data_3RNA # _model_server_result.job_id C2EedfViR3zu0CoJZ91hkg _model_server_result.datetime_utc '2024-12-26 17:05:26' _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 3rna # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":499}' # _entry.id 3RNA # _exptl.entry_id 3RNA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 55.845 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FE (III) 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 90 _cell.angle_gamma 120 _cell.entry_id 3RNA _cell.length_a 182.793 _cell.length_b 182.793 _cell.length_c 67.701 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RNA _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 ? hexameric 6 author_defined_assembly 1 PISA trimeric 3 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1,2 A,B,C,D,E,F,G,H,I 2 1 # 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' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 22.567 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E 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 A OE1 GLU 104 A GLU 104 1_555 E FE FE . A FE 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc2 A OE2 GLU 134 A GLU 134 1_555 D FE FE . A FE 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc3 A OE1 GLU 134 A GLU 134 1_555 E FE FE . A FE 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc4 A ND1 HIS 137 A HIS 137 1_555 E FE FE . A FE 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc5 A OE2 GLU 197 A GLU 197 1_555 D FE FE . A FE 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc6 A OE2 GLU 231 A GLU 231 1_555 D FE FE . A FE 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? metalc ? metalc7 A NE2 HIS 234 A HIS 234 1_555 D FE FE . A FE 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc8 D FE FE . A FE 499 1_555 F O OH . A OH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc9 D FE FE . A FE 499 1_555 G O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc10 E FE FE . A FE 500 1_555 F O OH . A OH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc11 E FE FE . A FE 500 1_555 G O HOH . A HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? metalc ? metalc12 E FE FE . A FE 500 1_555 G O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? # _chem_comp.formula 'Fe 3' _chem_comp.formula_weight 55.845 _chem_comp.id FE _chem_comp.mon_nstd_flag . _chem_comp.name 'FE (III) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3RNA _atom_sites.fract_transf_matrix[1][1] 0.005471 _atom_sites.fract_transf_matrix[1][2] 0.003158 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006317 _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] 0.014771 _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 D 4 FE A 1 499 1 FE FE . E 4 FE A 1 500 2 FE FE . F 5 OH A 1 501 52 OH OH . G 6 HOH A 1 502 1 HOH HOH . G 6 HOH A 2 503 2 HOH HOH . G 6 HOH A 3 504 3 HOH HOH . G 6 HOH A 4 505 4 HOH HOH . G 6 HOH A 5 506 5 HOH HOH . G 6 HOH A 6 507 9 HOH HOH . G 6 HOH A 7 508 13 HOH HOH . G 6 HOH A 8 509 18 HOH HOH . G 6 HOH A 9 510 19 HOH HOH . G 6 HOH A 10 511 23 HOH HOH . G 6 HOH A 11 512 26 HOH HOH . G 6 HOH A 12 513 27 HOH HOH . G 6 HOH A 13 514 29 HOH HOH . G 6 HOH A 14 515 31 HOH HOH . G 6 HOH A 15 516 32 HOH HOH . G 6 HOH A 16 517 36 HOH HOH . G 6 HOH A 17 518 37 HOH HOH . G 6 HOH A 18 519 41 HOH HOH . G 6 HOH A 19 520 44 HOH HOH . G 6 HOH A 20 521 48 HOH HOH . G 6 HOH A 21 522 49 HOH HOH . G 6 HOH A 22 523 50 HOH HOH . G 6 HOH A 23 524 53 HOH HOH . G 6 HOH A 24 525 54 HOH HOH . G 6 HOH A 25 526 55 HOH HOH . H 6 HOH B 1 331 7 HOH HOH . H 6 HOH B 2 332 8 HOH HOH . H 6 HOH B 3 333 10 HOH HOH . H 6 HOH B 4 334 11 HOH HOH . H 6 HOH B 5 335 12 HOH HOH . H 6 HOH B 6 336 14 HOH HOH . H 6 HOH B 7 337 17 HOH HOH . H 6 HOH B 8 338 20 HOH HOH . H 6 HOH B 9 339 25 HOH HOH . H 6 HOH B 10 340 30 HOH HOH . H 6 HOH B 11 341 34 HOH HOH . H 6 HOH B 12 342 35 HOH HOH . H 6 HOH B 13 343 39 HOH HOH . H 6 HOH B 14 344 42 HOH HOH . H 6 HOH B 15 345 43 HOH HOH . H 6 HOH B 16 346 45 HOH HOH . I 6 HOH C 1 87 6 HOH HOH . I 6 HOH C 2 88 15 HOH HOH . I 6 HOH C 3 89 16 HOH HOH . I 6 HOH C 4 90 21 HOH HOH . I 6 HOH C 5 91 24 HOH HOH . I 6 HOH C 6 92 33 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol FE _atom_site.label_atom_id FE _atom_site.label_comp_id FE _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x 19.962 _atom_site.Cartn_y -71.232 _atom_site.Cartn_z -2.018 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 60.7 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id FE _atom_site.auth_comp_id FE _atom_site.auth_seq_id 499 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 104 _model_server_stats.parse_time_ms 130 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #