data_3ABW # _model_server_result.job_id SGfCOOc1r7QF1kwpYBd-aw _model_server_result.datetime_utc '2024-11-02 19:40:05' _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 3abw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":318}' # _entry.id 3ABW # _exptl.entry_id 3ABW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 885.179 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE" _entity.pdbx_number_of_molecules 9 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 127.85 _cell.angle_gamma 90 _cell.entry_id 3ABW _cell.length_a 152.09 _cell.length_b 98.79 _cell.length_c 100.14 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ABW _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W _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 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 ? 4 F N N ? 4 G N N ? 4 H N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 Q N N ? 4 R N N ? 4 S 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 covale ? covale1 A NZ LYS 256 A LYS 256 1_555 D C15 RET . A RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale2 B NZ LYS 256 B LYS 256 1_555 J C15 RET . B RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale3 C NZ LYS 256 D LYS 256 1_555 P C15 RET . D RET 292 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? # _chem_comp.formula 'C46 H94 O11 P2 -2' _chem_comp.formula_weight 885.179 _chem_comp.id L3P _chem_comp.mon_nstd_flag . _chem_comp.name "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE" _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 C1 C2 L3P sing 304 n n C1 O1 L3P sing 305 n n C1 H12 L3P sing 306 n n C1 H11 L3P sing 307 n n C2 C3 L3P sing 308 n n C2 O2 L3P sing 309 n n C2 H2 L3P sing 310 n n C3 O3 L3P sing 311 n n C3 H32 L3P sing 312 n n C3 H31 L3P sing 313 n n C4 C5 L3P sing 314 n n C4 O4 L3P sing 315 n n C4 H42 L3P sing 316 n n C4 H41 L3P sing 317 n n C5 C6 L3P sing 318 n n C5 O5 L3P sing 319 n n C5 H5 L3P sing 320 n n C6 O6 L3P sing 321 n n C6 H62 L3P sing 322 n n C6 H61 L3P sing 323 n n O1 C11 L3P sing 324 n n O2 C41 L3P sing 325 n n O3 P1 L3P sing 326 n n O4 P1 L3P sing 327 n n O5 H5O L3P sing 328 n n O6 P2 L3P sing 329 n n O1P P1 L3P doub 330 n n O2P P1 L3P sing 331 n n O4P P2 L3P doub 332 n n O5P P2 L3P sing 333 n n O6P P2 L3P sing 334 n n O6P HOP6 L3P sing 335 n n C11 C12 L3P sing 336 n n C11 H112 L3P sing 337 n n C11 H111 L3P sing 338 n n C12 C13 L3P sing 339 n n C12 H122 L3P sing 340 n n C12 H121 L3P sing 341 n n C13 C14 L3P sing 342 n n C13 C15 L3P sing 343 n n C13 H13 L3P sing 344 n n C14 H143 L3P sing 345 n n C14 H142 L3P sing 346 n n C14 H141 L3P sing 347 n n C15 C16 L3P sing 348 n n C15 H152 L3P sing 349 n n C15 H151 L3P sing 350 n n C16 C17 L3P sing 351 n n C16 H162 L3P sing 352 n n C16 H161 L3P sing 353 n n C17 C18 L3P sing 354 n n C17 H172 L3P sing 355 n n C17 H171 L3P sing 356 n n C18 C19 L3P sing 357 n n C18 C20 L3P sing 358 n n C18 H18 L3P sing 359 n n C19 H193 L3P sing 360 n n C19 H192 L3P sing 361 n n C19 H191 L3P sing 362 n n C20 C21 L3P sing 363 n n C20 H202 L3P sing 364 n n C20 H201 L3P sing 365 n n C21 C22 L3P sing 366 n n C21 H212 L3P sing 367 n n C21 H211 L3P sing 368 n n C22 C23 L3P sing 369 n n C22 H222 L3P sing 370 n n C22 H221 L3P sing 371 n n C23 C24 L3P sing 372 n n C23 C25 L3P sing 373 n n C23 H23 L3P sing 374 n n C24 H243 L3P sing 375 n n C24 H242 L3P sing 376 n n C24 H241 L3P sing 377 n n C25 C26 L3P sing 378 n n C25 H252 L3P sing 379 n n C25 H251 L3P sing 380 n n C26 C27 L3P sing 381 n n C26 H262 L3P sing 382 n n C26 H261 L3P sing 383 n n C27 C28 L3P sing 384 n n C27 H272 L3P sing 385 n n C27 H271 L3P sing 386 n n C28 C29 L3P sing 387 n n C28 C30 L3P sing 388 n n C28 H28 L3P sing 389 n n C29 H293 L3P sing 390 n n C29 H292 L3P sing 391 n n C29 H291 L3P sing 392 n n C30 H303 L3P sing 393 n n C30 H302 L3P sing 394 n n C30 H301 L3P sing 395 n n C41 C42 L3P sing 396 n n C41 H412 L3P sing 397 n n C41 H411 L3P sing 398 n n C42 C43 L3P sing 399 n n C42 H422 L3P sing 400 n n C42 H421 L3P sing 401 n n C43 C44 L3P sing 402 n n C43 C45 L3P sing 403 n n C43 H43 L3P sing 404 n n C44 H443 L3P sing 405 n n C44 H442 L3P sing 406 n n C44 H441 L3P sing 407 n n C45 C46 L3P sing 408 n n C45 H452 L3P sing 409 n n C45 H451 L3P sing 410 n n C46 C47 L3P sing 411 n n C46 H462 L3P sing 412 n n C46 H461 L3P sing 413 n n C47 C48 L3P sing 414 n n C47 H472 L3P sing 415 n n C47 H471 L3P sing 416 n n C48 C49 L3P sing 417 n n C48 C50 L3P sing 418 n n C48 H48 L3P sing 419 n n C49 H493 L3P sing 420 n n C49 H492 L3P sing 421 n n C49 H491 L3P sing 422 n n C50 C51 L3P sing 423 n n C50 H502 L3P sing 424 n n C50 H501 L3P sing 425 n n C51 C52 L3P sing 426 n n C51 H512 L3P sing 427 n n C51 H511 L3P sing 428 n n C52 C53 L3P sing 429 n n C52 H522 L3P sing 430 n n C52 H521 L3P sing 431 n n C53 C54 L3P sing 432 n n C53 C55 L3P sing 433 n n C53 H53 L3P sing 434 n n C54 H543 L3P sing 435 n n C54 H542 L3P sing 436 n n C54 H541 L3P sing 437 n n C55 C56 L3P sing 438 n n C55 H552 L3P sing 439 n n C55 H551 L3P sing 440 n n C56 C57 L3P sing 441 n n C56 H562 L3P sing 442 n n C56 H561 L3P sing 443 n n C57 C58 L3P sing 444 n n C57 H572 L3P sing 445 n n C57 H571 L3P sing 446 n n C58 C59 L3P sing 447 n n C58 C60 L3P sing 448 n n C58 H58 L3P sing 449 n n C59 H593 L3P sing 450 n n C59 H592 L3P sing 451 n n C59 H591 L3P sing 452 n n C60 H603 L3P sing 453 n n C60 H602 L3P sing 454 n n C60 H601 L3P sing 455 n n # _atom_sites.entry_id 3ABW _atom_sites.fract_transf_matrix[1][1] 0.006575 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005109 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010122 _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] 0.012647 _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 D 2 RET A 1 292 290 RET RET . E 3 22B A 1 300 300 22B 22B . F 4 L3P A 1 310 310 L3P L3P . G 4 L3P A 1 313 313 L3P L3P . H 4 L3P A 1 317 317 L3P L3P . I 5 AZI A 1 401 401 AZI AZI . J 2 RET B 1 292 290 RET RET . K 4 L3P B 1 311 311 L3P L3P . L 4 L3P B 1 315 315 L3P L3P . M 4 L3P B 1 318 318 L3P L3P . N 3 22B B 1 300 300 22B 22B . O 5 AZI B 1 401 401 AZI AZI . P 2 RET D 1 292 290 RET RET . Q 4 L3P D 1 312 312 L3P L3P . R 4 L3P D 1 314 314 L3P L3P . S 4 L3P D 1 316 316 L3P L3P . T 5 AZI D 1 401 401 AZI AZI . U 6 HOH A 1 501 501 HOH HOH . U 6 HOH A 2 502 502 HOH HOH . U 6 HOH A 3 503 503 HOH HOH . U 6 HOH A 4 504 504 HOH HOH . U 6 HOH A 5 505 505 HOH HOH . U 6 HOH A 6 506 506 HOH HOH . U 6 HOH A 7 507 507 HOH HOH . U 6 HOH A 8 508 508 HOH HOH . U 6 HOH A 9 509 509 HOH HOH . U 6 HOH A 10 510 510 HOH HOH . U 6 HOH A 11 511 511 HOH HOH . U 6 HOH A 12 512 512 HOH HOH . U 6 HOH A 13 513 513 HOH HOH . U 6 HOH A 14 514 514 HOH HOH . U 6 HOH A 15 515 515 HOH HOH . U 6 HOH A 16 516 516 HOH HOH . U 6 HOH A 17 517 517 HOH HOH . U 6 HOH A 18 518 518 HOH HOH . U 6 HOH A 19 519 519 HOH HOH . U 6 HOH A 20 520 520 HOH HOH . U 6 HOH A 21 521 521 HOH HOH . U 6 HOH A 22 522 546 HOH HOH . U 6 HOH A 23 524 524 HOH HOH . U 6 HOH A 24 525 525 HOH HOH . U 6 HOH A 25 526 526 HOH HOH . U 6 HOH A 26 527 527 HOH HOH . U 6 HOH A 27 528 528 HOH HOH . U 6 HOH A 28 529 529 HOH HOH . U 6 HOH A 29 531 531 HOH HOH . U 6 HOH A 30 532 532 HOH HOH . U 6 HOH A 31 533 533 HOH HOH . U 6 HOH A 32 535 535 HOH HOH . U 6 HOH A 33 536 536 HOH HOH . U 6 HOH A 34 537 537 HOH HOH . U 6 HOH A 35 538 538 HOH HOH . U 6 HOH A 36 539 539 HOH HOH . U 6 HOH A 37 540 540 HOH HOH . U 6 HOH A 38 541 541 HOH HOH . U 6 HOH A 39 542 542 HOH HOH . U 6 HOH A 40 543 543 HOH HOH . U 6 HOH A 41 544 544 HOH HOH . U 6 HOH A 42 545 545 HOH HOH . U 6 HOH A 43 546 546 HOH HOH . U 6 HOH A 44 547 547 HOH HOH . U 6 HOH A 45 548 548 HOH HOH . U 6 HOH A 46 549 549 HOH HOH . U 6 HOH A 47 552 552 HOH HOH . U 6 HOH A 48 565 565 HOH HOH . U 6 HOH A 49 600 600 HOH HOH . V 6 HOH B 1 501 501 HOH HOH . V 6 HOH B 2 503 503 HOH HOH . V 6 HOH B 3 504 504 HOH HOH . V 6 HOH B 4 505 505 HOH HOH . V 6 HOH B 5 506 506 HOH HOH . V 6 HOH B 6 507 507 HOH HOH . V 6 HOH B 7 508 508 HOH HOH . V 6 HOH B 8 509 509 HOH HOH . V 6 HOH B 9 510 510 HOH HOH . V 6 HOH B 10 511 511 HOH HOH . V 6 HOH B 11 512 512 HOH HOH . V 6 HOH B 12 513 513 HOH HOH . V 6 HOH B 13 515 515 HOH HOH . V 6 HOH B 14 516 516 HOH HOH . V 6 HOH B 15 517 517 HOH HOH . V 6 HOH B 16 518 518 HOH HOH . V 6 HOH B 17 519 519 HOH HOH . V 6 HOH B 18 520 520 HOH HOH . V 6 HOH B 19 521 521 HOH HOH . V 6 HOH B 20 522 522 HOH HOH . V 6 HOH B 21 523 523 HOH HOH . V 6 HOH B 22 524 524 HOH HOH . V 6 HOH B 23 526 526 HOH HOH . V 6 HOH B 24 528 528 HOH HOH . V 6 HOH B 25 530 530 HOH HOH . V 6 HOH B 26 531 531 HOH HOH . V 6 HOH B 27 532 532 HOH HOH . V 6 HOH B 28 535 535 HOH HOH . V 6 HOH B 29 537 537 HOH HOH . V 6 HOH B 30 538 538 HOH HOH . V 6 HOH B 31 539 539 HOH HOH . V 6 HOH B 32 540 540 HOH HOH . V 6 HOH B 33 541 541 HOH HOH . V 6 HOH B 34 542 542 HOH HOH . V 6 HOH B 35 543 543 HOH HOH . V 6 HOH B 