data_2E76 # _model_server_result.job_id ymdsRxIQVPS6yy7jfVk9ug _model_server_result.datetime_utc '2024-11-22 06:03:01' _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 2e76 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":301}' # _entry.id 2E76 # _exptl.entry_id 2E76 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _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 120 _cell.entry_id 2E76 _cell.length_a 157.227 _cell.length_b 157.227 _cell.length_c 363.295 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2E76 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -78.6135 136.162576 60.549167 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 10 J N N ? 10 K N N ? 10 L N N ? 10 V 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 disulf ? disulf1 D SG CYS 108 D CYS 108 1_555 D SG CYS 126 D CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? disulf ? disulf2 D SG CYS 113 D CYS 113 1_555 D SG CYS 128 D CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A SG CYS 35 A CYS 35 1_555 L CAB HEM . A HEM 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? covale ? covale2 C SG CYS 25 C CYS 25 1_555 V CAC HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc1 A OE2 GLU 75 A GLU 75 1_555 I CD CD . A CD 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc2 A NE2 HIS 86 A HIS 86 1_555 J FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.73 ? metalc ? metalc3 A NE2 HIS 100 A HIS 100 1_555 K FE HEM . A HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc4 A NE2 HIS 187 A HIS 187 1_555 J FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc5 A NE2 HIS 202 A HIS 202 1_555 K FE HEM . A HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc6 I CD CD . A CD 216 1_555 C NE2 HIS 143 C HIS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc7 I CD CD . A CD 216 1_555 BA O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc8 L FE HEM . A HEM 303 1_555 Z O HOH . A HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc9 L FE HEM . A HEM 303 1_555 U OBD TDS . B TDS 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? metalc ? metalc10 R MG CLA . B CLA 201 1_555 AA O HOH . B HOH 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? metalc ? metalc11 C N TYR 1 C TYR 1 1_555 V FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc12 C NE2 HIS 26 C HIS 26 1_555 V FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc13 D SG CYS 108 D CYS 108 1_555 W FE1 FES . D FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc14 D ND1 HIS 110 D HIS 110 1_555 W FE2 FES . D FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc15 D SG CYS 126 D CYS 126 1_555 W FE1 FES . D FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc16 D ND1 HIS 129 D HIS 129 1_555 W FE2 FES . D FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.748 ? # _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 # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag CHA C1A HEM sing 375 n n CHA C4D HEM doub 376 n n CHA HHA HEM sing 377 n n CHB C4A HEM sing 378 n n CHB C1B HEM doub 379 n n CHB HHB HEM sing 380 n n CHC C4B HEM sing 381 n n CHC C1C HEM doub 382 n n CHC HHC HEM sing 383 n n CHD C4C HEM doub 384 n n CHD C1D HEM sing 385 n n CHD HHD HEM sing 386 n n C1A C2A HEM doub 387 n y C1A NA HEM sing 388 n y C2A C3A HEM sing 389 n y C2A CAA HEM sing 390 n n C3A C4A HEM doub 391 n y C3A CMA HEM sing 392 n n C4A NA HEM sing 393 n y CMA HMA HEM sing 394 n n CMA HMAA HEM sing 395 n n CMA HMAB HEM sing 396 n n CAA CBA HEM sing 397 n n CAA HAA HEM sing 398 n n CAA HAAA HEM sing 399 n n CBA CGA HEM sing 400 n n CBA HBA HEM sing 401 n n CBA HBAA HEM sing 402 n n CGA O1A HEM doub 403 n n CGA O2A HEM sing 404 n n C1B C2B HEM sing 405 n n C1B NB HEM sing 406 n n C2B C3B HEM doub 407 n n C2B CMB HEM sing 408 n n C3B C4B HEM sing 409 n n C3B CAB HEM sing 410 n n C4B NB HEM doub 411 n n CMB HMB HEM sing 412 n n CMB HMBA HEM sing 413 n n CMB HMBB HEM sing 414 n n CAB CBB HEM doub 415 n n CAB HAB HEM sing 416 n n CBB HBB HEM sing 417 n n CBB HBBA HEM sing 418 n n C1C C2C HEM sing 419 n y C1C NC HEM sing 420 n y C2C C3C HEM doub 421 n y C2C CMC HEM sing 422 n n C3C C4C HEM sing 423 n y C3C CAC HEM sing 424 n n C4C NC HEM sing 425 n y CMC HMC HEM sing 426 n n CMC HMCA HEM sing 427 n n CMC HMCB HEM sing 428 n n CAC CBC HEM doub 429 n n CAC HAC HEM sing 430 n n CBC HBC HEM sing 431 n n CBC HBCA HEM sing 432 n n C1D C2D HEM sing 433 n n C1D ND HEM doub 434 n n C2D C3D HEM doub 435 n n C2D CMD HEM sing 436 n n C3D C4D HEM sing 437 n n C3D CAD HEM sing 438 n n C4D ND HEM sing 439 n n CMD HMD HEM sing 440 n n CMD HMDA HEM sing 441 n n CMD HMDB HEM sing 442 n n CAD CBD HEM sing 443 n n CAD HAD HEM sing 444 n n CAD HADA HEM sing 445 n n CBD CGD HEM sing 446 n n CBD HBD HEM sing 447 n n CBD HBDA HEM sing 448 n n CGD O1D HEM doub 449 n n CGD O2D HEM sing 450 n n O2A H2A HEM sing 451 n n O2D H2D HEM sing 452 n n FE NA HEM sing 453 n n FE NB HEM sing 454 n n FE NC HEM sing 455 n n FE ND HEM sing 456 n n # _atom_sites.entry_id 2E76 _atom_sites.fract_transf_matrix[1][1] 0.00636 _atom_sites.fract_transf_matrix[1][2] 0.003672 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007344 _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] 0.002753 _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 I 9 CD A 1 216 1 CD CD . J 10 HEM A 1 301 301 HEM HEM . K 10 HEM A 1 302 302 HEM HEM . L 10 HEM A 1 303 303 HEM HEM . M 11 OPC A 1 1002 1002 OPC OPC . N 12 UMQ A 1 1101 1101 UMQ UMQ . O 12 UMQ A 1 1102 1102 UMQ UMQ . P 12 UMQ A 1 1103 1103 UMQ UMQ . Q 12 UMQ A 1 1104 1104 UMQ UMQ . R 13 CLA B 1 201 201 CLA CLA . S 11 OPC B 1 1001 1001 OPC OPC . T 14 TDS B 1 1201 1201 TDS TDS . U 14 TDS B 1 1202 1202 TDS TDS . V 10 HEM C 1 301 301 HEM HEM . W 15 FES D 1 200 200 FES FES . X 16 SQD D 1 201 11 SQD SQD . Y 17 BCR G 1 101 101 BCR BCR . Z 18 HOH A 1 1105 3 HOH HOH . Z 18 HOH A 2 1106 401 HOH HOH . AA 18 HOH B 1 211 211 HOH HOH . AA 18 HOH B 2 212 212 HOH HOH . BA 18 HOH C 1 302 2 HOH HOH . # 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 . . . V 10 -71.907 42.447 -13.249 1 27.54 ? CHA HEM 301 C 1 HETATM 2 C CHB HEM . . . V 10 -70.683 46.42 -10.813 1 37.6 ? CHB HEM 301 C 1 HETATM 3 C CHC HEM . . . V 10 -70.927 44.214 -6.495 1 18.27 ? CHC HEM 301 C 1 HETATM 4 C CHD HEM . . . V 10 -71.52 40.174 -9.048 1 35.16 ? CHD HEM 301 C 1 HETATM 5 C C1A HEM . . . V 10 -71.597 43.739 -12.837 1 40.94 ? C1A HEM 301 C 1 HETATM 6 C C2A HEM . . . V 10 -71.543 44.773 -13.784 1 36.87 ? C2A HEM 301 C 1 HETATM 7 C C3A HEM . . . V 10 -71.237 45.907 -13.17 1 44.58 ? C3A HEM 301 C 1 HETATM 8 C C4A HEM . . . V 10 -71.065 45.568 -11.763 1 15.53 ? C4A HEM 301 C 1 HETATM 9 C CMA HEM . . . V 10 -71.074 47.294 -13.895 1 17.4 ? CMA HEM 301 C 1 HETATM 10 C CAA HEM . . . V 10 -71.837 44.48 -15.268 1 69.02 ? CAA HEM 301 C 1 HETATM 11 C CBA HEM . . . V 10 -70.687 44.786 -16.235 1 69.13 ? CBA HEM 301 C 1 HETATM 12 C CGA HEM . . . V 10 -71.186 44.682 -17.669 1 79.17 ? CGA HEM 301 C 1 HETATM 13 O O1A HEM . . . V 10 -71.956 43.692 -17.973 1 89.67 ? O1A HEM 301 C 1 HETATM 14 O O2A HEM . . . V 10 -70.82 45.608 -18.472 1 51.75 ? O2A HEM 301 C 1 HETATM 15 C C1B HEM . . . V 10 -70.538 46.176 -9.499 1 27.79 ? C1B HEM 301 C 1 HETATM 16 C C2B HEM . . . V 10 -69.969 47.1 -8.508 1 49.54 ? C2B HEM 301 C 1 HETATM 17 C C3B HEM . . . V 10 -70.054 46.434 -7.319 1 34.82 ? C3B HEM 301 C 1 HETATM 18 C C4B HEM . . . V 10 -70.657 45.147 -7.513 1 39.8 ? C4B HEM 301 C 1 HETATM 19 C CMB HEM . . . V 10 -69.343 48.548 -8.788 1 20.83 ? CMB HEM 301 C 1 HETATM 20 C CAB HEM . . . V 10 -69.649 46.969 -5.943 1 37.64 ? CAB HEM 301 C 1 HETATM 21 C CBB HEM . . . V 10 -69.975 48.289 -5.925 1 18.32 ? CBB HEM 301 C 1 HETATM 22 C C1C HEM . . . V 10 -71.157 42.899 -6.845 1 20.55 ? C1C HEM 301 C 1 HETATM 23 C C2C HEM . . . V 10 -71.4 41.817 -5.962 1 11.63 ? C2C HEM 301 C 1 HETATM 24 C C3C HEM . . . V 10 -71.522 40.741 -6.705 1 29.24 ? C3C HEM 301 C 1 HETATM 25 C C4C HEM . . . V 10 -71.422 41.092 -8.088 1 17.6 ? C4C HEM 301 C 1 HETATM 26 C CMC HEM . . . V 10 -71.547 41.827 -4.447 1 30.27 ? CMC HEM 301 C 1 HETATM 27 C CAC HEM . . . V 10 -71.789 39.301 -6.211 1 12.68 ? CAC HEM 301 C 1 HETATM 28 C CBC HEM . . . V 10 -72.113 39.094 -4.937 1 3.76 ? CBC HEM 301 C 1 HETATM 29 C C1D HEM . . . V 10 -71.604 40.337 -10.38 1 49.3 ? C1D HEM 301 C 1 HETATM 30 C C2D HEM . . . V 10 -71.581 39.267 -11.403 1 60.75 ? C2D HEM 301 C 1 HETATM 31 C C3D HEM . . . V 10 -71.676 40.005 -12.732 1 41.17 ? C3D HEM 301 C 1 HETATM 32 C C4D HEM . . . V 10 -71.797 41.397 -12.37 1 48.37 ? C4D HEM 301 C 1 HETATM 33 C CMD HEM . . . V 10 -71.459 37.722 -11.242 1 26.24 ? CMD HEM 301 C 1 HETATM 34 C CAD HEM . . . V 10 -71.796 39.414 -14.137 1 71.62 ? CAD HEM 301 C 1 HETATM 35 C CBD HEM . . . V 10 -73.283 39.79 -14.483 1 104.02 ? CBD HEM 301 C 1 HETATM 36 C CGD HEM . . . V 10 -74.188 38.936 -15.389 1 91.55 ? CGD HEM 301 C 1 HETATM 37 O O1D HEM . . . V 10 -74.896 37.989 -14.903 1 70.95 ? O1D HEM 301 C 1 HETATM 38 O O2D HEM . . . V 10 -74.233 39.25 -16.613 1 67.34 ? O2D HEM 301 C 1 HETATM 39 N NA HEM . . . V 10 -71.298 44.275 -11.58 1 22.89 ? NA HEM 301 C 1 HETATM 40 N NB HEM . . . V 10 -70.936 45.037 -8.897 1 33.16 ? NB HEM 301 C 1 HETATM 41 N NC HEM . . . V 10 -71.164 42.395 -8.166 1 25.84 ? NC HEM 301 C 1 HETATM 42 N ND HEM . . . V 10 -71.726 41.56 -10.969 1 40.73 ? ND HEM 301 C 1 HETATM 43 FE FE HEM . . . V 10 -71.268 43.302 -9.97 1 31.87 ? FE HEM 301 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 43 #