data_2WDR # _model_server_result.job_id mtbkubOleXzKa0x_pAJzuw _model_server_result.datetime_utc '2024-11-23 17:28:14' _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 2wdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":1590}' # _entry.id 2WDR # _exptl.entry_id 2WDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 3 _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 2WDR _cell.length_a 119.955 _cell.length_b 186.128 _cell.length_c 204.034 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2WDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 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 PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA tetrameric 4 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,M,N,O,P,Q,R,S,T 1 1 E,F,G,H,U,V,W,X,Y,Z,AA,BA 2 1 I,J,K,L,CA,DA,EA,FA,GA,HA,IA,JA 3 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 ? 7 O N N ? 7 W N N ? 7 EA 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 A NE2 HIS 45 A HIS 45 1_555 M C8M FAD . A FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.507 ? covale ? covale2 E NE2 HIS 45 E HIS 45 1_555 U C8M FAD . E FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? covale ? covale3 I NE2 HIS 45 I HIS 45 1_555 CA C8M FAD . I FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? metalc ? metalc1 A O GLY 358 A GLY 358 1_555 O NA NA . A NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc2 A O GLU 388 A GLU 388 1_555 O NA NA . A NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc3 B SG CYS 55 B CYS 55 1_555 P FE1 FES . B FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 B SG CYS 60 B CYS 60 1_555 P FE1 FES . B FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc5 B OD1 ASP 63 B ASP 63 1_555 P FE2 FES . B FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc6 B SG CYS 75 B CYS 75 1_555 P FE2 FES . B FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc7 B SG CYS 149 B CYS 149 1_555 Q FE3 SF4 . B SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc8 B SG CYS 152 B CYS 152 1_555 Q FE4 SF4 . B SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc9 B SG CYS 155 B CYS 155 1_555 Q FE1 SF4 . B SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc10 B SG CYS 159 B CYS 159 1_555 R FE1 F3S . B F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc11 B SG CYS 206 B CYS 206 1_555 R FE3 F3S . B F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc12 B SG CYS 212 B CYS 212 1_555 R FE4 F3S . B F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc13 B SG CYS 216 B CYS 216 1_555 Q FE2 SF4 . B SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc14 C NE2 HIS 84 C HIS 84 1_555 S FE HEM . C HEM 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc15 S FE HEM . C HEM 1130 1_555 D NE2 HIS 71 D HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc16 E O GLY 358 E GLY 358 1_555 W NA NA . E NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc17 F SG CYS 55 F CYS 55 1_555 X FE1 FES . F FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc18 F SG CYS 60 F CYS 60 1_555 X FE1 FES . F FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc19 F OD1 ASP 63 F ASP 63 1_555 X FE2 FES . F FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc20 F SG CYS 75 F CYS 75 1_555 X FE2 FES . F FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc21 F SG CYS 149 F CYS 149 1_555 Y FE3 SF4 . F SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc22 F SG CYS 152 F CYS 152 1_555 Y FE4 SF4 . F SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc23 F SG CYS 155 F CYS 155 1_555 Y FE1 SF4 . F SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc24 F SG CYS 159 F CYS 159 1_555 Z FE1 F3S . F F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc25 F SG CYS 206 F CYS 206 1_555 Z FE3 F3S . F F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc26 F SG CYS 212 F CYS 212 1_555 Z FE4 F3S . F F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc27 F SG CYS 216 F CYS 216 1_555 Y FE2 SF4 . F SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc28 G NE2 HIS 84 G HIS 84 1_555 AA FE HEM . G HEM 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc29 AA FE HEM . G HEM 1130 1_555 H NE2 HIS 71 H HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc30 I O GLU 388 I GLU 388 1_555 EA NA NA . I NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc31 J SG CYS 55 J CYS 55 1_555 FA FE1 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc32 J SG CYS 60 J CYS 60 1_555 FA FE1 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc33 J OD1 ASP 63 J ASP 63 1_555 FA FE2 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.802 ? metalc ? metalc34 J OD2 ASP 63 J ASP 63 1_555 FA FE2 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc35 J SG CYS 75 J CYS 75 1_555 FA FE2 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc36 J SG CYS 149 J CYS 149 1_555 GA FE3 SF4 . J SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc37 J SG CYS 152 J CYS 152 1_555 GA FE4 SF4 . J SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc38 J SG CYS 155 J CYS 155 1_555 GA FE1 SF4 . J SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc39 J SG CYS 159 J CYS 159 1_555 HA FE1 F3S . J F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc40 J SG CYS 206 J CYS 206 1_555 HA FE3 F3S . J F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc41 J SG CYS 212 J CYS 212 1_555 HA FE4 F3S . J F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc42 J SG CYS 216 J CYS 216 1_555 GA FE2 SF4 . J SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc43 K NE2 HIS 84 K HIS 84 1_555 IA FE HEM . K HEM 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc44 IA FE HEM . K HEM 1130 1_555 L NE2 HIS 71 L HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? # _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 2WDR _atom_sites.fract_transf_matrix[1][1] 0.008336 _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] 0.005373 _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] 0.004901 _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 M 5 FAD A 1 601 601 FAD FAD . N 6 TEO A 1 1589 1589 TEO TEO . O 7 NA A 1 1590 1590 NA NA . P 8 FES B 1 302 302 FES FES . Q 9 SF4 B 1 303 303 SF4 SF4 . R 10 F3S B 1 304 304 F3S F3S . S 11 HEM C 1 1130 1130 HEM HEM . T 12 PCI C 1 1131 1131 PCI PCI . U 5 FAD E 1 601 601 FAD FAD . V 6 TEO E 1 1589 1589 TEO TEO . W 7 NA E 1 1590 1590 NA NA . X 8 FES F 1 302 302 FES FES . Y 9 SF4 F 1 303 303 SF4 SF4 . Z 10 F3S F 1 304 304 F3S F3S . AA 11 HEM G 1 1130 1130 HEM HEM . BA 12 PCI G 1 1131 1131 PCI PCI . CA 5 FAD I 1 601 601 FAD FAD . DA 6 TEO I 1 1589 1589 TEO TEO . EA 7 NA I 1 1590 1590 NA NA . FA 8 FES J 1 302 302 FES FES . GA 9 SF4 J 1 303 303 SF4 SF4 . HA 10 F3S J 1 304 304 F3S F3S . IA 11 HEM K 1 1130 1130 HEM HEM . JA 12 PCI K 1 1131 1131 PCI PCI . # _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 W _atom_site.label_entity_id 7 _atom_site.Cartn_x 7.954 _atom_site.Cartn_y -72.578 _atom_site.Cartn_z -27.716 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 12.1 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1590 _atom_site.auth_asym_id E _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #