data_2WDR # _model_server_result.job_id y1Vf_llGpInc4yQBxp44mA _model_server_result.datetime_utc '2024-11-05 22:53:12' _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":"S","auth_seq_id":1130}' # _entry.id 2WDR # _exptl.entry_id 2WDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _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 ? 11 S N N ? 11 AA N N ? 11 IA 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 ? metalc ? metalc1 O NA NA . A NA 1590 1_555 A O GLY 358 A GLY 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc2 O NA NA . A NA 1590 1_555 A O GLU 388 A GLU 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc3 P FE1 FES . B FES 302 1_555 B SG CYS 55 B CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 P FE1 FES . B FES 302 1_555 B SG CYS 60 B CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc5 P FE2 FES . B FES 302 1_555 B OD1 ASP 63 B ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc6 P FE2 FES . B FES 302 1_555 B SG CYS 75 B CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc7 Q FE1 SF4 . B SF4 303 1_555 B SG CYS 155 B CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc8 Q FE2 SF4 . B SF4 303 1_555 B SG CYS 216 B CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc9 Q FE3 SF4 . B SF4 303 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc10 Q FE4 SF4 . B SF4 303 1_555 B SG CYS 152 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc11 R FE1 F3S . B F3S 304 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc12 R FE3 F3S . B F3S 304 1_555 B SG CYS 206 B CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc13 R FE4 F3S . B F3S 304 1_555 B SG CYS 212 B CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc14 S FE HEM . C HEM 1130 1_555 D NE2 HIS 71 D HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc15 S FE HEM . C HEM 1130 1_555 C NE2 HIS 84 C HIS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? covale ? covale2 E NE2 HIS 45 E HIS 45 1_555 U C8M FAD . E FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? metalc ? metalc16 W NA NA . E NA 1590 1_555 E O GLY 358 E GLY 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc17 X FE2 FES . F FES 302 1_555 F OD1 ASP 63 F ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc18 X FE1 FES . F FES 302 1_555 F SG CYS 55 F CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc19 X FE1 FES . F FES 302 1_555 F SG CYS 60 F CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc20 X FE2 FES . F FES 302 1_555 F SG CYS 75 F CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc21 Y FE3 SF4 . F SF4 303 1_555 F SG CYS 149 F CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc22 Y FE2 SF4 . F SF4 303 1_555 F SG CYS 216 F CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc23 Y FE1 SF4 . F SF4 303 1_555 F SG CYS 155 F CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc24 Y FE4 SF4 . F SF4 303 1_555 F SG CYS 152 F CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc25 Z FE3 F3S . F F3S 304 1_555 F SG CYS 206 F CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc26 Z FE4 F3S . F F3S 304 1_555 F SG CYS 212 F CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc27 Z FE1 F3S . F F3S 304 1_555 F SG CYS 159 F CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc28 AA FE HEM . G HEM 1130 1_555 H NE2 HIS 71 H HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc29 AA FE HEM . G HEM 1130 1_555 G NE2 HIS 84 G HIS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? covale ? covale3 I NE2 HIS 45 I HIS 45 1_555 CA C8M FAD . I FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? metalc ? metalc30 EA NA NA . I NA 1590 1_555 I O GLU 388 I GLU 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc31 FA FE2 FES . J FES 302 1_555 J OD1 ASP 63 J ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.802 ? metalc ? metalc32 FA FE2 FES . J FES 302 1_555 J OD2 ASP 63 J ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc33 FA FE2 FES . J FES 302 1_555 J SG CYS 75 J CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc34 FA FE1 FES . J FES 302 1_555 J SG CYS 60 J CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc35 FA FE1 FES . J FES 302 1_555 J SG CYS 55 J CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc36 GA FE4 SF4 . J SF4 303 1_555 J SG CYS 152 J CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc37 GA FE3 SF4 . J SF4 303 1_555 J SG CYS 149 J CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc38 GA FE2 SF4 . J SF4 303 1_555 J SG CYS 216 J CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc39 GA FE1 SF4 . J SF4 303 1_555 J SG CYS 155 J CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc40 HA FE3 F3S . J F3S 304 1_555 J SG CYS 206 J CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc41 HA FE1 F3S . J F3S 304 1_555 J SG CYS 159 J CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc42 HA FE4 F3S . J F3S 304 1_555 J SG CYS 212 J CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc43 IA FE HEM . K HEM 1130 1_555 L NE2 HIS 71 L HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc44 IA FE HEM . K HEM 1130 1_555 K NE2 HIS 84 K HIS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # _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 . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CHA HEM . . . S 11 55.438 -14.407 -34.147 1 40.67 ? CHA HEM 1130 C 1 HETATM 2 C CHB HEM . . . S 11 59.354 -13.353 -36.762 1 41.67 ? CHB HEM 1130 C 1 HETATM 3 C CHC HEM . . . S 11 62.369 -14.681 -33.179 1 41.12 ? CHC HEM 1130 C 1 HETATM 4 C CHD HEM . . . S 11 58.433 -15.401 -30.443 1 40.25 ? CHD HEM 1130 C 1 HETATM 5 C C1A HEM . . . S 11 56.251 -14.023 -35.188 1 40.64 ? C1A HEM 1130 C 1 HETATM 6 C C2A HEM . . . S 11 55.804 -13.618 -36.509 1 40.6 ? C2A HEM 1130 C 1 HETATM 7 C C3A HEM . . . S 11 56.889 -13.327 -37.23 1 40.2 ? C3A HEM 1130 C 1 HETATM 8 C C4A HEM . . . S 11 58.05 -13.544 -36.384 1 40.85 ? C4A HEM 1130 C 1 HETATM 9 C CMA HEM . . . S 11 56.92 -12.845 -38.697 1 38.77 ? CMA HEM 1130 C 1 HETATM 10 C CAA HEM . . . S 11 54.329 -13.535 -36.972 1 41.24 ? CAA HEM 1130 C 1 HETATM 11 C CBA HEM . . . S 11 53.782 -12.178 -36.551 1 42.76 ? CBA HEM 1130 C 1 HETATM 12 C CGA HEM . . . S 11 52.286 -12.163 -36.369 1 43.87 ? CGA HEM 1130 C 1 HETATM 13 O O1A HEM . . . S 11 51.754 -11.026 -36.234 1 43.79 ? O1A HEM 1130 C 1 HETATM 14 O O2A HEM . . . S 11 51.646 -13.257 -36.342 1 44.5 ? O2A HEM 1130 C 1 HETATM 15 C C1B HEM . . . S 11 60.483 -13.653 -36.043 1 41.5 ? C1B HEM 1130 C 1 HETATM 16 C C2B HEM . . . S 11 61.83 -13.584 -36.573 1 41.6 ? C2B HEM 1130 C 1 HETATM 17 C C3B HEM . . . S 11 62.662 -13.941 -35.611 1 41.5 ? C3B HEM 1130 C 1 HETATM 18 C C4B HEM . . . S 11 61.891 -14.262 -34.415 1 41.26 ? C4B HEM 1130 C 1 HETATM 19 C CMB HEM . . . S 11 62.253 -13.172 -37.999 1 41.34 ? CMB HEM 1130 C 1 HETATM 20 C CAB HEM . . . S 11 64.179 -13.986 -35.812 1 41.95 ? CAB HEM 1130 C 1 HETATM 21 C CBB HEM . . . S 11 64.927 -14.336 -34.769 1 44.04 ? CBB HEM 1130 C 1 HETATM 22 C C1C HEM . . . S 11 61.56 -14.972 -32.077 1 41.54 ? C1C HEM 1130 C 1 HETATM 23 C C2C HEM . . . S 11 61.979 -15.34 -30.723 1 40.28 ? C2C HEM 1130 C 1 HETATM 24 C C3C HEM . . . S 11 60.873 -15.534 -30.011 1 39.13 ? C3C HEM 1130 C 1 HETATM 25 C C4C HEM . . . S 11 59.726 -15.302 -30.844 1 39.57 ? C4C HEM 1130 C 1 HETATM 26 C CMC HEM . . . S 11 63.418 -15.487 -30.187 1 39.61 ? CMC HEM 1130 C 1 HETATM 27 C CAC HEM . . . S 11 60.776 -15.921 -28.543 1 38.02 ? CAC HEM 1130 C 1 HETATM 28 C CBC HEM . . . S 11 59.842 -15.287 -27.833 1 37.43 ? CBC HEM 1130 C 1 HETATM 29 C C1D HEM . . . S 11 57.309 -15.354 -31.218 1 40.43 ? C1D HEM 1130 C 1 HETATM 30 C C2D HEM . . . S 11 56.05 -15.935 -30.839 1 40.76 ? C2D HEM 1130 C 1 HETATM 31 C C3D HEM . . . S 11 55.095 -15.643 -31.982 1 40.8 ? C3D HEM 1130 C 1 HETATM 32 C C4D HEM . . . S 11 55.878 -14.898 -32.939 1 40.74 ? C4D HEM 1130 C 1 HETATM 33 C CMD HEM . . . S 11 55.731 -16.702 -29.54 1 41.14 ? CMD HEM 1130 C 1 HETATM 34 C CAD HEM . . . S 11 53.633 -16.109 -32.002 1 42.94 ? CAD HEM 1130 C 1 HETATM 35 C CBD HEM . . . S 11 52.712 -15.284 -32.89 1 46.22 ? CBD HEM 1130 C 1 HETATM 36 C CGD HEM . . . S 11 51.487 -16.14 -33.079 1 47.48 ? CGD HEM 1130 C 1 HETATM 37 O O1D HEM . . . S 11 51.538 -17.066 -33.94 1 46.87 ? O1D HEM 1130 C 1 HETATM 38 O O2D HEM . . . S 11 50.486 -15.903 -32.341 1 48.69 ? O2D HEM 1130 C 1 HETATM 39 N NA HEM . . . S 11 57.634 -13.974 -35.142 1 40.79 ? NA HEM 1130 C 1 HETATM 40 N NB HEM . . . S 11 60.545 -14.064 -34.723 1 41.2 ? NB HEM 1130 C 1 HETATM 41 N NC HEM . . . S 11 60.16 -14.963 -32.092 1 40.75 ? NC HEM 1130 C 1 HETATM 42 N ND HEM . . . S 11 57.176 -14.754 -32.449 1 40.78 ? ND HEM 1130 C 1 HETATM 43 FE FE HEM . . . S 11 58.888 -14.578 -33.525 1 41.08 ? FE HEM 1130 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #