data_5LYM # _model_server_result.job_id ul0lfr01qwARpT4utYWF9Q _model_server_result.datetime_utc '2024-12-24 02:03:46' _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 5lym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":512}' # _entry.id 5LYM # _exptl.entry_id 5LYM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.005 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NITRATE ION' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.8 _cell.angle_gamma 90 _cell.entry_id 5LYM _cell.length_a 28 _cell.length_b 62.5 _cell.length_c 60.9 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LYM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,D,E,I 1 1 B,F,G,H,J 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 6 A CYS 6 1_555 A SG CYS 127 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 B SG CYS 6 B CYS 6 1_555 B SG CYS 127 B CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 B SG CYS 30 B CYS 30 1_555 B SG CYS 115 B CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf7 B SG CYS 64 B CYS 64 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf8 B SG CYS 76 B CYS 76 1_555 B SG CYS 94 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? # _chem_comp.formula 'N O3 -1' _chem_comp.formula_weight 62.005 _chem_comp.id NO3 _chem_comp.mon_nstd_flag . _chem_comp.name 'NITRATE ION' _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 N O1 NO3 doub 237 n n N O2 NO3 sing 238 n n N O3 NO3 sing 239 n n # _atom_sites.entry_id 5LYM _atom_sites.fract_transf_matrix[1][1] 0.035714 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000499 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016 _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] 0.016422 _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 NO3 A 1 513 513 NO3 NO3 . D 2 NO3 A 1 514 514 NO3 NO3 . E 2 NO3 A 1 517 517 NO3 NO3 . F 2 NO3 B 1 512 512 NO3 NO3 . G 2 NO3 B 1 515 515 NO3 NO3 . H 2 NO3 B 1 516 516 NO3 NO3 . I 3 HOH A 1 401 401 HOH HOH . I 3 HOH A 2 407 407 HOH HOH . I 3 HOH A 3 410 410 HOH HOH . I 3 HOH A 4 415 415 HOH HOH . I 3 HOH A 5 416 416 HOH HOH . I 3 HOH A 6 417 417 HOH HOH . I 3 HOH A 7 418 418 HOH HOH . I 3 HOH A 8 422 422 HOH HOH . I 3 HOH A 9 426 426 HOH HOH . I 3 HOH A 10 428 428 HOH HOH . I 3 HOH A 11 430 430 HOH HOH . I 3 HOH A 12 431 431 HOH HOH . I 3 HOH A 13 433 433 HOH HOH . I 3 HOH A 14 434 434 HOH HOH . I 3 HOH A 15 435 435 HOH HOH . I 3 HOH A 16 436 436 HOH HOH . I 3 HOH A 17 439 439 HOH HOH . I 3 HOH A 18 442 442 HOH HOH . I 3 HOH A 19 443 443 HOH HOH . I 3 HOH A 20 444 444 HOH HOH . I 3 HOH A 21 445 445 HOH HOH . I 3 HOH A 22 446 446 HOH HOH . I 3 HOH A 23 447 447 HOH HOH . I 3 HOH A 24 448 448 HOH HOH . I 3 HOH A 25 454 454 HOH HOH . I 3 HOH A 26 455 455 HOH HOH . I 3 HOH A 27 458 458 HOH HOH . I 3 HOH A 28 459 459 HOH HOH . I 3 HOH A 29 461 461 HOH HOH . I 3 HOH A 30 465 465 HOH HOH . I 3 HOH A 31 467 467 HOH HOH . I 3 HOH A 32 468 468 HOH HOH . I 3 HOH A 33 469 469 HOH HOH . I 3 HOH A 34 470 470 HOH HOH . I 3 HOH A 35 471 471 HOH HOH . I 3 HOH A 36 474 474 HOH HOH . I 3 HOH A 37 475 475 HOH HOH . I 3 HOH A 38 479 479 HOH HOH . I 3 HOH A 39 481 481 HOH HOH . I 3 HOH A 40 482 482 HOH HOH . I 3 HOH A 41 483 483 HOH HOH . I 3 HOH A 42 484 484 HOH HOH . I 3 HOH A 43 485 485 HOH HOH . I 3 HOH A 44 486 486 HOH HOH . I 3 HOH A 45 487 487 HOH HOH . I 3 HOH A 46 489 489 HOH HOH . I 3 HOH A 47 490 490 HOH HOH . I 3 HOH A 48 491 491 HOH HOH . I 3 HOH A 49 492 492 HOH HOH . I 3 HOH A 50 493 493 HOH HOH . I 3 HOH A 51 494 494 HOH HOH . I 3 HOH A 52 495 495 HOH HOH . I 3 HOH A 53 496 496 HOH HOH . I 3 HOH A 54 497 497 HOH HOH . I 3 HOH A 55 501 501 HOH HOH . I 3 HOH A 56 504 504 HOH HOH . I 3 HOH A 57 507 507 HOH HOH . I 3 HOH A 58 508 508 HOH HOH . I 3 HOH A 59 509 509 HOH HOH . I 3 HOH A 60 510 510 HOH HOH . I 3 HOH A 61 511 511 HOH HOH . J 3 HOH B 1 402 402 HOH HOH . J 3 HOH B 2 403 403 HOH HOH . J 3 HOH B 3 404 404 HOH HOH . J 3 HOH B 4 405 405 HOH HOH . J 3 HOH B 5 406 406 HOH HOH . J 3 HOH B 6 408 408 HOH HOH . J 3 HOH B 7 409 409 HOH HOH . J 3 HOH B 8 411 411 HOH HOH . J 3 HOH B 9 412 412 HOH HOH . J 3 HOH B 10 413 413 HOH HOH . J 3 HOH B 11 414 414 HOH HOH . J 3 HOH B 12 419 419 HOH HOH . J 3 HOH B 13 420 420 HOH HOH . J 3 HOH B 14 421 421 HOH HOH . J 3 HOH B 15 423 423 HOH HOH . J 3 HOH B 16 424 424 HOH HOH . J 3 HOH B 17 425 425 HOH HOH . J 3 HOH B 18 427 427 HOH HOH . J 3 HOH B 19 429 429 HOH HOH . J 3 HOH B 20 432 432 HOH HOH . J 3 HOH B 21 437 437 HOH HOH . J 3 HOH B 22 438 438 HOH HOH . J 3 HOH B 23 440 440 HOH HOH . J 3 HOH B 24 441 441 HOH HOH . J 3 HOH B 25 449 449 HOH HOH . J 3 HOH B 26 450 450 HOH HOH . J 3 HOH B 27 451 451 HOH HOH . J 3 HOH B 28 452 452 HOH HOH . J 3 HOH B 29 453 453 HOH HOH . J 3 HOH B 30 456 456 HOH HOH . J 3 HOH B 31 457 457 HOH HOH . J 3 HOH B 32 460 460 HOH HOH . J 3 HOH B 33 462 462 HOH HOH . J 3 HOH B 34 463 463 HOH HOH . J 3 HOH B 35 464 464 HOH HOH . J 3 HOH B 36 466 466 HOH HOH . J 3 HOH B 37 472 472 HOH HOH . J 3 HOH B 38 473 473 HOH HOH . J 3 HOH B 39 476 476 HOH HOH . J 3 HOH B 40 477 477 HOH HOH . J 3 HOH B 41 478 478 HOH HOH . J 3 HOH B 42 480 480 HOH HOH . J 3 HOH B 43 488 488 HOH HOH . J 3 HOH B 44 498 498 HOH HOH . J 3 HOH B 45 499 499 HOH HOH . J 3 HOH B 46 500 500 HOH HOH . J 3 HOH B 47 502 502 HOH HOH . J 3 HOH B 48 503 503 HOH HOH . J 3 HOH B 49 505 505 HOH HOH . J 3 HOH B 50 506 506 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 N N NO3 . . . F 2 15.085 26.25 37.523 1 31.1 ? N NO3 512 B 1 HETATM 2 O O1 NO3 . . . F 2 16.29 25.688 37.084 1 33.4 ? O1 NO3 512 B 1 HETATM 3 O O2 NO3 . . . F 2 14.921 26.59 38.869 1 34.3 ? O2 NO3 512 B 1 HETATM 4 O O3 NO3 . . . F 2 14.044 26.472 36.616 1 35.9 ? O3 NO3 512 B 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 78 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 4 #