data_3SPC # _model_server_result.job_id zYPSuP0r3tRBMEPF62pBlQ _model_server_result.datetime_utc '2024-11-24 00:48:34' _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 3spc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":379}' # _entry.id 3SPC # _exptl.entry_id 3SPC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 504.446 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-3-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}propane-1,2-diyl dioctanoate' _entity.pdbx_number_of_molecules 1 _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 3SPC _cell.length_a 82.904 _cell.length_b 82.904 _cell.length_c 191.159 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SPC _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _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,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 88 A CYS 123 1_555 A SG CYS 120 A CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc1 A O THR 108 A THR 143 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc2 A OG1 THR 108 A THR 143 1_555 E K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc3 A O THR 108 A THR 143 1_555 E K K . A K 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc4 A O ILE 109 A ILE 144 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? metalc ? metalc5 A O ILE 109 A ILE 144 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc6 A O GLY 110 A GLY 145 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc7 A O GLY 110 A GLY 145 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc8 A O TYR 111 A TYR 146 1_555 B K K . A K 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc9 I O HOH . A HOH 404 1_555 G K K . A K 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.069 ? # _chem_comp.formula 'C19 H38 O11 P2' _chem_comp.formula_weight 504.446 _chem_comp.id P8P _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-3-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}propane-1,2-diyl dioctanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'dioctanoylglycerol pyrophosphate' # 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 O1 P2 P8P sing 237 n n P1 O1 P8P sing 238 n n P1 O11 P8P sing 239 n n P2 O22 P8P sing 240 n n P2 O23 P8P sing 241 n n O11 HO11 P8P sing 242 n n O12 P1 P8P doub 243 n n O13 P1 P8P sing 244 n n C1A O2C P8P sing 245 n n C1A O1A P8P doub 246 n n C1B O1B P8P doub 247 n n C1B O3C P8P sing 248 n n C1C O13 P8P sing 249 n n C1C H1C P8P sing 250 n n C1C H1CA P8P sing 251 n n O21 P2 P8P doub 252 n n O22 HO22 P8P sing 253 n n O23 HO23 P8P sing 254 n n C2A C1A P8P sing 255 n n C2A H2A P8P sing 256 n n C2A H2AA P8P sing 257 n n C2B C1B P8P sing 258 n n C2B C3B P8P sing 259 n n C2B H2B P8P sing 260 n n C2B H2BA P8P sing 261 n n C2C C1C P8P sing 262 n n C2C O2C P8P sing 263 n n C2C H2C P8P sing 264 n n C3A C2A P8P sing 265 n n C3A H3A P8P sing 266 n n C3A H3AA P8P sing 267 n n C3B H3B P8P sing 268 n n C3B H3BA P8P sing 269 n n C3C C2C P8P sing 270 n n C3C H3C P8P sing 271 n n C3C H3CA P8P sing 272 n n O3C C3C P8P sing 