data_4UB1 # _model_server_result.job_id jrPfXDCaFU54fFERDnlilQ _model_server_result.datetime_utc '2024-12-01 00:01:34' _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 4ub1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 4UB1 # _exptl.entry_id 4UB1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 109.58 _cell.angle_gamma 90 _cell.entry_id 4UB1 _cell.length_a 55.131 _cell.length_b 80.8 _cell.length_c 55.462 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4UB1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,I,J _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 ? 5 E N N ? 5 F 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 C O3' DC 10 P DC 10 1_555 C P 8OG 11 P 8OG 11 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.6 ? metalc ? metalc1 E NA NA . A NA 401 1_555 I O HOH . P HOH 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.093 ? hydrog WATSON-CRICK hydrog1 B N3 DC 1 T DC 1 1_555 D N1 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 1 T DC 1 1_555 D O6 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 1 T DC 1 1_555 D N2 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DC 2 T DC 2 1_555 D N1 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N4 DC 2 T DC 2 1_555 D O6 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O2 DC 2 T DC 2 1_555 D N2 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DG 3 T DG 3 1_555 D N3 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N2 DG 3 T DG 3 1_555 D O2 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O6 DG 3 T DG 3 1_555 D N4 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 4 T DA 4 1_555 D N3 DT 2 D DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 4 T DA 4 1_555 D O4 DT 2 D DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DC 5 T DC 5 1_555 D N1 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N4 DC 5 T DC 5 1_555 D O6 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O2 DC 5 T DC 5 1_555 D N2 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-8OG MISPAIR' hydrog15 B N6 DA 6 T DA 6 1_555 C N3 8OG 11 P 8OG 11 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 7 T DG 7 1_555 C N3 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 7 T DG 7 1_555 C O2 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 7 T DG 7 1_555 C N4 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DC 8 T DC 8 1_555 C N1 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N4 DC 8 T DC 8 1_555 C O6 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O2 DC 8 T DC 8 1_555 C N2 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DG 9 T DG 9 1_555 C N3 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 DG 9 T DG 9 1_555 C O2 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 DG 9 T DG 9 1_555 C N4 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 DC 10 T DC 10 1_555 C N1 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N4 DC 10 T DC 10 1_555 C O6 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O2 DC 10 T DC 10 1_555 C N2 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N1 DA 11 T DA 11 1_555 C N3 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N6 DA 11 T DA 11 1_555 C O4 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N3 DT 12 T DT 12 1_555 C N1 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B O4 DT 12 T DT 12 1_555 C N6 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B N3 DC 13 T DC 13 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N4 DC 13 T DC 13 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B O2 DC 13 T DC 13 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N1 DA 14 T DA 14 1_555 C N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B N6 DA 14 T DA 14 1_555 C O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B N1 DG 15 T DG 15 1_555 C N3 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 B N2 DG 15 T DG 15 1_555 C O2 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 B O6 DG 15 T DG 15 1_555 C N4 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 B N3 DC 16 T DC 16 1_555 C N1 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 B N4 DC 16 T DC 16 1_555 C O6 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 B O2 DC 16 T DC 16 1_555 C N2 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 4UB1 _atom_sites.fract_transf_matrix[1][1] 0.018139 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006452 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012376 _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] 0.019137 _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 E 5 NA A 1 401 1 NA NA . F 5 NA A 1 402 2 NA NA . G 6 HOH A 1 501 47 HOH HOH . G 6 HOH A 2 502 25 HOH HOH . G 6 HOH A 3 503 15 HOH HOH . G 6 HOH A 4 504 59 HOH HOH . G 6 HOH A 5 505 34 HOH HOH . G 6 HOH A 6 506 55 HOH HOH . G 6 HOH A 7 507 16 HOH HOH . G 6 HOH A 8 508 33 HOH HOH . G 6 HOH A 9 509 70 HOH HOH . G 6 HOH A 10 510 81 HOH HOH . G 6 HOH A 11 511 3 HOH HOH . G 6 HOH A 12 512 4 HOH HOH . G 6 HOH A 13 513 5 HOH HOH . G 6 HOH A 14 514 6 HOH HOH . G 6 HOH A 15 515 8 HOH HOH . G 6 HOH A 16 516 9 HOH HOH . G 6 HOH A 17 517 10 HOH HOH . G 6 HOH A 18 518 11 HOH HOH . G 6 HOH A 19 519 13 HOH HOH . G 6 HOH A 20 520 14 HOH HOH . G 6 HOH A 21 521 17 HOH HOH . G 6 HOH A 22 522 18 HOH HOH . G 6 HOH A 23 523 19 HOH HOH . G 6 HOH A 24 524 20 HOH HOH . G 6 HOH A 25 525 21 HOH HOH . G 6 HOH A 26 526 29 HOH HOH . G 6 HOH A 27 527 32 HOH HOH . G 6 HOH A 28 528 35 HOH HOH . G 6 HOH A 29 529 37 HOH HOH . G 6 HOH A 30 530 38 HOH HOH . G 6 HOH A 31 531 39 HOH HOH . G 6 HOH A 32 532 40 HOH HOH . G 6 HOH A 33 533 42 HOH HOH . G 6 HOH A 34 534 43 HOH HOH . G 6 HOH A 35 535 48 HOH HOH . G 6 HOH A 36 536 49 HOH HOH . G 6 HOH A 37 537 51 HOH HOH . G 6 HOH A 38 538 57 HOH HOH . G 6 HOH A 39 539 58 HOH HOH . G 6 HOH A 40 540 61 HOH HOH . G 6 HOH A 41 541 62 HOH HOH . G 6 HOH A 42 542 63 HOH HOH . G 6 HOH A 43 543 64 HOH HOH . G 6 HOH A 44 544 66 HOH HOH . G 6 HOH A 45 545 67 HOH HOH . G 6 HOH A 46 546 68 HOH HOH . G 6 HOH A 47 547 71 HOH HOH . G 6 HOH A 48 548 74 HOH HOH . G 6 HOH A 49 549 76 HOH HOH . G 6 HOH A 50 550 79 HOH HOH . G 6 HOH A 51 551 82 HOH HOH . G 6 HOH A 52 552 83 HOH HOH . G 6 HOH A 53 553 84 HOH HOH . G 6 HOH A 54 554 85 HOH HOH . G 6 HOH A 55 555 86 HOH HOH . H 6 HOH T 1 101 73 HOH HOH . H 6 HOH T 2 102 53 HOH HOH . H 6 HOH T 3 103 7 HOH HOH . H 6 HOH T 4 104 27 HOH HOH . H 6 HOH T 5 105 31 HOH HOH . H 6 HOH T 6 106 36 HOH HOH . H 6 HOH T 7 107 41 HOH HOH . H 6 HOH T 8 108 44 HOH HOH . H 6 HOH T 9 109 54 HOH HOH . H 6 HOH T 10 110 56 HOH HOH . H 6 HOH T 11 111 60 HOH HOH . H 6 HOH T 12 112 72 HOH HOH . H 6 HOH T 13 113 75 HOH HOH . H 6 HOH T 14 114 78 HOH HOH . I 6 HOH P 1 101 12 HOH HOH . I 6 HOH P 2 102 22 HOH HOH . I 6 HOH P 3 103 23 HOH HOH . I 6 HOH P 4 104 24 HOH HOH . I 6 HOH P 5 105 26 HOH HOH . I 6 HOH P 6 106 30 HOH HOH . I 6 HOH P 7 107 45 HOH HOH . I 6 HOH P 8 108 46 HOH HOH . I 6 HOH P 9 109 50 HOH HOH . I 6 HOH P 10 110 65 HOH HOH . I 6 HOH P 11 111 69 HOH HOH . I 6 HOH P 12 112 77 HOH HOH . I 6 HOH P 13 113 80 HOH HOH . J 6 HOH D 1 101 28 HOH HOH . J 6 HOH D 2 102 52 HOH HOH . J 6 HOH D 3 103 87 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 E _atom_site.label_entity_id 5 _atom_site.Cartn_x 13.533 _atom_site.Cartn_y -6.255 _atom_site.Cartn_z 22.586 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 35.4 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 229 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 1 #