data_4M2Y # _model_server_result.job_id xARMJkD3pK0owEvchetvAw _model_server_result.datetime_utc '2024-11-23 19:18:22' _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 4m2y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 4M2Y # _exptl.entry_id 4M2Y _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 105.48 _cell.angle_gamma 90 _cell.entry_id 4M2Y _cell.length_a 54.554 _cell.length_b 79.271 _cell.length_c 54.915 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M2Y _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 B O3' DC 5 T DC 5 1_555 B P BGM 6 T BGM 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.623 ? covale ? covale2 B O3' BGM 6 T BGM 6 1_555 B P DT 7 T DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? metalc ? metalc1 A O LYS 50 A LYS 60 1_555 F NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc2 A O LEU 52 A LEU 62 1_555 F NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? metalc ? metalc3 A O VAL 55 A VAL 65 1_555 F NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc4 A O THR 91 A THR 101 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc5 A O VAL 93 A VAL 103 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc6 A O ILE 96 A ILE 106 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc7 E NA NA . A NA 401 1_555 C OP1 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc8 E NA NA . A NA 401 1_555 I O HOH . P HOH 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc9 F NA NA . A NA 402 1_555 D OP1 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? 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 WATSON-CRICK hydrog15 B N3 DT 7 T DT 7 1_555 C N1 DA 10 P DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O4 DT 7 T DT 7 1_555 C N6 DA 10 P DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DC 8 T DC 8 1_555 C N1 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N4 DC 8 T DC 8 1_555 C O6 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O2 DC 8 T DC 8 1_555 C N2 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 DG 9 T DG 9 1_555 C N3 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N2 DG 9 T DG 9 1_555 C O2 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O6 DG 9 T DG 9 1_555 C N4 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N3 DC 10 T DC 10 1_555 C N1 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N4 DC 10 T DC 10 1_555 C O6 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O2 DC 10 T DC 10 1_555 C N2 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N1 DA 11 T DA 11 1_555 C N3 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N6 DA 11 T DA 11 1_555 C O4 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N3 DT 12 T DT 12 1_555 C N1 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B O4 DT 12 T DT 12 1_555 C N6 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N3 DC 13 T DC 13 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N4 DC 13 T DC 13 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B O2 DC 13 T DC 13 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N1 DA 14 T DA 14 1_555 C N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B N6 DA 14 T DA 14 1_555 C O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N1 DG 15 T DG 15 1_555 C N3 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B N2 DG 15 T DG 15 1_555 C O2 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B O6 DG 15 T DG 15 1_555 C N4 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 B N3 DC 16 T DC 16 1_555 C N1 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 B N4 DC 16 T DC 16 1_555 C O6 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 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 4M2Y _atom_sites.fract_transf_matrix[1][1] 0.01833 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005075 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012615 _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] 0.018895 _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 1 401 341 NA NA . F 5 NA A 1 402 342 NA NA . G 6 HOH A 1 501 1 HOH HOH . G 6 HOH A 2 502 2 HOH HOH . G 6 HOH A 3 503 4 HOH HOH . G 6 HOH A 4 504 5 HOH HOH . G 6 HOH A 5 505 8 HOH HOH . G 6 HOH A 6 506 9 HOH HOH . G 6 HOH A 7 507 10 HOH HOH . G 6 HOH A 8 508 11 HOH HOH . G 6 HOH A 9 509 12 HOH HOH . G 6 HOH A 10 510 13 HOH HOH . G 6 HOH A 11 511 14 HOH HOH . G 6 HOH A 12 512 17 HOH HOH . G 6 HOH A 13 513 18 HOH HOH . G 6 HOH A 14 514 19 HOH HOH . G 6 HOH A 15 515 20 HOH HOH . G 6 HOH A 16 516 21 HOH HOH . G 6 HOH A 17 517 22 HOH HOH . G 6 HOH A 18 518 23 HOH HOH . G 6 HOH A 19 519 24 HOH HOH . G 6 HOH A 20 520 25 HOH HOH . G 6 HOH A 21 521 26 HOH HOH . G 6 HOH A 22 522 27 HOH HOH . G 6 HOH A 23 523 29 HOH HOH . G 6 HOH A 24 524 30 HOH HOH . G 6 HOH A 25 525 33 HOH HOH . G 6 HOH A 26 526 36 HOH HOH . G 6 HOH A 27 527 37 HOH HOH . G 6 HOH A 28 528 39 HOH HOH . G 6 HOH A 29 529 42 HOH HOH . G 6 HOH A 30 530 43 HOH HOH . G 6 HOH A 31 531 44 HOH HOH . G 6 HOH A 32 532 45 HOH HOH . G 6 HOH A 33 533 47 HOH HOH . G 6 HOH A 34 534 48 HOH HOH . G 6 HOH A 35 535 49 HOH HOH . G 6 HOH A 36 536 50 HOH HOH . G 6 HOH A 37 537 53 HOH HOH . G 6 HOH A 38 538 56 HOH HOH . G 6 HOH A 39 539 57 HOH HOH . G 6 HOH A 40 540 61 HOH HOH . G 6 HOH A 41 541 63 HOH HOH . G 6 HOH A 42 542 67 HOH HOH . G 6 HOH A 43 543 68 HOH HOH . G 6 HOH A 44 544 69 HOH HOH . G 6 HOH A 45 545 71 HOH HOH . G 6 HOH A 46 546 72 HOH HOH . G 6 HOH A 47 547 73 HOH HOH . G 6 HOH A 48 548 74 HOH HOH . G 6 HOH A 49 549 75 HOH HOH . G 6 HOH A 50 550 77 HOH HOH . G 6 HOH A 51 551 78 HOH HOH . G 6 HOH A 52 552 79 HOH HOH . G 6 HOH A 53 553 81 HOH HOH . G 6 HOH A 54 554 3 HOH HOH . G 6 HOH A 55 555 54 HOH HOH . H 6 HOH T 1 101 6 HOH HOH . H 6 HOH T 2 102 16 HOH HOH . H 6 HOH T 3 103 28 HOH HOH . H 6 HOH T 4 104 32 HOH HOH . H 6 HOH T 5 105 34 HOH HOH . H 6 HOH T 6 106 35 HOH HOH . H 6 HOH T 7 107 38 HOH HOH . H 6 HOH T 8 108 41 HOH HOH . H 6 HOH T 9 109 64 HOH HOH . H 6 HOH T 10 110 65 HOH HOH . I 6 HOH P 1 101 7 HOH HOH . I 6 HOH P 2 102 15 HOH HOH . I 6 HOH P 3 103 31 HOH HOH . I 6 HOH P 4 104 40 HOH HOH . I 6 HOH P 5 105 46 HOH HOH . J 6 HOH D 1 101 58 HOH HOH . J 6 HOH D 2 102 59 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 19.703 _atom_site.Cartn_y 2.068 _atom_site.Cartn_z 22.07 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 13.6 _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 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 802 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 1 #