K A1D . 
KA 13 HEM M 1 401 401 HEM HEM . 
LA 11 6PH N 1 401 401 6PH 6PH . 
MA 18 7PH N 1 402 402 7PH 7PH . 
NA 14 8PE Q 1 101 101 8PE 8PE . 
#
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 P 8PE . . . NA 14 166.365 149.191 133.369 1 19.17 ? P 8PE 101 Q 1 
HETATM 2 N N 8PE . . . NA 14 163.695 149.632 136.77 1 19.17 ? N 8PE 101 Q 1 
HETATM 3 O O11 8PE . . . NA 14 166.051 149.856 131.891 1 19.17 ? O11 8PE 101 Q 1 
HETATM 4 O O12 8PE . . . NA 14 167.037 150.243 134.217 1 19.17 ? O12 8PE 101 Q 1 
HETATM 5 O O13 8PE . . . NA 14 164.988 148.658 134.104 1 19.17 ? O13 8PE 101 Q 1 
HETATM 6 O O14 8PE . . . NA 14 167.306 148.022 133.221 1 19.17 ? O14 8PE 101 Q 1 
HETATM 7 C C11 8PE . . . NA 14 163.928 149.54 134.342 1 19.17 ? C11 8PE 101 Q 1 
HETATM 8 C C12 8PE . . . NA 14 164.161 150.36 135.605 1 19.17 ? C12 8PE 101 Q 1 
HETATM 9 C C1 8PE . . . NA 14 164.938 149.448 131.149 1 19.17 ? C1 8PE 101 Q 1 
HETATM 10 C C2 8PE . . . NA 14 165.382 148.589 129.974 1 19.17 ? C2 8PE 101 Q 1 
HETATM 11 C C3 8PE . . . NA 14 164.174 148.237 129.118 1 19.17 ? C3 8PE 101 Q 1 
HETATM 12 O O31 8PE . . . NA 14 163.99 146.859 129.127 1 19.17 ? O31 8PE 101 Q 1 
HETATM 13 O O32 8PE . . . NA 14 164.904 146.41 127.151 1 19.17 ? O32 8PE 101 Q 1 
HETATM 14 C C31 8PE . . . NA 14 163.974 146.277 127.864 1 19.17 ? C31 8PE 101 Q 1 
HETATM 15 C C32 8PE . . . NA 14 162.762 145.451 127.451 1 19.17 ? C32 8PE 101 Q 1 
HETATM 16 C C33 8PE . . . NA 14 162.431 145.571 125.968 1 19.17 ? C33 8PE 101 Q 1 
HETATM 17 C C34 8PE . . . NA 14 163.499 144.976 125.053 1 19.17 ? C34 8PE 101 Q 1 
HETATM 18 C C35 8PE . . . NA 14 164.218 146.023 124.199 1 19.17 ? C35 8PE 101 Q 1 
HETATM 19 C C36 8PE . . . NA 14 164.503 145.474 122.805 1 19.17 ? C36 8PE 101 Q 1 
HETATM 20 C C37 8PE . . . NA 14 163.248 145.53 121.941 1 19.17 ? C37 8PE 101 Q 1 
HETATM 21 C C38 8PE . . . NA 14 163.611 145.084 120.523 1 19.17 ? C38 8PE 101 Q 1 
HETATM 22 C C39 8PE . . . NA 14 162.72 143.967 119.967 1 19.17 ? C39 8PE 101 Q 1 
HETATM 23 C C3A 8PE . . . NA 14 163.526 142.963 119.124 1 19.17 ? C3A 8PE 101 Q 1 
HETATM 24 C C3B 8PE . . . NA 14 162.769 141.64 118.969 1 19.17 ? C3B 8PE 101 Q 1 
HETATM 25 C C3C 8PE . . . NA 14 163.639 140.397 119.205 1 19.17 ? C3C 8PE 101 Q 1 
HETATM 26 C C3D 8PE . . . NA 14 162.887 139.327 120.002 1 19.17 ? C3D 8PE 101 Q 1 
HETATM 27 C C3E 8PE . . . NA 14 163.136 137.896 119.536 1 19.17 ? C3E 8PE 101 Q 1 
HETATM 28 C C3F 8PE . . . NA 14 161.785 137.204 119.464 1 19.17 ? C3F 8PE 101 Q 1 
HETATM 29 C C3G 8PE . . . NA 14 161.952 135.748 119.063 1 19.17 ? C3G 8PE 101 Q 1 
HETATM 30 C C3H 8PE . . . NA 14 160.595 135.089 119.232 1 19.17 ? C3H 8PE 101 Q 1 
HETATM 31 C C3I 8PE . . . NA 14 160.452 133.912 118.28 1 19.17 ? C3I 8PE 101 Q 1 
HETATM 32 O O21 8PE . . . NA 14 166.32 149.324 129.255 1 19.17 ? O21 8PE 101 Q 1 
HETATM 33 O O22 8PE . . . NA 14 167.193 147.457 128.356 1 19.17 ? O22 8PE 101 Q 1 
HETATM 34 C C21 8PE . . . NA 14 167.014 148.624 128.272 1 19.17 ? C21 8PE 101 Q 1 
HETATM 35 C C22 8PE . . . NA 14 167.528 149.398 127.074 1 19.17 ? C22 8PE 101 Q 1 
HETATM 36 C C23 8PE . . . NA 14 166.326 149.803 126.231 1 19.17 ? C23 8PE 101 Q 1 
HETATM 37 C C24 8PE . . . NA 14 166.786 150.205 124.837 1 19.17 ? C24 8PE 101 Q 1 
HETATM 38 C C25 8PE . . . NA 14 166.066 149.352 123.807 1 19.17 ? C25 8PE 101 Q 1 
HETATM 39 C C26 8PE . . . NA 14 166.699 149.621 122.449 1 19.17 ? C26 8PE 101 Q 1 
HETATM 40 C C27 8PE . . . NA 14 167.899 148.716 122.163 1 19.17 ? C27 8PE 101 Q 1 
HETATM 41 C C28 8PE . . . NA 14 167.712 147.995 120.832 1 19.17 ? C28 8PE 101 Q 1 
HETATM 42 C C29 8PE . . . NA 14 167.931 148.996 119.688 1 19.17 ? C29 8PE 101 Q 1 
HETATM 43 C C2A 8PE . . . NA 14 167.778 148.429 118.269 1 19.17 ? C2A 8PE 101 Q 1 
HETATM 44 C C2B 8PE . . . NA 14 166.817 147.24 118.169 1 19.17 ? C2B 8PE 101 Q 1 
HETATM 45 C C2C 8PE . . . NA 14 166.419 146.981 116.719 1 19.17 ? C2C 8PE 101 Q 1 
HETATM 46 C C2D 8PE . . . NA 14 165.122 146.176 116.673 1 19.17 ? C2D 8PE 101 Q 1 
HETATM 47 C C2E 8PE . . . NA 14 164.549 146.234 115.263 1 19.17 ? C2E 8PE 101 Q 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           353 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           47 
#