data_6YBY # _model_server_result.job_id QUhf-ijpZtyQ11wDgzUAYA _model_server_result.datetime_utc '2024-11-16 17:58:06' _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 6yby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6YBY # _exptl.entry_id 6YBY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 6YBY _cell.length_a 40.887 _cell.length_b 83.601 _cell.length_c 233.83 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A NZ LYS 254 A LYS 255 1_555 KA C15 RET . A RET 336 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A NZ LYS 254 A LYS 255 1_555 KA C15 RET . A RET 336 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.456 ? metalc ? metalc1 A OH TYR 24 A TYR 25 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc2 A O THR 82 A THR 83 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc3 A O PHE 85 A PHE 86 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc4 B NA NA . A NA 301 1_555 LA O HOH . A HOH 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc5 B NA NA . A NA 301 1_555 LA O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc6 B NA NA . A NA 301 1_555 LA O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6YBY _atom_sites.fract_transf_matrix[1][1] 0.024458 _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] 0.011962 _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] 0.004277 _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 NA A 1 301 301 NA NA . C 3 LFA A 1 302 302 LFA LFA . D 3 LFA A 1 303 303 LFA LFA . E 3 LFA A 1 304 304 LFA LFA . F 3 LFA A 1 305 305 LFA LFA . G 3 LFA A 1 306 306 LFA LFA . H 3 LFA A 1 307 307 LFA LFA . I 3 LFA A 1 308 308 LFA LFA . J 3 LFA A 1 309 309 LFA LFA . K 3 LFA A 1 310 310 LFA LFA . L 3 LFA A 1 311 311 LFA LFA . M 3 LFA A 1 312 312 LFA LFA . N 3 LFA A 1 313 313 LFA LFA . O 3 LFA A 1 314 314 LFA LFA . P 3 LFA A 1 315 315 LFA LFA . Q 3 LFA A 1 316 316 LFA LFA . R 3 LFA A 1 317 317 LFA LFA . S 3 LFA A 1 318 318 LFA LFA . T 3 LFA A 1 319 319 LFA LFA . U 3 LFA A 1 320 320 LFA LFA . V 3 LFA A 1 321 321 LFA LFA . W 3 LFA A 1 322 322 LFA LFA . X 3 LFA A 1 323 323 LFA LFA . Y 3 LFA A 1 324 324 LFA LFA . Z 3 LFA A 1 325 325 LFA LFA . AA 3 LFA A 1 326 326 LFA LFA . BA 3 LFA A 1 327 327 LFA LFA . CA 3 LFA A 1 328 328 LFA LFA . DA 3 LFA A 1 329 329 LFA LFA . EA 3 LFA A 1 330 330 LFA LFA . FA 3 LFA A 1 331 331 LFA LFA . GA 3 LFA A 1 332 332 LFA LFA . HA 3 LFA A 1 333 333 LFA LFA . IA 3 LFA A 1 334 334 LFA LFA . JA 3 LFA A 1 335 335 LFA LFA . KA 4 RET A 1 336 255 RET LYR . LA 5 HOH A 1 401 401 HOH HOH . LA 5 HOH A 2 402 409 HOH HOH . LA 5 HOH A 3 403 474 HOH HOH . LA 5 HOH A 4 404 427 HOH HOH . LA 5 HOH A 5 405 449 HOH HOH . LA 5 HOH A 6 406 3 HOH HOH . LA 5 HOH A 7 407 423 HOH HOH . LA 5 HOH A 8 408 439 HOH HOH . LA 5 HOH A 9 409 434 HOH HOH . LA 5 HOH A 10 410 520 HOH HOH . LA 5 HOH A 11 411 471 HOH HOH . LA 5 HOH A 12 412 481 HOH HOH . LA 5 HOH A 13 413 406 HOH HOH . LA 5 HOH A 14 414 486 HOH HOH . LA 5 HOH A 15 415 450 HOH HOH . LA 5 HOH A 16 416 485 HOH HOH . LA 5 HOH A 17 417 402 HOH HOH . LA 5 HOH A 18 418 477 HOH HOH . LA 5 HOH A 19 419 412 HOH HOH . LA 5 HOH A 20 420 519 HOH HOH . LA 5 HOH A 21 421 490 HOH HOH . LA 5 HOH A 22 422 524 HOH HOH . LA 5 HOH A 23 423 494 HOH HOH . LA 5 HOH A 24 424 442 HOH HOH . LA 5 HOH A 25 425 459 HOH HOH . LA 5 HOH A 26 426 447 HOH HOH . LA 5 HOH A 27 427 438 HOH HOH . LA 5 HOH A 28 428 511 HOH HOH . LA 5 HOH A 29 429 404 HOH HOH . LA 5 HOH A 30 430 498 HOH HOH . LA 5 HOH A 31 431 413 HOH HOH . LA 5 HOH A 32 432 491 HOH HOH . LA 5 HOH A 33 433 444 HOH HOH . LA 5 HOH A 34 434 467 HOH HOH . LA 5 HOH A 35 435 527 HOH HOH . LA 5 HOH A 36 436 443 HOH HOH . LA 5 HOH A 37 437 403 HOH HOH . LA 5 HOH A 38 438 405 HOH HOH . LA 5 HOH A 39 439 542 HOH HOH . LA 5 HOH A 40 440 466 HOH HOH . LA 5 HOH A 41 441 480 HOH HOH . LA 5 HOH A 42 442 457 HOH HOH . LA 5 HOH A 43 443 435 HOH HOH . LA 5 HOH A 44 444 429 HOH HOH . LA 5 HOH A 45 445 501 HOH HOH . LA 5 HOH A 46 446 445 HOH HOH . LA 5 HOH A 47 447 473 HOH HOH . LA 5 HOH A 48 448 468 HOH HOH . LA 5 HOH A 49 449 440 HOH HOH . LA 5 HOH A 50 450 408 HOH HOH . LA 5 HOH A 51 451 407 HOH HOH . LA 5 HOH A 52 452 458 HOH HOH . LA 5 HOH A 53 453 456 HOH HOH . LA 5 HOH A 54 454 455 HOH HOH . LA 5 HOH A 55 455 415 HOH HOH . LA 5 HOH A 56 456 503 HOH HOH . LA 5 HOH A 57 457 497 HOH HOH . LA 5 HOH A 58 458 448 HOH HOH . LA 5 HOH A 59 459 426 HOH HOH . LA 5 HOH A 60 460 8 HOH HOH . LA 5 HOH A 61 461 436 HOH HOH . LA 5 HOH A 62 462 417 HOH HOH . LA 5 HOH A 63 463 437 HOH HOH . LA 5 HOH A 64 464 441 HOH HOH . LA 5 HOH A 65 465 464 HOH HOH . LA 5 HOH A 66 466 410 HOH HOH . LA 5 HOH A 67 467 453 HOH HOH . LA 5 HOH A 68 468 461 HOH HOH . LA 5 HOH A 69 469 460 HOH HOH . LA 5 HOH A 70 470 424 HOH HOH . LA 5 HOH A 71 471 529 HOH HOH . LA 5 HOH A 72 472 530 HOH HOH . LA 5 HOH A 73 473 495 HOH HOH . LA 5 HOH A 74 474 418 HOH HOH . LA 5 HOH A 75 475 414 HOH HOH . LA 5 HOH A 76 476 475 HOH HOH . LA 5 HOH A 77 477 419 HOH HOH . LA 5 HOH A 78 478 516 HOH HOH . LA 5 HOH A 79 479 463 HOH HOH . LA 5 HOH A 80 480 411 HOH HOH . LA 5 HOH A 81 481 420 HOH HOH . LA 5 HOH A 82 482 421 HOH HOH . LA 5 HOH A 83 483 539 HOH HOH . LA 5 HOH A 84 484 489 HOH HOH . LA 5 HOH A 85 485 454 HOH HOH . LA 5 HOH A 86 486 517 HOH HOH . LA 5 HOH A 87 487 492 HOH HOH . LA 5 HOH A 88 488 425 HOH HOH . LA 5 HOH A 89 489 534 HOH HOH . LA 5 HOH A 90 490 478 HOH HOH . LA 5 HOH A 91 491 507 HOH HOH . LA 5 HOH A 92 492 422 HOH HOH . LA 5 HOH A 93 493 451 HOH HOH . LA 5 HOH A 94 494 496 HOH HOH . LA 5 HOH A 95 495 533 HOH HOH . LA 5 HOH A 96 496 528 HOH HOH . LA 5 HOH A 97 497 510 HOH HOH . LA 5 HOH A 98 498 505 HOH HOH . LA 5 HOH A 99 499 521 HOH HOH . LA 5 HOH A 100 500 487 HOH HOH . LA 5 HOH A 101 501 484 HOH HOH . LA 5 HOH A 102 502 470 HOH HOH . LA 5 HOH A 103 503 531 HOH HOH . LA 5 HOH A 104 504 488 HOH HOH . LA 5 HOH A 105 505 2 HOH HOH . LA 5 HOH A 106 506 9 HOH HOH . LA 5 HOH A 107 507 537 HOH HOH . LA 5 HOH A 108 508 428 HOH HOH . LA 5 HOH A 109 509 513 HOH HOH . LA 5 HOH A 110 510 536 HOH HOH . LA 5 HOH A 111 511 10 HOH HOH . LA 5 HOH A 112 512 1 HOH HOH . LA 5 HOH A 113 513 472 HOH HOH . LA 5 HOH A 114 514 416 HOH HOH . LA 5 HOH A 115 515 502 HOH HOH . LA 5 HOH A 116 516 452 HOH HOH . LA 5 HOH A 117 517 430 HOH HOH . LA 5 HOH A 118 518 462 HOH HOH . LA 5 HOH A 119 519 482 HOH HOH . LA 5 HOH A 120 520 465 HOH HOH . LA 5 HOH A 121 521 446 HOH HOH . LA 5 HOH A 122 522 535 HOH HOH . LA 5 HOH A 123 523 493 HOH HOH . LA 5 HOH A 124 524 469 HOH HOH . LA 5 HOH A 125 525 538 HOH HOH . LA 5 HOH A 126 526 4 HOH HOH . LA 5 HOH A 127 527 523 HOH HOH . LA 5 HOH A 128 528 7 HOH HOH . LA 5 HOH A 129 529 512 HOH HOH . LA 5 HOH A 130 530 506 HOH HOH . LA 5 HOH A 131 531 526 HOH HOH . LA 5 HOH A 132 532 476 HOH HOH . LA 5 HOH A 133 533 532 HOH HOH . LA 5 HOH A 134 534 431 HOH HOH . LA 5 HOH A 135 535 514 HOH HOH . LA 5 HOH A 136 536 541 HOH HOH . LA 5 HOH A 137 537 515 HOH HOH . LA 5 HOH A 138 538 508 HOH HOH . LA 5 HOH A 139 539 479 HOH HOH . LA 5 HOH A 140 540 432 HOH HOH . LA 5 HOH A 141 541 518 HOH HOH . LA 5 HOH A 142 542 433 HOH HOH . LA 5 HOH A 143 543 543 HOH HOH . LA 5 HOH A 144 544 504 HOH HOH . LA 5 HOH A 145 545 540 HOH HOH . LA 5 HOH A 146 546 6 HOH HOH . LA 5 HOH A 147 547 499 HOH HOH . LA 5 HOH A 148 548 500 HOH HOH . LA 5 HOH A 149 549 5 HOH HOH . LA 5 HOH A 150 550 525 HOH HOH . LA 5 HOH A 151 551 544 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id B _atom_site.label_entity_id 2 _atom_site.Cartn_x 14.811 _atom_site.Cartn_y 33.665 _atom_site.Cartn_z 7.562 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 55.12 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 301 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 369 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 1 #