data_9AYH # _model_server_result.job_id '_Mbpr3r0NbK_72MvtX-CrQ' _model_server_result.datetime_utc '2024-11-14 17:02:49' _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 9ayh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":2407}' # _entry.id 9AYH # _exptl.entry_id 9AYH _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 9AYH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9AYH _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 1584 A CYS 1821 1_555 A SG CYS 1591 A CYS 1828 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A OE2 GLU 421 A GLU 378 1_555 E CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc2 A OE1 GLU 737 A GLU 974 1_555 E CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? metalc ? metalc3 A OD1 ASP 1267 A ASP 1504 1_555 E CA CA . A CA 2404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? # _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 221 n n C13 C14 JL3 sing 222 n n C12 C11 JL3 sing 223 n n O16 C15 JL3 doub 224 n n C10 C11 JL3 sing 225 n n C10 C09 JL3 sing 226 n n C14 C15 JL3 sing 227 n n C15 O17 JL3 sing 228 n n C09 C08 JL3 sing 229 n n C07 C08 JL3 sing 230 n n C07 C06 JL3 sing 231 n n O17 C18 JL3 sing 232 n n O24 P22 JL3 doub 233 n n C18 C19 JL3 sing 234 n n C06 C05 JL3 sing 235 n n C05 C04 JL3 sing 236 n n C20 C19 JL3 sing 237 n n C20 O21 JL3 sing 238 n n O23 P22 JL3 sing 239 n n C19 O29 JL3 sing 240 n n P22 O21 JL3 sing 241 n n P22 O25 JL3 sing 242 n n C04 C03 JL3 sing 243 n n C33 C34 JL3 sing 244 n n C33 C32 JL3 sing 245 n n C36 C37 JL3 sing 246 n n C36 C35 JL3 sing 247 n n C37 C38 JL3 sing 248 n n C35 C34 JL3 sing 249 n n C03 C02 JL3 sing 250 n n O25 C26 JL3 sing 251 n n O29 C30 JL3 sing 252 n n C32 C30 JL3 sing 253 n n C38 C39 JL3 sing 254 n n C30 O31 JL3 doub 255 n n C39 C40 JL3 sing 256 n n C40 C41 JL3 sing 257 n n C42 C41 JL3 sing 258 n n C42 C43 JL3 sing 259 n n C44 C43 JL3 sing 260 n n C44 C45 JL3 sing 261 n n C02 C01 JL3 sing 262 n n C26 C27 JL3 sing 263 n n N28 C27 JL3 sing 264 n n C01 H1 JL3 sing 265 n n C01 H2 JL3 sing 266 n n C01 H3 JL3 sing 267 n n C02 H4 JL3 sing 268 n n C02 H5 JL3 sing 269 n n C03 H6 JL3 sing 270 n n C03 H7 JL3 sing 271 n n C04 H8 JL3 sing 272 n n C04 H9 JL3 sing 273 n n C05 H10 JL3 sing 274 n n C05 H11 JL3 sing 275 n n C06 H12 JL3 sing 276 n n C06 H13 JL3 sing 277 n n C07 H14 JL3 sing 278 n n C07 H15 JL3 sing 279 n n C08 H16 JL3 sing 280 n n C08 H17 JL3 sing 281 n n C09 H18 JL3 sing 282 n n C09 H19 JL3 sing 283 n n C10 H20 JL3 sing 284 n n C10 H21 JL3 sing 285 n n C11 H22 JL3 sing 286 n n C11 H23 JL3 sing 287 n n C12 H24 JL3 sing 288 n n C12 H25 JL3 sing 289 n n C13 H26 JL3 sing 290 n n C13 H27 JL3 sing 291 n n C14 H28 JL3 sing 292 n n C14 H29 JL3 sing 293 n n C18 H30 JL3 sing 294 n n C18 H31 JL3 sing 295 n n C19 H32 JL3 sing 296 n n C20 H33 JL3 sing 297 n n C20 H34 JL3 sing 298 n n O23 H35 JL3 sing 299 n n C26 H36 JL3 sing 300 n n C26 H37 JL3 sing 301 n n C27 H38 JL3 sing 302 n n C27 H39 JL3 sing 303 n n N28 H40 JL3 sing 304 n n N28 H41 JL3 sing 305 n n C32 H43 JL3 sing 306 n n C32 H44 JL3 sing 307 n n C33 H45 JL3 sing 308 n n C33 H46 JL3 sing 309 n n C34 H47 JL3 sing 310 n n C34 H48 JL3 sing 311 n n C35 H49 JL3 sing 312 n n C35 H50 JL3 sing 313 n n C36 H51 JL3 sing 314 n n C36 H52 JL3 sing 315 n n C37 H53 JL3 sing 316 n n C37 H54 JL3 sing 317 n n C38 H55 JL3 sing 318 n n C38 H56 JL3 sing 319 n n C39 H57 JL3 sing 320 n n C39 H58 JL3 sing 321 n n C40 H59 JL3 sing 322 n n C40 H60 JL3 sing 323 n n C41 H61 JL3 sing 324 n n C41 H62 JL3 sing 325 n n C42 H63 JL3 sing 326 n n C42 H64 JL3 sing 327 n n C43 H65 JL3 sing 328 n n C43 H66 JL3 sing 329 n n C44 H67 JL3 sing 330 n n C44 H68 JL3 sing 331 n n C45 H69 JL3 sing 332 n n C45 H70 JL3 sing 333 n n C45 H71 JL3 sing 334 n n # _atom_sites.entry_id 9AYH _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 A1AHH A 1 2401 1901 A1AHH 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 . . . H 7 112.529 117.258 162.332 1 89.7 ? P22 JL3 2407 A 1 HETATM 2 C C01 JL3 . . . H 7 116.164 116.072 144.348 1 62.16 ? C01 JL3 2407 A 1 HETATM 3 C C02 JL3 . . . H 7 116.725 116.952 145.437 1 61.98 ? C02 JL3 2407 A 1 HETATM 4 C C03 JL3 . . . H 7 117.147 118.325 144.969 1 65.93 ? C03 JL3 2407 A 1 HETATM 5 C C04 JL3 . . . H 7 117.308 119.35 146.07 1 63.42 ? C04 JL3 2407 A 1 HETATM 6 C C05 JL3 . . . H 7 117.875 118.807 147.356 1 61.13 ? C05 JL3 2407 A 1 HETATM 7 C C06 JL3 . . . H 7 118.371 119.863 148.311 1 54.71 ? C06 JL3 2407 A 1 HETATM 8 C C07 JL3 . . . H 7 118.33 119.455 149.763 1 52.75 ? C07 JL3 2407 A 1 HETATM 9 C C08 JL3 . . . H 7 116.944 119.205 150.298 1 54.67 ? C08 JL3 2407 A 1 HETATM 10 C C09 JL3 . . . H 7 116.809 119.406 151.787 1 57.75 ? C09 JL3 2407 A 1 HETATM 11 C C10 JL3 . . . H 7 115.518 120.05 152.215 1 57.26 ? C10 JL3 2407 A 1 HETATM 12 C C11 JL3 . . . H 7 114.676 119.204 153.135 1 57.93 ? C11 JL3 2407 A 1 HETATM 13 C C12 JL3 . . . H 7 114.918 119.459 154.597 1 57.49 ? C12 JL3 2407 A 1 HETATM 14 C C13 JL3 . . . H 7 114.442 118.346 155.513 1 59.8 ? C13 JL3 2407 A 1 HETATM 15 C C14 JL3 . . . H 7 115.503 117.324 155.771 1 61.68 ? C14 JL3 2407 A 1 HETATM 16 C C15 JL3 . . . H 7 115.006 116.112 156.506 1 65.82 ? C15 JL3 2407 A 1 HETATM 17 O O16 JL3 . . . H 7 114.84 115.024 156.022 1 63.41 ? O16 JL3 2407 A 1 HETATM 18 O O17 JL3 . . . H 7 114.771 116.382 157.785 1 66.56 ? O17 JL3 2407 A 1 HETATM 19 C C18 JL3 . . . H 7 113.385 116.518 158.162 1 63.92 ? C18 JL3 2407 A 1 HETATM 20 C C19 JL3 . . . H 7 113.079 115.51 159.247 1 60.94 ? C19 JL3 2407 A 1 HETATM 21 C C20 JL3 . . . H 7 113.8 115.777 160.546 1 59.22 ? C20 JL3 2407 A 1 HETATM 22 O O21 JL3 . . . H 7 113.467 117.103 161.039 1 68.54 ? O21 JL3 2407 A 1 HETATM 23 O O23 JL3 . . . H 7 112.624 118.689 162.785 1 67.98 ? O23 JL3 2407 A 1 HETATM 24 O O24 JL3 . . . H 7 111.19 116.665 161.992 1 71.1 ? O24 JL3 2407 A 1 HETATM 25 O O25 JL3 . . . H 7 113.252 116.335 163.43 1 68.22 ? O25 JL3 2407 A 1 HETATM 26 C C26 JL3 . . . H 7 112.618 115.093 163.848 1 66.7 ? C26 JL3 2407 A 1 HETATM 27 C C27 JL3 . . . H 7 113.436 114.439 164.929 1 68.64 ? C27 JL3 2407 A 1 HETATM 28 N N28 JL3 . . . H 7 112.692 113.391 165.631 1 65.23 ? N28 JL3 2407 A 1 HETATM 29 O O29 JL3 . . . H 7 113.464 114.182 158.801 1 70.6 ? O29 JL3 2407 A 1 HETATM 30 C C30 JL3 . . . H 7 112.608 113.175 159.026 1 72.09 ? C30 JL3 2407 A 1 HETATM 31 O O31 JL3 . . . H 7 112.504 112.665 160.11 1 67.16 ? O31 JL3 2407 A 1 HETATM 32 C C32 JL3 . . . H 7 111.815 112.76 157.816 1 67.62 ? C32 JL3 2407 A 1 HETATM 33 C C33 JL3 . . . H 7 111.548 113.876 156.847 1 63.89 ? C33 JL3 2407 A 1 HETATM 34 C C34 JL3 . . . H 7 111.049 113.382 155.506 1 62.56 ? C34 JL3 2407 A 1 HETATM 35 C C35 JL3 . . . H 7 112.078 112.616 154.723 1 63.76 ? C35 JL3 2407 A 1 HETATM 36 C C36 JL3 . . . H 7 112.553 113.302 153.479 1 62.57 ? C36 JL3 2407 A 1 HETATM 37 C C37 JL3 . . . H 7 111.676 113.072 152.282 1 65.61 ? C37 JL3 2407 A 1 HETATM 38 C C38 JL3 . . . H 7 111.52 114.279 151.404 1 64.28 ? C38 JL3 2407 A 1 HETATM 39 C C39 JL3 . . . H 7 112.781 114.677 150.685 1 63.63 ? C39 JL3 2407 A 1 HETATM 40 C C40 JL3 . . . H 7 113.504 115.845 151.302 1 64.55 ? C40 JL3 2407 A 1 HETATM 41 C C41 JL3 . . . H 7 112.809 117.166 151.109 1 64.42 ? C41 JL3 2407 A 1 HETATM 42 C C42 JL3 . . . H 7 113.545 118.122 150.21 1 67.51 ? C42 JL3 2407 A 1 HETATM 43 C C43 JL3 . . . H 7 113.151 118.032 148.763 1 64.43 ? C43 JL3 2407 A 1 HETATM 44 C C44 JL3 . . . H 7 114.188 118.56 147.809 1 62.77 ? C44 JL3 2407 A 1 HETATM 45 C C45 JL3 . . . H 7 113.736 118.603 146.371 1 61.06 ? C45 JL3 2407 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 45 #