36 545 545 HOH HOH . V 6 HOH B 37 547 547 HOH HOH . V 6 HOH B 38 549 549 HOH HOH . V 6 HOH B 39 550 550 HOH HOH . V 6 HOH B 40 552 552 HOH HOH . V 6 HOH B 41 553 553 HOH HOH . V 6 HOH B 42 556 556 HOH HOH . V 6 HOH B 43 557 557 HOH HOH . V 6 HOH B 44 559 559 HOH HOH . V 6 HOH B 45 560 560 HOH HOH . V 6 HOH B 46 561 561 HOH HOH . V 6 HOH B 47 563 563 HOH HOH . V 6 HOH B 48 564 564 HOH HOH . W 6 HOH D 1 501 501 HOH HOH . W 6 HOH D 2 503 503 HOH HOH . W 6 HOH D 3 504 504 HOH HOH . W 6 HOH D 4 505 505 HOH HOH . W 6 HOH D 5 506 506 HOH HOH . W 6 HOH D 6 507 507 HOH HOH . W 6 HOH D 7 508 508 HOH HOH . W 6 HOH D 8 509 509 HOH HOH . W 6 HOH D 9 510 510 HOH HOH . W 6 HOH D 10 511 511 HOH HOH . W 6 HOH D 11 512 512 HOH HOH . W 6 HOH D 12 515 515 HOH HOH . W 6 HOH D 13 516 516 HOH HOH . W 6 HOH D 14 517 517 HOH HOH . W 6 HOH D 15 518 518 HOH HOH . W 6 HOH D 16 520 520 HOH HOH . W 6 HOH D 17 521 521 HOH HOH . W 6 HOH D 18 523 523 HOH HOH . W 6 HOH D 19 525 525 HOH HOH . W 6 HOH D 20 530 530 HOH HOH . W 6 HOH D 21 531 531 HOH HOH . W 6 HOH D 22 539 539 HOH HOH . W 6 HOH D 23 540 540 HOH HOH . W 6 HOH D 24 543 543 HOH HOH . W 6 HOH D 25 544 544 HOH HOH . W 6 HOH D 26 545 545 HOH HOH . W 6 HOH D 27 546 546 HOH HOH . W 6 HOH D 28 547 547 HOH HOH . W 6 HOH D 29 548 548 HOH HOH . W 6 HOH D 30 553 553 HOH HOH . W 6 HOH D 31 554 554 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 C C11 L3P . . . M 4 13.993 1.61 14.636 1 90.04 ? C11 L3P 318 B 1 HETATM 2 C C12 L3P . . . M 4 15.116 2.74 14.892 1 91 ? C12 L3P 318 B 1 HETATM 3 C C13 L3P . . . M 4 14.992 3.691 16.187 1 91.66 ? C13 L3P 318 B 1 HETATM 4 C C14 L3P . . . M 4 13.593 4.476 16.161 1 91.76 ? C14 L3P 318 B 1 HETATM 5 C C15 L3P . . . M 4 16.281 4.756 16.208 1 92.43 ? C15 L3P 318 B 1 HETATM 6 C C16 L3P . . . M 4 17.692 3.984 16.244 1 93.39 ? C16 L3P 318 B 1 HETATM 7 C C17 L3P . . . M 4 18.875 4.421 17.207 1 93.97 ? C17 L3P 318 B 1 HETATM 8 C C18 L3P . . . M 4 18.828 5.69 18.278 1 94.42 ? C18 L3P 318 B 1 HETATM 9 C C19 L3P . . . M 4 17.664 5.666 19.386 1 94.51 ? C19 L3P 318 B 1 HETATM 10 C C20 L3P . . . M 4 18.743 7.051 17.45 1 94.48 ? C20 L3P 318 B 1 HETATM 11 C C21 L3P . . . M 4 20.036 7.775 16.892 1 94.67 ? C21 L3P 318 B 1 HETATM 12 C C22 L3P . . . M 4 19.713 9.287 16.5 1 94.89 ? C22 L3P 318 B 1 HETATM 13 C C23 L3P . . . M 4 20.963 10.099 15.928 1 95.11 ? C23 L3P 318 B 1 HETATM 14 C C24 L3P . . . M 4 22.103 10.109 16.967 1 95.4 ? C24 L3P 318 B 1 HETATM 15 C C25 L3P . . . M 4 20.547 11.656 15.534 1 94.83 ? C25 L3P 318 B 1 HETATM 16 C C26 L3P . . . M 4 21.416 12.709 14.664 1 94.6 ? C26 L3P 318 B 1 HETATM 17 C C27 L3P . . . M 4 20.768 14.184 14.426 1 94.74 ? C27 L3P 318 B 1 HETATM 18 C C28 L3P . . . M 4 21.552 15.285 15.286 1 94.89 ? C28 L3P 318 B 1 HETATM 19 C C29 L3P . . . M 4 22.05 16.367 14.388 1 94.73 ? C29 L3P 318 B 1 HETATM 20 C C30 L3P . . . M 4 20.678 15.947 16.27 1 95.2 ? C30 L3P 318 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #