data_5HVD # _model_server_result.job_id 7DqibAWt5J5DxsAFX3ox2g _model_server_result.datetime_utc '2024-12-02 10:13:23' _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 5hvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5HVD # _exptl.entry_id 5HVD _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 3 _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 5HVD _cell.length_a 109.58 _cell.length_b 109.58 _cell.length_c 209.71 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 2 2' # _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 _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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 109.58 109.58 0 3 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 109.58 0 0 4 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 109.58 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 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 metalc ? metalc1 B NA NA . A NA 301 1_555 H O HOH . A HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? metalc ? metalc2 B NA NA . A NA 301 1_555 H O HOH . A HOH 424 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? metalc ? metalc3 C NA NA . A NA 302 1_555 H O HOH . A HOH 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? metalc ? metalc4 C NA NA . A NA 302 1_555 H O HOH . A HOH 427 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? # _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 5HVD _atom_sites.fract_transf_matrix[1][1] 0.009126 _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] 0.009126 _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] 0.004768 _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 2 NA A 1 302 302 NA NA . D 2 NA A 1 303 303 NA NA . E 3 2CV A 1 304 401 2CV 2CV . F 4 12P A 1 305 501 12P 12P . G 5 MES A 1 306 1 MES MES . H 6 HOH A 1 401 110 HOH HOH . H 6 HOH A 2 402 54 HOH HOH . H 6 HOH A 3 403 101 HOH HOH . H 6 HOH A 4 404 3 HOH HOH . H 6 HOH A 5 405 51 HOH HOH . H 6 HOH A 6 406 7 HOH HOH . H 6 HOH A 7 407 95 HOH HOH . H 6 HOH A 8 408 8 HOH HOH . H 6 HOH A 9 409 17 HOH HOH . H 6 HOH A 10 410 11 HOH HOH . H 6 HOH A 11 411 108 HOH HOH . H 6 HOH A 12 412 9 HOH HOH . H 6 HOH A 13 413 2 HOH HOH . H 6 HOH A 14 414 106 HOH HOH . H 6 HOH A 15 415 96 HOH HOH . H 6 HOH A 16 416 6 HOH HOH . H 6 HOH A 17 417 36 HOH HOH . H 6 HOH A 18 418 28 HOH HOH . H 6 HOH A 19 419 65 HOH HOH . H 6 HOH A 20 420 22 HOH HOH . H 6 HOH A 21 421 5 HOH HOH . H 6 HOH A 22 422 21 HOH HOH . H 6 HOH A 23 423 1 HOH HOH . H 6 HOH A 24 424 75 HOH HOH . H 6 HOH A 25 425 32 HOH HOH . H 6 HOH A 26 426 94 HOH HOH . H 6 HOH A 27 427 74 HOH HOH . H 6 HOH A 28 428 97 HOH HOH . H 6 HOH A 29 429 78 HOH HOH . H 6 HOH A 30 430 13 HOH HOH . H 6 HOH A 31 431 55 HOH HOH . H 6 HOH A 32 432 23 HOH HOH . H 6 HOH A 33 433 15 HOH HOH . H 6 HOH A 34 434 85 HOH HOH . H 6 HOH A 35 435 89 HOH HOH . H 6 HOH A 36 436 86 HOH HOH . H 6 HOH A 37 437 67 HOH HOH . H 6 HOH A 38 438 31 HOH HOH . H 6 HOH A 39 439 25 HOH HOH . H 6 HOH A 40 440 88 HOH HOH . H 6 HOH A 41 441 98 HOH HOH . H 6 HOH A 42 442 10 HOH HOH . H 6 HOH A 43 443 60 HOH HOH . H 6 HOH A 44 444 46 HOH HOH . H 6 HOH A 45 445 12 HOH HOH . H 6 HOH A 46 446 70 HOH HOH . H 6 HOH A 47 447 20 HOH HOH . H 6 HOH A 48 448 29 HOH HOH . H 6 HOH A 49 449 16 HOH HOH . H 6 HOH A 50 450 72 HOH HOH . H 6 HOH A 51 451 83 HOH HOH . H 6 HOH A 52 452 99 HOH HOH . H 6 HOH A 53 453 49 HOH HOH . H 6 HOH A 54 454 27 HOH HOH . H 6 HOH A 55 455 69 HOH HOH . H 6 HOH A 56 456 39 HOH HOH . H 6 HOH A 57 457 14 HOH HOH . H 6 HOH A 58 458 56 HOH HOH . H 6 HOH A 59 459 37 HOH HOH . H 6 HOH A 60 460 30 HOH HOH . H 6 HOH A 61 461 81 HOH HOH . H 6 HOH A 62 462 18 HOH HOH . H 6 HOH A 63 463 58 HOH HOH . H 6 HOH A 64 464 4 HOH HOH . H 6 HOH A 65 465 40 HOH HOH . H 6 HOH A 66 466 79 HOH HOH . H 6 HOH A 67 467 33 HOH HOH . H 6 HOH A 68 468 38 HOH HOH . H 6 HOH A 69 469 104 HOH HOH . H 6 HOH A 70 470 63 HOH HOH . H 6 HOH A 71 471 92 HOH HOH . H 6 HOH A 72 472 43 HOH HOH . H 6 HOH A 73 473 19 HOH HOH . H 6 HOH A 74 474 47 HOH HOH . H 6 HOH A 75 475 77 HOH HOH . H 6 HOH A 76 476 84 HOH HOH . H 6 HOH A 77 477 109 HOH HOH . H 6 HOH A 78 478 87 HOH HOH . H 6 HOH A 79 479 105 HOH HOH . H 6 HOH A 80 480 24 HOH HOH . H 6 HOH A 81 481 41 HOH HOH . H 6 HOH A 82 482 76 HOH HOH . H 6 HOH A 83 483 35 HOH HOH . H 6 HOH A 84 484 102 HOH HOH . H 6 HOH A 85 485 107 HOH HOH . H 6 HOH A 86 486 93 HOH HOH . H 6 HOH A 87 487 34 HOH HOH . H 6 HOH A 88 488 42 HOH HOH . H 6 HOH A 89 489 103 HOH HOH . H 6 HOH A 90 490 44 HOH HOH . H 6 HOH A 91 491 66 HOH HOH . H 6 HOH A 92 492 26 HOH HOH . H 6 HOH A 93 493 111 HOH HOH . H 6 HOH A 94 494 68 HOH HOH . H 6 HOH A 95 495 53 HOH HOH . H 6 HOH A 96 496 91 HOH HOH . H 6 HOH A 97 497 71 HOH HOH . H 6 HOH A 98 498 52 HOH HOH . H 6 HOH A 99 499 48 HOH HOH . H 6 HOH A 100 500 45 HOH HOH . H 6 HOH A 101 501 62 HOH HOH . H 6 HOH A 102 502 64 HOH HOH . H 6 HOH A 103 503 61 HOH HOH . H 6 HOH A 104 504 59 HOH HOH . H 6 HOH A 105 505 90 HOH HOH . H 6 HOH A 106 506 50 HOH HOH . H 6 HOH A 107 507 82 HOH HOH . H 6 HOH A 108 508 57 HOH HOH . H 6 HOH A 109 509 73 HOH HOH . H 6 HOH A 110 510 80 HOH HOH . H 6 HOH A 111 511 100 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 54.79 _atom_site.Cartn_y 54.79 _atom_site.Cartn_z 20.226 _atom_site.occupancy 0.25 _atom_site.B_iso_or_equiv 85.12 _atom_site.pdbx_formal_charge 1 _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 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #