data_3VBO # _model_server_result.job_id ena3JxMOD5e4InTPw2tQ-g _model_server_result.datetime_utc '2024-11-24 14:00:10' _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 3vbo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 3VBO # _exptl.entry_id 3VBO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 1 _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 3VBO _cell.length_a 353.1 _cell.length_b 353.1 _cell.length_c 353.1 _cell.Z_PDB 120 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VBO _symmetry.cell_setting ? _symmetry.Int_Tables_number 208 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 180-meric 180 'complete icosahedral assembly' 1 ? trimeric 3 'icosahedral asymmetric unit' 2 ? pentadecameric 15 'icosahedral pentamer' 3 ? octadecameric 18 'icosahedral 23 hexamer' 4 ? trimeric 3 'icosahedral asymmetric unit, std point frame' 5 ? pentadecameric 15 'crystal asymmetric unit, crystal frame' 6 # 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 1 (1-60) A,B,C,D,E,F,G 2 1 A,B,C,D,E,F,G 3 (1-5) A,B,C,D,E,F,G 4 (1,2,6,10,23,24) A,B,C,D,E,F,G 5 P A,B,C,D,E,F,G 6 (X0)(1-5) # 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] P 'transform to point frame' ? ? 0 -1 0 1 0 0 0 0 1 0 0 0 X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 0 0 0 3 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 0 0 0 4 'point symmetry operation' ? ? -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 0 0 0 5 'point symmetry operation' ? ? 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 0 0 0 6 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 0 0 0 7 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 0 0 0 8 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 0.809017 0.309017 0.5 0 0 0 9 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 0 0 0 10 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 0 0 0 11 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 0 0 12 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 0 0 0 13 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 0 0 0 14 'point symmetry operation' ? ? -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 0 0 0 15 'point symmetry operation' ? ? 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 0 0 0 16 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0 0 0 17 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 0 0 0 18 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 0 0 0 19 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 0 0 0 20 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 0 0 0 21 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 0 0 0 22 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 0 0 0 23 'point symmetry operation' ? ? -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 0 0 0 24 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 0 0 0 25 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 0 0 0 26 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 0 0 0 27 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 0 0 0 28 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 0 0 0 29 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 0 0 0 30 'point symmetry operation' ? ? -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 0 0 0 31 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 0 32 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 0 0 0 33 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 0 0 0 34 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 0 0 0 35 'point symmetry operation' ? ? -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 0 0 0 36 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 0 0 0 37 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 0 0 0 38 'point symmetry operation' ? ? -0.5 0.809017 0.309017 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 0 0 0 39 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 0 0 0 40 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 0 0 0 41 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 0 0 0 42 'point symmetry operation' ? ? 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 0 0 0 43 'point symmetry operation' ? ? 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 0 0 0 44 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0 0 0 45 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 0 0 0 46 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 47 'point symmetry operation' ? ? 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 0 0 0 48 'point symmetry operation' ? ? 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 0 0 0 49 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0 0 0 50 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 0 0 0 51 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 0 0 0 52 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 0 0 0 53 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 0 0 0 54 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 0 0 0 55 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 0 0 0 56 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 0 0 0 57 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 0 0 0 58 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 0 0 0 59 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 0 0 0 60 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 GLN 189 A GLN 189 1_555 D NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc2 D NA NA . A NA 301 1_555 C O VAL 20 C VAL 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? # _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 3VBO _atom_sites.fract_transf_matrix[1][1] 0.002832 _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] 0.002832 _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] 0.002832 _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 NA A 1 301 100 NA NA . E 5 HOH A 1 401 10 HOH HOH . E 5 HOH A 2 402 16 HOH HOH . E 5 HOH A 3 403 17 HOH HOH . E 5 HOH A 4 404 18 HOH HOH . E 5 HOH A 5 405 19 HOH HOH . E 5 HOH A 6 406 20 HOH HOH . E 5 HOH A 7 407 21 HOH HOH . E 5 HOH A 8 408 22 HOH HOH . E 5 HOH A 9 409 23 HOH HOH . E 5 HOH A 10 410 24 HOH HOH . E 5 HOH A 11 411 25 HOH HOH . E 5 HOH A 12 412 26 HOH HOH . E 5 HOH A 13 413 27 HOH HOH . E 5 HOH A 14 414 28 HOH HOH . E 5 HOH A 15 415 29 HOH HOH . E 5 HOH A 16 416 30 HOH HOH . E 5 HOH A 17 417 31 HOH HOH . E 5 HOH A 18 418 37 HOH HOH . E 5 HOH A 19 419 38 HOH HOH . E 5 HOH A 20 420 39 HOH HOH . F 5 HOH B 1 401 1 HOH HOH . F 5 HOH B 2 402 2 HOH HOH . F 5 HOH B 3 403 6 HOH HOH . F 5 HOH B 4 404 7 HOH HOH . F 5 HOH B 5 405 9 HOH HOH . F 5 HOH B 6 406 36 HOH HOH . F 5 HOH B 7 407 40 HOH HOH . F 5 HOH B 8 408 41 HOH HOH . F 5 HOH B 9 409 42 HOH HOH . F 5 HOH B 10 410 43 HOH HOH . F 5 HOH B 11 411 44 HOH HOH . F 5 HOH B 12 412 45 HOH HOH . F 5 HOH B 13 413 46 HOH HOH . F 5 HOH B 14 414 47 HOH HOH . F 5 HOH B 15 415 48 HOH HOH . F 5 HOH B 16 416 50 HOH HOH . F 5 HOH B 17 417 51 HOH HOH . F 5 HOH B 18 418 52 HOH HOH . F 5 HOH B 19 419 53 HOH HOH . F 5 HOH B 20 420 54 HOH HOH . F 5 HOH B 21 421 55 HOH HOH . F 5 HOH B 22 422 62 HOH HOH . F 5 HOH B 23 423 68 HOH HOH . G 5 HOH C 1 301 3 HOH HOH . G 5 HOH C 2 302 4 HOH HOH . G 5 HOH C 3 303 5 HOH HOH . G 5 HOH C 4 304 8 HOH HOH . G 5 HOH C 5 305 11 HOH HOH . G 5 HOH C 6 306 12 HOH HOH . G 5 HOH C 7 307 13 HOH HOH . G 5 HOH C 8 308 14 HOH HOH . G 5 HOH C 9 309 15 HOH HOH . G 5 HOH C 10 310 32 HOH HOH . G 5 HOH C 11 311 33 HOH HOH . G 5 HOH C 12 312 34 HOH HOH . G 5 HOH C 13 313 35 HOH HOH . G 5 HOH C 14 314 49 HOH HOH . G 5 HOH C 15 315 56 HOH HOH . G 5 HOH C 16 316 57 HOH HOH . G 5 HOH C 17 317 58 HOH HOH . G 5 HOH C 18 318 59 HOH HOH . G 5 HOH C 19 319 60 HOH HOH . G 5 HOH C 20 320 61 HOH HOH . G 5 HOH C 21 321 63 HOH HOH . G 5 HOH C 22 322 64 HOH HOH . G 5 HOH C 23 323 65 HOH HOH . G 5 HOH C 24 324 66 HOH HOH . G 5 HOH C 25 325 67 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 D _atom_site.label_entity_id 4 _atom_site.Cartn_x 62.552 _atom_site.Cartn_y -10.845 _atom_site.Cartn_z 115.948 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 56.11 _atom_site.pdbx_formal_charge ? _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 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 399 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 1 #