data_4PYK # _model_server_result.job_id DQrI_gLmvNkqwsC5km3DrQ _model_server_result.datetime_utc '2024-11-25 04:01:38' _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 4pyk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4PYK # _exptl.entry_id 4PYK _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 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 4PYK _cell.length_a 54.786 _cell.length_b 66.825 _cell.length_c 128.032 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PYK _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 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 1 1 A,B,C,D,E 2 1,2 # 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 OD1 ASP 141 A ASP 191 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc2 A OD2 ASP 169 A ASP 219 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc3 A OD1 ASN 170 A ASN 220 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc4 A O VAL 183 A VAL 233 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc5 A O ARG 184 A ARG 234 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc6 A O SER 186 A SER 236 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc7 A O PHE 189 A PHE 239 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc8 A OE2 GLU 202 A GLU 252 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc9 B NA NA . A NA 301 1_555 E O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc10 B NA NA . A NA 301 1_555 E O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc11 C MG MG . A MG 302 1_555 E O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? # _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 4PYK _atom_sites.fract_transf_matrix[1][1] 0.018253 _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] 0.014964 _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] 0.007811 _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 3 MG A 1 302 303 MG MG . D 4 CL A 1 303 302 CL CL . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 2 HOH HOH . E 5 HOH A 3 403 3 HOH HOH . E 5 HOH A 4 404 4 HOH HOH . E 5 HOH A 5 405 5 HOH HOH . E 5 HOH A 6 406 6 HOH HOH . E 5 HOH A 7 407 7 HOH HOH . E 5 HOH A 8 408 8 HOH HOH . E 5 HOH A 9 409 9 HOH HOH . E 5 HOH A 10 410 10 HOH HOH . E 5 HOH A 11 411 11 HOH HOH . E 5 HOH A 12 412 12 HOH HOH . E 5 HOH A 13 413 13 HOH HOH . E 5 HOH A 14 414 14 HOH HOH . E 5 HOH A 15 415 15 HOH HOH . E 5 HOH A 16 416 16 HOH HOH . E 5 HOH A 17 417 17 HOH HOH . E 5 HOH A 18 418 18 HOH HOH . E 5 HOH A 19 419 19 HOH HOH . E 5 HOH A 20 420 20 HOH HOH . E 5 HOH A 21 421 21 HOH HOH . E 5 HOH A 22 422 22 HOH HOH . E 5 HOH A 23 423 23 HOH HOH . E 5 HOH A 24 424 24 HOH HOH . E 5 HOH A 25 425 25 HOH HOH . E 5 HOH A 26 426 26 HOH HOH . E 5 HOH A 27 427 27 HOH HOH . E 5 HOH A 28 428 28 HOH HOH . E 5 HOH A 29 429 29 HOH HOH . E 5 HOH A 30 430 30 HOH HOH . E 5 HOH A 31 431 31 HOH HOH . E 5 HOH A 32 432 32 HOH HOH . E 5 HOH A 33 433 33 HOH HOH . E 5 HOH A 34 434 34 HOH HOH . E 5 HOH A 35 435 35 HOH HOH . E 5 HOH A 36 436 36 HOH HOH . E 5 HOH A 37 437 37 HOH HOH . E 5 HOH A 38 438 38 HOH HOH . E 5 HOH A 39 439 39 HOH HOH . E 5 HOH A 40 440 40 HOH HOH . E 5 HOH A 41 441 41 HOH HOH . E 5 HOH A 42 442 42 HOH HOH . E 5 HOH A 43 443 43 HOH HOH . E 5 HOH A 44 444 44 HOH HOH . E 5 HOH A 45 445 45 HOH HOH . E 5 HOH A 46 446 46 HOH HOH . E 5 HOH A 47 447 47 HOH HOH . E 5 HOH A 48 448 48 HOH HOH . E 5 HOH A 49 449 49 HOH HOH . E 5 HOH A 50 450 50 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 6.922 _atom_site.Cartn_y 6.379 _atom_site.Cartn_z -22.056 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 38.89 _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 9 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #