data_4NV5 # _model_server_result.job_id ON-j9GS5v8uQeWXX696uWQ _model_server_result.datetime_utc '2024-11-24 05:08:45' _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 4nv5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 4NV5 # _exptl.entry_id 4NV5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 863.343 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description UBIQUINONE-10 _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 89.85 _cell.angle_gamma 90 _cell.entry_id 4NV5 _cell.length_a 140.842 _cell.length_b 118.822 _cell.length_c 68.034 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NV5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C 1 1 B,D 2 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 ? 2 C N N ? 2 D 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 56 A CYS 56 1_555 A SG CYS 130 A CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 209 A CYS 209 1_555 A SG CYS 212 A CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 231 A CYS 231 1_555 A SG CYS 244 A CYS 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 56 B CYS 56 1_555 B SG CYS 130 B CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 B SG CYS 209 B CYS 209 1_555 B SG CYS 212 B CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 B SG CYS 231 B CYS 231 1_555 B SG CYS 244 B CYS 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C59 H90 O4' _chem_comp.formula_weight 863.343 _chem_comp.id U10 _chem_comp.mon_nstd_flag . _chem_comp.name UBIQUINONE-10 _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Coenzyme Q10' # 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 U10 sing 356 n n C1 C6 U10 doub 357 n n C1 C1M U10 sing 358 n n C2 C3 U10 sing 359 n n C2 O2 U10 doub 360 n n C3 C4 U10 doub 361 n n C3 O3 U10 sing 362 n n C4 C5 U10 sing 363 n n C4 O4 U10 sing 364 n n C5 C6 U10 sing 365 n n C5 O5 U10 doub 366 n n C6 C7 U10 sing 367 n n C1M H1M1 U10 sing 368 n n C1M H1M2 U10 sing 369 n n C1M H1M3 U10 sing 370 n n C3M O3 U10 sing 371 n n C3M H3M1 U10 sing 372 n n C3M H3M2 U10 sing 373 n n C3M H3M3 U10 sing 374 n n C4M O4 U10 sing 375 n n C4M H4M1 U10 sing 376 n n C4M H4M2 U10 sing 377 n n C4M H4M3 U10 sing 378 n n C7 C8 U10 sing 379 n n C7 H71 U10 sing 380 n n C7 H72 U10 sing 381 n n C8 C9 U10 doub 382 e n C8 H8 U10 sing 383 n n C9 C10 U10 sing 384 n n C9 C11 U10 sing 385 n n C10 H101 U10 sing 386 n n C10 H102 U10 sing 387 n n C10 H103 U10 sing 388 n n C11 C12 U10 sing 389 n n C11 H111 U10 sing 390 n n C11 H112 U10 sing 391 n n C12 C13 U10 sing 392 n n C12 H121 U10 sing 393 n n C12 H122 U10 sing 394 n n C13 C14 U10 doub 395 e n C13 H13 U10 sing 396 n n C14 C15 U10 sing 397 n n C14 C16 U10 sing 398 n n C15 H151 U10 sing 399 n n C15 H152 U10 sing 400 n n C15 H153 U10 sing 401 n n C16 C17 U10 sing 402 n n C16 H161 U10 sing 403 n n C16 H162 U10 sing 404 n n C17 C18 U10 sing 405 n n C17 H171 U10 sing 406 n n C17 H172 U10 sing 407 n n C18 C19 U10 doub 408 e n C18 H18 U10 sing 409 n n C19 C20 U10 sing 410 n n C19 C21 U10 sing 411 n n C20 H201 U10 sing 412 n n C20 H202 U10 sing 413 n n C20 H203 U10 sing 414 n n C21 C22 U10 sing 415 n n C21 H211 U10 sing 416 n n C21 H212 U10 sing 417 n n C22 C23 U10 sing 418 n n C22 H221 U10 sing 419 n n C22 H222 U10 sing 420 n n C23 C24 U10 doub 421 e n C23 H23 U10 sing 422 n n C24 C25 U10 sing 423 n n C24 C26 U10 sing 424 n n C25 H251 U10 sing 425 n n C25 H252 U10 sing 426 n n C25 H253 U10 sing 427 n n C26 C27 U10 sing 428 n n C26 H261 U10 sing 429 n n C26 H262 U10 sing 430 n n C27 C28 U10 sing 431 n n C27 H271 U10 sing 432 n n C27 H272 U10 sing 433 n n C28 C29 U10 doub 434 e n C28 H28 U10 sing 435 n n C29 C30 U10 sing 436 n n C29 C31 U10 sing 437 n n C30 H301 U10 sing 438 n n C30 H302 U10 sing 439 n n C30 H303 U10 sing 440 n n C31 C32 U10 sing 441 n n C31 H311 U10 sing 442 n n C31 H312 U10 sing 443 n n C32 C33 U10 sing 444 n n C32 H321 U10 sing 445 n n C32 H322 U10 sing 446 n n C33 C34 U10 doub 447 e n C33 H33 U10 sing 448 n n C34 C35 U10 sing 449 n n C34 C36 U10 sing 450 n n C35 H351 U10 sing 451 n n C35 H352 U10 sing 452 n n C35 H353 U10 sing 453 n n C36 C37 U10 sing 454 n n C36 H361 U10 sing 455 n n C36 H362 U10 sing 456 n n C37 C38 U10 sing 457 n n C37 H371 U10 sing 458 n n C37 H372 U10 sing 459 n n C38 C39 U10 doub 460 e n C38 H38 U10 sing 461 n n C39 C40 U10 sing 462 n n C39 C41 U10 sing 463 n n C40 H401 U10 sing 464 n n C40 H402 U10 sing 465 n n C40 H403 U10 sing 466 n n C41 C42 U10 sing 467 n n C41 H411 U10 sing 468 n n C41 H412 U10 sing 469 n n C42 C43 U10 sing 470 n n C42 H421 U10 sing 471 n n C42 H422 U10 sing 472 n n C43 C44 U10 doub 473 e n C43 H43 U10 sing 474 n n C44 C45 U10 sing 475 n n C44 C46 U10 sing 476 n n C45 H451 U10 sing 477 n n C45 H452 U10 sing 478 n n C45 H453 U10 sing 479 n n C46 C47 U10 sing 480 n n C46 H461 U10 sing 481 n n C46 H462 U10 sing 482 n n C47 C48 U10 sing 483 n n C47 H471 U10 sing 484 n n C47 H472 U10 sing 485 n n C48 C49 U10 doub 486 e n C48 H48 U10 sing 487 n n C49 C50 U10 sing 488 n n C49 C51 U10 sing 489 n n C50 H501 U10 sing 490 n n C50 H502 U10 sing 491 n n C50 H503 U10 sing 492 n n C51 C52 U10 sing 493 n n C51 H511 U10 sing 494 n n C51 H512 U10 sing 495 n n C52 C53 U10 sing 496 n n C52 H521 U10 sing 497 n n C52 H522 U10 sing 498 n n C53 C54 U10 doub 499 n n C53 H53 U10 sing 500 n n C54 C55 U10 sing 501 n n C54 C56 U10 sing 502 n n C55 H551 U10 sing 503 n n C55 H552 U10 sing 504 n n C55 H553 U10 sing 505 n n C56 H561 U10 sing 506 n n C56 H562 U10 sing 507 n n C56 H563 U10 sing 508 n n # _atom_sites.entry_id 4NV5 _atom_sites.fract_transf_matrix[1][1] 0.0071 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000019 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008416 _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] 0.014699 _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 C 2 U10 A 1 501 501 U10 U10 . D 2 U10 B 1 501 501 U10 U10 . # 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 C1 U10 . . . D 2 -47.84 10.212 16.954 1 75.24 ? C1 U10 501 B 1 HETATM 2 C C2 U10 . . . D 2 -49.117 9.677 16.397 1 74.54 ? C2 U10 501 B 1 HETATM 3 C C3 U10 . . . D 2 -49.358 8.21 16.348 1 74.66 ? C3 U10 501 B 1 HETATM 4 C C4 U10 . . . D 2 -48.325 7.272 16.866 1 75.91 ? C4 U10 501 B 1 HETATM 5 C C5 U10 . . . D 2 -47.052 7.795 17.427 1 76.45 ? C5 U10 501 B 1 HETATM 6 C C6 U10 . . . D 2 -46.808 9.269 17.474 1 76.85 ? C6 U10 501 B 1 HETATM 7 C C1M U10 . . . D 2 -47.592 11.703 17.005 1 74.86 ? C1M U10 501 B 1 HETATM 8 C C3M U10 . . . D 2 -50.655 7.351 14.473 1 74.54 ? C3M U10 501 B 1 HETATM 9 C C4M U10 . . . D 2 -49.265 5.295 17.875 1 78.71 ? C4M U10 501 B 1 HETATM 10 C C7 U10 . . . D 2 -45.512 9.809 18.038 1 78.69 ? C7 U10 501 B 1 HETATM 11 C C8 U10 . . . D 2 -44.418 9.465 17.056 1 80.59 ? C8 U10 501 B 1 HETATM 12 C C9 U10 . . . D 2 -43.312 8.788 17.406 1 80.73 ? C9 U10 501 B 1 HETATM 13 C C10 U10 . . . D 2 -43.093 8.33 18.82 1 80.71 ? C10 U10 501 B 1 HETATM 14 C C11 U10 . . . D 2 -42.266 8.467 16.364 1 80.89 ? C11 U10 501 B 1 HETATM 15 C C12 U10 . . . D 2 -42.038 9.616 15.386 1 81.71 ? C12 U10 501 B 1 HETATM 16 C C13 U10 . . . D 2 -40.825 9.266 14.554 1 82.66 ? C13 U10 501 B 1 HETATM 17 C C14 U10 . . . D 2 -39.689 9.987 14.575 1 82.5 ? C14 U10 501 B 1 HETATM 18 C C15 U10 . . . D 2 -39.557 11.204 15.446 1 82.24 ? C15 U10 501 B 1 HETATM 19 C C16 U10 . . . D 2 -38.513 9.556 13.726 1 83.26 ? C16 U10 501 B 1 HETATM 20 C C17 U10 . . . D 2 -38.74 9.824 12.245 1 82.69 ? C17 U10 501 B 1 HETATM 21 C C18 U10 . . . D 2 -37.655 9.121 11.457 1 83.26 ? C18 U10 501 B 1 HETATM 22 C C19 U10 . . . D 2 -37.607 9.13 10.113 1 83.89 ? C19 U10 501 B 1 HETATM 23 C C20 U10 . . . D 2 -38.649 9.863 9.314 1 82.69 ? C20 U10 501 B 1 HETATM 24 C C21 U10 . . . D 2 -36.482 8.4 9.41 1 84.08 ? C21 U10 501 B 1 HETATM 25 C C22 U10 . . . D 2 -37.017 7.334 8.454 1 85.24 ? C22 U10 501 B 1 HETATM 26 C C23 U10 . . . D 2 -36.71 7.742 7.028 1 85.9 ? C23 U10 501 B 1 HETATM 27 C C24 U10 . . . D 2 -37.647 7.883 6.071 1 85.91 ? C24 U10 501 B 1 HETATM 28 C C25 U10 . . . D 2 -39.106 7.638 6.34 1 86.32 ? C25 U10 501 B 1 HETATM 29 C C26 U10 . . . D 2 -37.219 8.297 4.683 1 85.39 ? C26 U10 501 B 1 HETATM 30 O O2 U10 . . . D 2 -49.996 10.45 15.959 1 74.77 ? O2 U10 501 B 1 HETATM 31 O O3 U10 . . . D 2 -50.535 7.723 15.84 1 73.31 ? O3 U10 501 B 1 HETATM 32 O O4 U10 . . . D 2 -48.544 5.922 16.822 1 76.11 ? O4 U10 501 B 1 HETATM 33 O O5 U10 . . . D 2 -46.195 6.987 17.856 1 75.99 ? O5 U10 501 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 33 #