data_2WDV # _model_server_result.job_id knhl56qG2WtT4bJIkscoUg _model_server_result.datetime_utc '2024-11-05 23:16:15' _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 2wdv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GA","auth_seq_id":1129}' # _entry.id 2WDV # _exptl.entry_id 2WDV _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 2WDV _cell.length_a 120.34 _cell.length_b 184.847 _cell.length_c 204.72 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2WDV _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 1 1 E,F,G,H,T,U,V,W,X,Y,Z 2 1 I,J,K,L,AA,BA,CA,DA,EA,FA,GA 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 Z N N ? 11 GA 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? metalc ? metalc1 O NA NA . A NA 1590 1_555 A O ALA 390 A ALA 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc2 O NA NA . A NA 1590 1_555 A O GLY 358 A GLY 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc3 O NA NA . A NA 1590 1_555 A O GLU 388 A GLU 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc4 O NA NA . A NA 1590 1_555 A O MET 356 A MET 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc5 P FE1 FES . B FES 302 1_555 B SG CYS 60 B CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc6 P FE1 FES . B FES 302 1_555 B SG CYS 55 B CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc7 P FE2 FES . B FES 302 1_555 B OD1 ASP 63 B ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? metalc ? metalc8 P FE2 FES . B FES 302 1_555 B SG CYS 75 B CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc9 Q FE1 SF4 . B SF4 303 1_555 B SG CYS 155 B CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc10 Q FE2 SF4 . B SF4 303 1_555 B SG CYS 216 B CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc11 Q FE3 SF4 . B SF4 303 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc12 Q FE4 SF4 . B SF4 303 1_555 B SG CYS 152 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc13 R FE1 F3S . B F3S 304 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc14 R FE3 F3S . B F3S 304 1_555 B SG CYS 206 B CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc15 R FE4 F3S . B F3S 304 1_555 B SG CYS 212 B CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc16 S FE HEM . C HEM 1129 1_555 D NE2 HIS 71 D HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc17 S FE HEM . C HEM 1129 1_555 C NE2 HIS 84 C HIS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? covale ? covale2 E NE2 HIS 45 E HIS 45 1_555 T C8M FAD . E FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.508 ? metalc ? metalc18 V NA NA . E NA 1590 1_555 E O GLY 358 E GLY 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc19 V NA NA . E NA 1590 1_555 E O MET 356 E MET 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc20 V NA NA . E NA 1590 1_555 E O GLU 388 E GLU 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc21 W FE1 FES . F FES 302 1_555 F SG CYS 60 F CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc22 W FE2 FES . F FES 302 1_555 F SG CYS 75 F CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc23 W FE2 FES . F FES 302 1_555 F OD1 ASP 63 F ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc24 W FE1 FES . F FES 302 1_555 F SG CYS 55 F CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc25 X FE2 SF4 . F SF4 303 1_555 F SG CYS 149 F CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc26 X FE3 SF4 . F SF4 303 1_555 F SG CYS 152 F CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc27 X FE4 SF4 . F SF4 303 1_555 F SG CYS 216 F CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc28 X FE1 SF4 . F SF4 303 1_555 F SG CYS 155 F CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc29 Y FE4 F3S . F F3S 304 1_555 F SG CYS 212 F CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc30 Y FE3 F3S . F F3S 304 1_555 F SG CYS 206 F CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc31 Y FE1 F3S . F F3S 304 1_555 F SG CYS 159 F CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc32 Z FE HEM . G HEM 1129 1_555 H NE2 HIS 71 H HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc33 Z FE HEM . G HEM 1129 1_555 G NE2 HIS 84 G HIS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? covale ? covale3 I NE2 HIS 45 I HIS 45 1_555 AA C8M FAD . I FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc34 DA FE2 FES . J FES 302 1_555 J OD1 ASP 63 J ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? metalc ? metalc35 DA FE2 FES . J FES 302 1_555 J SG CYS 75 J CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc36 DA FE2 FES . J FES 302 1_555 J OD2 ASP 63 J ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc37 DA FE1 FES . J FES 302 1_555 J SG CYS 60 J CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc38 DA FE1 FES . J FES 302 1_555 J SG CYS 55 J CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc39 EA FE4 SF4 . J SF4 303 1_555 J SG CYS 152 J CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc40 EA FE3 SF4 . J SF4 303 1_555 J SG CYS 149 J CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc41 EA FE2 SF4 . J SF4 303 1_555 J SG CYS 216 J CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc42 EA FE1 SF4 . J SF4 303 1_555 J SG CYS 155 J CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc43 FA FE3 F3S . J F3S 304 1_555 J SG CYS 206 J CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc44 FA FE1 F3S . J F3S 304 1_555 J SG CYS 159 J CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc45 FA FE4 F3S . J F3S 304 1_555 J SG CYS 212 J CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc46 GA FE HEM . K HEM 1129 1_555 L NE2 HIS 71 L HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc47 GA FE HEM . K HEM 1129 1_555 K NE2 HIS 84 K HIS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? # _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 2WDV _atom_sites.fract_transf_matrix[1][1] 0.00831 _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] 0.00541 _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] 0.004885 _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 1129 1129 HEM HEM . T 5 FAD E 1 601 601 FAD FAD . U 6 TEO E 1 1589 1589 TEO TEO . V 7 NA E 1 1590 1590 NA NA . W 8 FES F 1 302 302 FES FES . X 9 SF4 F 1 303 303 SF4 SF4 . Y 10 F3S F 1 304 304 F3S F3S . Z 11 HEM G 1 1129 1129 HEM HEM . AA 5 FAD I 1 601 601 FAD FAD . BA 6 TEO I 1 1589 1589 TEO TEO . CA 7 NA I 1 1590 1590 NA NA . DA 8 FES J 1 302 302 FES FES . EA 9 SF4 J 1 303 303 SF4 SF4 . FA 10 F3S J 1 304 304 F3S F3S . GA 11 HEM K 1 1129 1129 HEM HEM . # 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 . . . GA 11 58.868 -30.873 -64.916 1 55.86 ? CHA HEM 1129 K 1 HETATM 2 C CHB HEM . . . GA 11 63.385 -32.068 -63.705 1 55.02 ? CHB HEM 1129 K 1 HETATM 3 C CHC HEM . . . GA 11 64.798 -27.452 -64.213 1 55.31 ? CHC HEM 1129 K 1 HETATM 4 C CHD HEM . . . GA 11 60.275 -26.286 -65.463 1 55.94 ? CHD HEM 1129 K 1 HETATM 5 C C1A HEM . . . GA 11 59.973 -31.59 -64.542 1 55.3 ? C1A HEM 1129 K 1 HETATM 6 C C2A HEM . . . GA 11 59.977 -33.007 -64.248 1 55.96 ? C2A HEM 1129 K 1 HETATM 7 C C3A HEM . . . GA 11 61.225 -33.342 -63.906 1 55.4 ? C3A HEM 1129 K 1 HETATM 8 C C4A HEM . . . GA 11 62.04 -32.144 -63.976 1 54.82 ? C4A HEM 1129 K 1 HETATM 9 C CMA HEM . . . GA 11 61.739 -34.745 -63.505 1 55.01 ? CMA HEM 1129 K 1 HETATM 10 C CAA HEM . . . GA 11 58.738 -33.928 -64.346 1 58.12 ? CAA HEM 1129 K 1 HETATM 11 C CBA HEM . . . GA 11 58.011 -33.537 -65.634 1 61.36 ? CBA HEM 1129 K 1 HETATM 12 C CGA HEM . . . GA 11 56.84 -34.405 -65.985 1 64.18 ? CGA HEM 1129 K 1 HETATM 13 O O1A HEM . . . GA 11 56.573 -34.496 -67.216 1 65.6 ? O1A HEM 1129 K 1 HETATM 14 O O2A HEM . . . GA 11 56.184 -34.986 -65.07 1 65.54 ? O2A HEM 1129 K 1 HETATM 15 C C1B HEM . . . GA 11 64.156 -30.924 -63.737 1 55.35 ? C1B HEM 1129 K 1 HETATM 16 C C2B HEM . . . GA 11 65.561 -30.845 -63.393 1 55.62 ? C2B HEM 1129 K 1 HETATM 17 C C3B HEM . . . GA 11 65.956 -29.593 -63.527 1 55.59 ? C3B HEM 1129 K 1 HETATM 18 C C4B HEM . . . GA 11 64.817 -28.804 -63.966 1 54.97 ? C4B HEM 1129 K 1 HETATM 19 C CMB HEM . . . GA 11 66.48 -31.991 -62.932 1 56.25 ? CMB HEM 1129 K 1 HETATM 20 C CAB HEM . . . GA 11 67.4 -29.141 -63.24 1 56.14 ? CAB HEM 1129 K 1 HETATM 21 C CBB HEM . . . GA 11 67.623 -27.996 -62.595 1 57.04 ? CBB HEM 1129 K 1 HETATM 22 C C1C HEM . . . GA 11 63.688 -26.739 -64.623 1 55.97 ? C1C HEM 1129 K 1 HETATM 23 C C2C HEM . . . GA 11 63.672 -25.336 -65.007 1 56.47 ? C2C HEM 1129 K 1 HETATM 24 C C3C HEM . . . GA 11 62.428 -25.021 -65.353 1 56.07 ? C3C HEM 1129 K 1 HETATM 25 C C4C HEM . . . GA 11 61.613 -26.203 -65.198 1 55.12 ? C4C HEM 1129 K 1 HETATM 26 C CMC HEM . . . GA 11 64.886 -24.374 -65.019 1 56.66 ? CMC HEM 1129 K 1 HETATM 27 C CAC HEM . . . GA 11 61.973 -23.621 -65.824 1 57.4 ? CAC HEM 1129 K 1 HETATM 28 C CBC HEM . . . GA 11 60.838 -23.442 -66.517 1 58.43 ? CBC HEM 1129 K 1 HETATM 29 C C1D HEM . . . GA 11 59.448 -27.37 -65.281 1 56.11 ? C1D HEM 1129 K 1 HETATM 30 C C2D HEM . . . GA 11 58.007 -27.302 -65.147 1 56.84 ? C2D HEM 1129 K 1 HETATM 31 C C3D HEM . . . GA 11 57.553 -28.751 -64.976 1 57.09 ? C3D HEM 1129 K 1 HETATM 32 C C4D HEM . . . GA 11 58.772 -29.521 -65.017 1 55.92 ? C4D HEM 1129 K 1 HETATM 33 C CMD HEM . . . GA 11 57.113 -26.035 -65.167 1 55.93 ? CMD HEM 1129 K 1 HETATM 34 C CAD HEM . . . GA 11 56.102 -29.223 -64.745 1 59.77 ? CAD HEM 1129 K 1 HETATM 35 C CBD HEM . . . GA 11 55.478 -30.083 -65.835 1 63.35 ? CBD HEM 1129 K 1 HETATM 36 C CGD HEM . . . GA 11 54.097 -30.441 -65.336 1 64.99 ? CGD HEM 1129 K 1 HETATM 37 O O1D HEM . . . GA 11 53.134 -29.701 -65.693 1 65.48 ? O1D HEM 1129 K 1 HETATM 38 O O2D HEM . . . GA 11 53.968 -31.448 -64.575 1 65.41 ? O2D HEM 1129 K 1 HETATM 39 N NA HEM . . . GA 11 61.24 -31.092 -64.368 1 54.4 ? NA HEM 1129 K 1 HETATM 40 N NB HEM . . . GA 11 63.73 -29.651 -64.079 1 54.76 ? NB HEM 1129 K 1 HETATM 41 N NC HEM . . . GA 11 62.403 -27.237 -64.753 1 55.07 ? NC HEM 1129 K 1 HETATM 42 N ND HEM . . . GA 11 59.857 -28.689 -65.196 1 55.34 ? ND HEM 1129 K 1 HETATM 43 FE FE HEM . . . GA 11 61.766 -29.201 -64.504 1 54.34 ? FE HEM 1129 K 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #