data_9AYK
#
_model_server_result.job_id            BfmsX7F_EZ7bnKk6spH4mA 
_model_server_result.datetime_utc      '2024-11-27 15:44:24' 
_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          9ayk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":2409}' 
#
_entry.id    9AYK 
#
_exptl.entry_id    9AYK 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              663.906 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate' 
_entity.pdbx_number_of_molecules    4 
_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            9AYK 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9AYK 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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
? 7 H N N 
? 7 J N N 
? 7 K N N 
? 7 L 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 A SG CYS 166 A CYS 123 1_555 A SG CYS 702 A CYS 939 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 A SG CYS 303 A CYS 260 1_555 A SG CYS 345 A CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 A SG CYS 334 A CYS 291 1_555 A SG CYS 390 A CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf4 A SG CYS 1222 A CYS 1459 1_555 A SG CYS 1236 A CYS 1473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 1539 A CYS 1776 1_555 A SG CYS 1545 A CYS 1782 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf6 A SG CYS 1584 A CYS 1821 1_555 A SG CYS 1591 A CYS 1828 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 A OE2 GLU 421 A GLU 378 1_555 E CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc2 A OD2 ASP 1267 A ASP 1504 1_555 E CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? 
#
_chem_comp.formula           'C35 H70 N O8 P' 
_chem_comp.formula_weight    663.906 
_chem_comp.id                JL3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1,2-Dipentadecanoyl-sn-glycero-3-phosphoethanolamine;PE(15:0/15:0) 
#
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
C13 C12 JL3 sing 223 n n 
C13 C14 JL3 sing 224 n n 
C12 C11 JL3 sing 225 n n 
O16 C15 JL3 doub 226 n n 
C10 C11 JL3 sing 227 n n 
C10 C09 JL3 sing 228 n n 
C14 C15 JL3 sing 229 n n 
C15 O17 JL3 sing 230 n n 
C09 C08 JL3 sing 231 n n 
C07 C08 JL3 sing 232 n n 
C07 C06 JL3 sing 233 n n 
O17 C18 JL3 sing 234 n n 
O24 P22 JL3 doub 235 n n 
C18 C19 JL3 sing 236 n n 
C06 C05 JL3 sing 237 n n 
C05 C04 JL3 sing 238 n n 
C20 C19 JL3 sing 239 n n 
C20 O21 JL3 sing 240 n n 
O23 P22 JL3 sing 241 n n 
C19 O29 JL3 sing 242 n n 
P22 O21 JL3 sing 243 n n 
P22 O25 JL3 sing 244 n n 
C04 C03 JL3 sing 245 n n 
C33 C34 JL3 sing 246 n n 
C33 C32 JL3 sing 247 n n 
C36 C37 JL3 sing 248 n n 
C36 C35 JL3 sing 249 n n 
C37 C38 JL3 sing 250 n n 
C35 C34 JL3 sing 251 n n 
C03 C02 JL3 sing 252 n n 
O25 C26 JL3 sing 253 n n 
O29 C30 JL3 sing 254 n n 
C32 C30 JL3 sing 255 n n 
C38 C39 JL3 sing 256 n n 
C30 O31 JL3 doub 257 n n 
C39 C40 JL3 sing 258 n n 
C40 C41 JL3 sing 259 n n 
C42 C41 JL3 sing 260 n n 
C42 C43 JL3 sing 261 n n 
C44 C43 JL3 sing 262 n n 
C44 C45 JL3 sing 263 n n 
C02 C01 JL3 sing 264 n n 
C26 C27 JL3 sing 265 n n 
N28 C27 JL3 sing 266 n n 
C01 H1 JL3 sing 267 n n 
C01 H2 JL3 sing 268 n n 
C01 H3 JL3 sing 269 n n 
C02 H4 JL3 sing 270 n n 
C02 H5 JL3 sing 271 n n 
C03 H6 JL3 sing 272 n n 
C03 H7 JL3 sing 273 n n 
C04 H8 JL3 sing 274 n n 
C04 H9 JL3 sing 275 n n 
C05 H10 JL3 sing 276 n n 
C05 H11 JL3 sing 277 n n 
C06 H12 JL3 sing 278 n n 
C06 H13 JL3 sing 279 n n 
C07 H14 JL3 sing 280 n n 
C07 H15 JL3 sing 281 n n 
C08 H16 JL3 sing 282 n n 
C08 H17 JL3 sing 283 n n 
C09 H18 JL3 sing 284 n n 
C09 H19 JL3 sing 285 n n 
C10 H20 JL3 sing 286 n n 
C10 H21 JL3 sing 287 n n 
C11 H22 JL3 sing 288 n n 
C11 H23 JL3 sing 289 n n 
C12 H24 JL3 sing 290 n n 
C12 H25 JL3 sing 291 n n 
C13 H26 JL3 sing 292 n n 
C13 H27 JL3 sing 293 n n 
C14 H28 JL3 sing 294 n n 
C14 H29 JL3 sing 295 n n 
C18 H30 JL3 sing 296 n n 
C18 H31 JL3 sing 297 n n 
C19 H32 JL3 sing 298 n n 
C20 H33 JL3 sing 299 n n 
C20 H34 JL3 sing 300 n n 
O23 H35 JL3 sing 301 n n 
C26 H36 JL3 sing 302 n n 
C26 H37 JL3 sing 303 n n 
C27 H38 JL3 sing 304 n n 
C27 H39 JL3 sing 305 n n 
N28 H40 JL3 sing 306 n n 
N28 H41 JL3 sing 307 n n 
C32 H43 JL3 sing 308 n n 
C32 H44 JL3 sing 309 n n 
C33 H45 JL3 sing 310 n n 
C33 H46 JL3 sing 311 n n 
C34 H47 JL3 sing 312 n n 
C34 H48 JL3 sing 313 n n 
C35 H49 JL3 sing 314 n n 
C35 H50 JL3 sing 315 n n 
C36 H51 JL3 sing 316 n n 
C36 H52 JL3 sing 317 n n 
C37 H53 JL3 sing 318 n n 
C37 H54 JL3 sing 319 n n 
C38 H55 JL3 sing 320 n n 
C38 H56 JL3 sing 321 n n 
C39 H57 JL3 sing 322 n n 
C39 H58 JL3 sing 323 n n 
C40 H59 JL3 sing 324 n n 
C40 H60 JL3 sing 325 n n 
C41 H61 JL3 sing 326 n n 
C41 H62 JL3 sing 327 n n 
C42 H63 JL3 sing 328 n n 
C42 H64 JL3 sing 329 n n 
C43 H65 JL3 sing 330 n n 
C43 H66 JL3 sing 331 n n 
C44 H67 JL3 sing 332 n n 
C44 H68 JL3 sing 333 n n 
C45 H69 JL3 sing 334 n n 
C45 H70 JL3 sing 335 n n 
C45 H71 JL3 sing 336 n n 
#
_atom_sites.entry_id                     9AYK 
_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
B 2 A1AHJ A 1 2401 1901 A1AHJ LIG . 
C 3 NAG A 1 2402 1 NAG NAG . 
D 3 NAG A 1 2403 2 NAG NAG . 
E 4 CA A 1 2404 3 CA CA . 
F 5 LPE A 1 2405 10 LPE LPE . 
G 6 Y01 A 1 2406 11 Y01 Y01 . 
H 7 JL3 A 1 2407 12 JL3 3PE . 
I 6 Y01 A 1 2408 13 Y01 Y01 . 
J 7 JL3 A 1 2409 14 JL3 3PE . 
K 7 JL3 A 1 2410 15 JL3 3PE . 
L 7 JL3 A 1 2411 16 JL3 3PE . 
M 6 Y01 A 1 2412 17 Y01 Y01 . 
N 6 Y01 A 1 2413 18 Y01 Y01 . 
#
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 P22 JL3 . . . J 7 112.312 124.749 168.216 1 88.62 ? P22 JL3 2409 A 1 
HETATM 2 C C01 JL3 . . . J 7 111.923 131.424 149.755 1 50.76 ? C01 JL3 2409 A 1 
HETATM 3 C C02 JL3 . . . J 7 112.13 130.529 150.969 1 53.61 ? C02 JL3 2409 A 1 
HETATM 4 C C03 JL3 . . . J 7 111.068 129.448 151.112 1 57.68 ? C03 JL3 2409 A 1 
HETATM 5 C C04 JL3 . . . J 7 111.409 128.417 152.177 1 52.59 ? C04 JL3 2409 A 1 
HETATM 6 C C05 JL3 . . . J 7 111.324 128.951 153.599 1 50.3 ? C05 JL3 2409 A 1 
HETATM 7 C C06 JL3 . . . J 7 112.459 128.451 154.479 1 53.76 ? C06 JL3 2409 A 1 
HETATM 8 C C07 JL3 . . . J 7 112.124 128.429 155.964 1 59.2 ? C07 JL3 2409 A 1 
HETATM 9 C C08 JL3 . . . J 7 111.205 127.274 156.339 1 52.41 ? C08 JL3 2409 A 1 
HETATM 10 C C09 JL3 . . . J 7 110.76 127.289 157.794 1 51.68 ? C09 JL3 2409 A 1 
HETATM 11 C C10 JL3 . . . J 7 111.888 126.951 158.759 1 52.33 ? C10 JL3 2409 A 1 
HETATM 12 C C11 JL3 . . . J 7 111.495 127.042 160.227 1 53.99 ? C11 JL3 2409 A 1 
HETATM 13 C C12 JL3 . . . J 7 110.227 126.265 160.553 1 56.6 ? C12 JL3 2409 A 1 
HETATM 14 C C13 JL3 . . . J 7 110.15 125.802 162.003 1 55.93 ? C13 JL3 2409 A 1 
HETATM 15 C C14 JL3 . . . J 7 110.058 126.974 162.968 1 61.27 ? C14 JL3 2409 A 1 
HETATM 16 C C15 JL3 . . . J 7 110.202 126.581 164.412 1 64.66 ? C15 JL3 2409 A 1 
HETATM 17 O O16 JL3 . . . J 7 110.746 127.235 165.265 1 59.81 ? O16 JL3 2409 A 1 
HETATM 18 O O17 JL3 . . . J 7 109.634 125.396 164.634 1 66.83 ? O17 JL3 2409 A 1 
HETATM 19 C C18 JL3 . . . J 7 109.466 124.945 165.976 1 60.89 ? C18 JL3 2409 A 1 
HETATM 20 C C19 JL3 . . . J 7 109.694 123.447 165.981 1 65.09 ? C19 JL3 2409 A 1 
HETATM 21 C C20 JL3 . . . J 7 110.65 123.019 167.089 1 61.9 ? C20 JL3 2409 A 1 
HETATM 22 O O21 JL3 . . . J 7 111.848 123.757 166.988 1 70.99 ? O21 JL3 2409 A 1 
HETATM 23 O O23 JL3 . . . J 7 112.712 126.025 167.557 1 56.3 ? O23 JL3 2409 A 1 
HETATM 24 O O24 JL3 . . . J 7 111.343 124.673 169.347 1 64.63 ? O24 JL3 2409 A 1 
HETATM 25 O O25 JL3 . . . J 7 113.66 123.972 168.775 1 69.56 ? O25 JL3 2409 A 1 
HETATM 26 C C26 JL3 . . . J 7 114.71 124.722 169.339 1 60.42 ? C26 JL3 2409 A 1 
HETATM 27 C C27 JL3 . . . J 7 115.452 123.84 170.318 1 62.84 ? C27 JL3 2409 A 1 
HETATM 28 N N28 JL3 . . . J 7 115.549 124.478 171.656 1 61.85 ? N28 JL3 2409 A 1 
HETATM 29 O O29 JL3 . . . J 7 110.202 123.133 164.677 1 66.88 ? O29 JL3 2409 A 1 
HETATM 30 C C30 JL3 . . . J 7 109.89 121.996 164.088 1 66.69 ? C30 JL3 2409 A 1 
HETATM 31 O O31 JL3 . . . J 7 110.533 120.977 164.231 1 62.11 ? O31 JL3 2409 A 1 
HETATM 32 C C32 JL3 . . . J 7 108.663 122.13 163.231 1 64.36 ? C32 JL3 2409 A 1 
HETATM 33 C C33 JL3 . . . J 7 108.915 121.967 161.741 1 59.07 ? C33 JL3 2409 A 1 
HETATM 34 C C34 JL3 . . . J 7 107.657 122.238 160.926 1 57.82 ? C34 JL3 2409 A 1 
HETATM 35 C C35 JL3 . . . J 7 107.94 122.47 159.447 1 58.59 ? C35 JL3 2409 A 1 
HETATM 36 C C36 JL3 . . . J 7 107.193 123.667 158.873 1 58.33 ? C36 JL3 2409 A 1 
HETATM 37 C C37 JL3 . . . J 7 107.826 124.235 157.609 1 58.13 ? C37 JL3 2409 A 1 
HETATM 38 C C38 JL3 . . . J 7 108.072 123.192 156.525 1 60.16 ? C38 JL3 2409 A 1 
HETATM 39 C C39 JL3 . . . J 7 106.808 122.476 156.067 1 63.24 ? C39 JL3 2409 A 1 
HETATM 40 C C40 JL3 . . . J 7 107.039 121.539 154.886 1 66.24 ? C40 JL3 2409 A 1 
HETATM 41 C C41 JL3 . . . J 7 107.385 122.261 153.59 1 61.09 ? C41 JL3 2409 A 1 
HETATM 42 C C42 JL3 . . . J 7 107.541 121.321 152.401 1 56.49 ? C42 JL3 2409 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           42 
#