273 n n C4A C3A P8P sing 274 n n C4A H4A P8P sing 275 n n C4A H4AA P8P sing 276 n n C4B C3B P8P sing 277 n n C4B H4B P8P sing 278 n n C4B H4BA P8P sing 279 n n C4B C16 P8P sing 280 n n C5A C4A P8P sing 281 n n C5A H5A P8P sing 282 n n C5A H5AA P8P sing 283 n n C6A C5A P8P sing 284 n n C6A H6A P8P sing 285 n n C6A H6AA P8P sing 286 n n C7A C6A P8P sing 287 n n C7A C8A P8P sing 288 n n C7A H7A P8P sing 289 n n C7A H7AA P8P sing 290 n n C8A H8A P8P sing 291 n n C8A H8AA P8P sing 292 n n C8A H8AB P8P sing 293 n n C16 C17 P8P sing 294 n n C17 C18 P8P sing 295 n n C18 C19 P8P sing 296 n n C16 H30 P8P sing 297 n n C16 H31 P8P sing 298 n n C17 H32 P8P sing 299 n n C17 H33 P8P sing 300 n n C18 H34 P8P sing 301 n n C18 H35 P8P sing 302 n n C19 H36 P8P sing 303 n n C19 H37 P8P sing 304 n n C19 H38 P8P sing 305 n n # _atom_sites.entry_id 3SPC _atom_sites.fract_transf_matrix[1][1] 0.012062 _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] 0.012062 _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] 0.005231 _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 K A 1 501 501 K K . C 2 K A 1 502 502 K K . D 2 K A 1 503 503 K K . E 2 K A 1 504 504 K K . F 2 K A 1 508 508 K K . G 2 K A 1 510 510 K K . H 3 P8P A 1 379 4 P8P P8P . I 4 HOH A 1 1 1 HOH HOH . I 4 HOH A 2 2 2 HOH HOH . I 4 HOH A 3 3 3 HOH HOH . I 4 HOH A 4 4 4 HOH HOH . I 4 HOH A 5 5 5 HOH HOH . I 4 HOH A 6 6 6 HOH HOH . I 4 HOH A 7 7 7 HOH HOH . I 4 HOH A 8 8 8 HOH HOH . I 4 HOH A 9 9 9 HOH HOH . I 4 HOH A 10 10 10 HOH HOH . I 4 HOH A 11 11 11 HOH HOH . I 4 HOH A 12 12 12 HOH HOH . I 4 HOH A 13 13 13 HOH HOH . I 4 HOH A 14 14 14 HOH HOH . I 4 HOH A 15 15 15 HOH HOH . I 4 HOH A 16 16 16 HOH HOH . I 4 HOH A 17 17 17 HOH HOH . I 4 HOH A 18 18 18 HOH HOH . I 4 HOH A 19 19 19 HOH HOH . I 4 HOH A 20 20 20 HOH HOH . I 4 HOH A 21 21 21 HOH HOH . I 4 HOH A 22 22 22 HOH HOH . I 4 HOH A 23 23 23 HOH HOH . I 4 HOH A 24 24 24 HOH HOH . I 4 HOH A 25 25 25 HOH HOH . I 4 HOH A 26 26 26 HOH HOH . I 4 HOH A 27 27 27 HOH HOH . I 4 HOH A 28 28 28 HOH HOH . I 4 HOH A 29 29 29 HOH HOH . I 4 HOH A 30 30 30 HOH HOH . I 4 HOH A 31 31 31 HOH HOH . I 4 HOH A 32 32 32 HOH HOH . I 4 HOH A 33 33 33 HOH HOH . I 4 HOH A 34 34 34 HOH HOH . I 4 HOH A 35 35 35 HOH HOH . I 4 HOH A 36 380 36 HOH HOH . I 4 HOH A 37 381 37 HOH HOH . I 4 HOH A 38 382 38 HOH HOH . I 4 HOH A 39 383 39 HOH HOH . I 4 HOH A 40 384 40 HOH HOH . I 4 HOH A 41 385 41 HOH HOH . I 4 HOH A 42 386 42 HOH HOH . I 4 HOH A 43 387 43 HOH HOH . I 4 HOH A 44 388 44 HOH HOH . I 4 HOH A 45 389 45 HOH HOH . I 4 HOH A 46 390 46 HOH HOH . I 4 HOH A 47 391 47 HOH HOH . I 4 HOH A 48 392 48 HOH HOH . I 4 HOH A 49 393 49 HOH HOH . I 4 HOH A 50 394 50 HOH HOH . I 4 HOH A 51 395 51 HOH HOH . I 4 HOH A 52 396 52 HOH HOH . I 4 HOH A 53 397 53 HOH HOH . I 4 HOH A 54 398 54 HOH HOH . I 4 HOH A 55 399 55 HOH HOH . I 4 HOH A 56 400 57 HOH HOH . I 4 HOH A 57 401 58 HOH HOH . I 4 HOH A 58 402 59 HOH HOH . I 4 HOH A 59 403 60 HOH HOH . I 4 HOH A 60 404 61 HOH HOH . I 4 HOH A 61 405 62 HOH HOH . I 4 HOH A 62 406 63 HOH HOH . I 4 HOH A 63 407 64 HOH HOH . I 4 HOH A 64 408 65 HOH HOH . I 4 HOH A 65 409 66 HOH HOH . I 4 HOH A 66 410 67 HOH HOH . I 4 HOH A 67 411 68 HOH HOH . I 4 HOH A 68 412 69 HOH HOH . I 4 HOH A 69 413 70 HOH HOH . I 4 HOH A 70 414 71 HOH HOH . I 4 HOH A 71 415 72 HOH HOH . I 4 HOH A 72 416 73 HOH HOH . I 4 HOH A 73 417 74 HOH HOH . I 4 HOH A 74 418 75 HOH HOH . I 4 HOH A 75 419 76 HOH HOH . I 4 HOH A 76 420 77 HOH HOH . I 4 HOH A 77 421 78 HOH HOH . I 4 HOH A 78 422 79 HOH HOH . I 4 HOH A 79 423 80 HOH HOH . I 4 HOH A 80 424 81 HOH HOH . I 4 HOH A 81 425 82 HOH HOH . I 4 HOH A 82 426 83 HOH HOH . I 4 HOH A 83 427 84 HOH HOH . I 4 HOH A 84 428 85 HOH HOH . I 4 HOH A 85 429 86 HOH HOH . I 4 HOH A 86 430 87 HOH HOH . I 4 HOH A 87 431 88 HOH HOH . I 4 HOH A 88 432 89 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 O1 P8P . . . H 3 18.491 8.897 62.701 1 146 ? O1 P8P 379 A 1 HETATM 2 P P1 P8P . . . H 3 19.309 9.077 61.321 1 125.45 ? P1 P8P 379 A 1 HETATM 3 P P2 P8P . . . H 3 18.905 7.801 63.809 1 150.17 ? P2 P8P 379 A 1 HETATM 4 O O11 P8P . . . H 3 20.384 10.121 61.522 1 125.53 ? O11 P8P 379 A 1 HETATM 5 O O12 P8P . . . H 3 19.684 7.706 60.806 1 124.69 ? O12 P8P 379 A 1 HETATM 6 O O13 P8P . . . H 3 18.156 9.701 60.38 1 144.79 ? O13 P8P 379 A 1 HETATM 7 C C1A P8P . . . H 3 14.691 10.299 58.777 1 133.7 ? C1A P8P 379 A 1 HETATM 8 O O1A P8P . . . H 3 14.105 11.035 59.554 1 133.01 ? O1A P8P 379 A 1 HETATM 9 C C1B P8P . . . H 3 18.998 9.088 55.37 1 149.99 ? C1B P8P 379 A 1 HETATM 10 O O1B P8P . . . H 3 18.817 7.887 55.493 1 151.51 ? O1B P8P 379 A 1 HETATM 11 C C1C P8P . . . H 3 18.409 10.205 59.069 1 143.64 ? C1C P8P 379 A 1 HETATM 12 O O21 P8P . . . H 3 17.86 7.962 64.89 1 148.14 ? O21 P8P 379 A 1 HETATM 13 O O22 P8P . . . H 3 20.302 8.205 64.219 1 151.94 ? O22 P8P 379 A 1 HETATM 14 O O23 P8P . . . H 3 18.84 6.487 63.069 1 150.64 ? O23 P8P 379 A 1 HETATM 15 C C2A P8P . . . H 3 14.01 9.862 57.5 1 130.34 ? C2A P8P 379 A 1 HETATM 16 C C2B P8P . . . H 3 19.935 9.616 54.308 1 149.24 ? C2B P8P 379 A 1 HETATM 17 C C2C P8P . . . H 3 17.086 10.333 58.316 1 142.35 ? C2C P8P 379 A 1 HETATM 18 O O2C P8P . . . H 3 16.026 9.831 59.136 1 138.16 ? O2C P8P 379 A 1 HETATM 19 C C3A P8P . . . H 3 12.602 10.447 57.452 1 126.91 ? C3A P8P 379 A 1 HETATM 20 C C3B P8P . . . H 3 21.359 9.647 54.852 1 148.75 ? C3B P8P 379 A 1 HETATM 21 C C3C P8P . . . H 3 17.201 9.519 57.035 1 145.31 ? C3C P8P 379 A 1 HETATM 22 O O3C P8P . . . H 3 18.308 9.998 56.272 1 147.96 ? O3C P8P 379 A 1 HETATM 23 C C4A P8P . . . H 3 11.928 10.148 56.118 1 124.11 ? C4A P8P 379 A 1 HETATM 24 C C4B P8P . . . H 3 22.354 9.981 53.747 1 148.28 ? C4B P8P 379 A 1 HETATM 25 C C5A P8P . . . H 3 10.619 10.917 55.977 1 122.73 ? C5A P8P 379 A 1 HETATM 26 C C6A P8P . . . H 3 10.052 10.761 54.571 1 121.98 ? C6A P8P 379 A 1 HETATM 27 C C7A P8P . . . H 3 8.726 11.499 54.41 1 121.13 ? C7A P8P 379 A 1 HETATM 28 C C8A P8P . . . H 3 8.902 12.996 54.547 1 120.58 ? C8A P8P 379 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #