data_5M7J # _model_server_result.job_id LXSYXF7tuGLw6aKwyq6Wcw _model_server_result.datetime_utc '2024-11-23 16:19:13' _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 5m7j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":404}' # _entry.id 5M7J # _exptl.entry_id 5M7J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 90 _cell.entry_id 5M7J _cell.length_a 57.9 _cell.length_b 84.8 _cell.length_c 384.3 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M7J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H 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 D C FME 1 D FME 1 1_555 D N TYR 2 D TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A NE2 HIS 111 A HIS 91 1_555 E FE HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc2 A NE2 HIS 144 A HIS 124 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc3 A NE2 HIS 156 A HIS 136 1_555 F FE HEC . A HEC 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc4 A NE2 HIS 268 A HIS 248 1_555 G FE HEC . A HEC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc5 A NE2 HIS 329 A HIS 309 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc6 B NE2 HIS 191 B HIS 190 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc7 B NE2 HIS 231 B HIS 230 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc8 P FE FE2 . B FE2 307 1_555 C NE2 HIS 218 C HIS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc9 P FE FE2 . B FE2 307 1_555 C OE1 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc10 P FE FE2 . B FE2 307 1_555 C OE2 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc11 P FE FE2 . B FE2 307 1_555 C NE2 HIS 265 C HIS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 FE NA HEC sing 561 n n FE NB HEC sing 562 n n FE NC HEC sing 563 n n FE ND HEC sing 564 n n CHA C1A HEC doub 565 n n CHA C4D HEC sing 566 n n CHA HHA HEC sing 567 n n CHB C4A HEC doub 568 n n CHB C1B HEC sing 569 n n CHB HHB HEC sing 570 n n CHC C4B HEC doub 571 n n CHC C1C HEC sing 572 n n CHC HHC HEC sing 573 n n CHD C4C HEC doub 574 n n CHD C1D HEC sing 575 n n CHD HHD HEC sing 576 n n NA C1A HEC sing 577 n y NA C4A HEC sing 578 n y C1A C2A HEC sing 579 n y C2A C3A HEC doub 580 n y C2A CAA HEC sing 581 n n C3A C4A HEC sing 582 n y C3A CMA HEC sing 583 n n CMA HMA1 HEC sing 584 n n CMA HMA2 HEC sing 585 n n CMA HMA3 HEC sing 586 n n CAA CBA HEC sing 587 n n CAA HAA1 HEC sing 588 n n CAA HAA2 HEC sing 589 n n CBA CGA HEC sing 590 n n CBA HBA1 HEC sing 591 n n CBA HBA2 HEC sing 592 n n CGA O1A HEC doub 593 n n CGA O2A HEC sing 594 n n O2A H2A HEC sing 595 n n NB C1B HEC sing 596 n y NB C4B HEC sing 597 n y C1B C2B HEC doub 598 n y C2B C3B HEC sing 599 n y C2B CMB HEC sing 600 n n C3B C4B HEC sing 601 n y C3B CAB HEC doub 602 e n CMB HMB1 HEC sing 603 n n CMB HMB2 HEC sing 604 n n CMB HMB3 HEC sing 605 n n CAB CBB HEC sing 606 n n CAB HAB HEC sing 607 n n CBB HBB1 HEC sing 608 n n CBB HBB2 HEC sing 609 n n CBB HBB3 HEC sing 610 n n NC C1C HEC sing 611 n y NC C4C HEC sing 612 n y C1C C2C HEC doub 613 n y C2C C3C HEC sing 614 n y C2C CMC HEC sing 615 n n C3C C4C HEC sing 616 n y C3C CAC HEC doub 617 e n CMC HMC1 HEC sing 618 n n CMC HMC2 HEC sing 619 n n CMC HMC3 HEC sing 620 n n CAC CBC HEC sing 621 n n CAC HAC HEC sing 622 n n CBC HBC1 HEC sing 623 n n CBC HBC2 HEC sing 624 n n CBC HBC3 HEC sing 625 n n ND C1D HEC sing 626 n y ND C4D HEC sing 627 n y C1D C2D HEC doub 628 n y C2D C3D HEC sing 629 n y C2D CMD HEC sing 630 n n C3D C4D HEC doub 631 n y C3D CAD HEC sing 632 n n CMD HMD1 HEC sing 633 n n CMD HMD2 HEC sing 634 n n CMD HMD3 HEC sing 635 n n CAD CBD HEC sing 636 n n CAD HAD1 HEC sing 637 n n CAD HAD2 HEC sing 638 n n CBD CGD HEC sing 639 n n CBD HBD1 HEC sing 640 n n CBD HBD2 HEC sing 641 n n CGD O1D HEC doub 642 n n CGD O2D HEC sing 643 n n O2D H2D HEC sing 644 n n # _atom_sites.entry_id 5M7J _atom_sites.fract_transf_matrix[1][1] 0.017271 _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] 0.011792 _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] 0.002602 _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 E 5 HEC A 1 401 1333 HEC HEM . F 5 HEC A 1 402 1334 HEC HEM . G 5 HEC A 1 403 1335 HEC HEM . H 5 HEC A 1 404 1336 HEC HEM . I 6 DGA A 1 405 1278 DGA DGA . J 7 BCL B 1 301 1274 BCL BCL . K 7 BCL B 1 302 1275 BCL BCL . L 7 BCL B 1 303 1276 BCL BCL . M 8 BPB B 1 304 1277 BPB BPB . N 9 MPG B 1 305 1279 MPG MPG . O 9 MPG B 1 306 1280 MPG MPG . P 10 FE2 B 1 307 1326 FE2 FE2 . Q 7 BCL C 1 401 1324 BCL BCL . R 8 BPB C 1 402 1325 BPB BPB . S 11 MQ7 C 1 403 1327 MQ7 MQ7 . T 12 NS5 C 1 404 1328 NS5 NS5 . U 13 OTP C 1 405 1329 OTP OTP . V 9 MPG C 1 406 1330 MPG MPG . W 14 PO4 C 1 407 1331 PO4 PO4 . X 14 PO4 C 1 408 1332 PO4 PO4 . # 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 FE FE HEC . . . H 5 -5.912 -22.998 87.99 1 30.42 ? FE HEC 404 A 1 HETATM 2 C CHA HEC . . . H 5 -7.511 -20.031 88.32 1 36.32 ? CHA HEC 404 A 1 HETATM 3 C CHB HEC . . . H 5 -4.497 -21.93 85.02 1 27.69 ? CHB HEC 404 A 1 HETATM 4 C CHC HEC . . . H 5 -4.391 -26.048 87.554 1 36.59 ? CHC HEC 404 A 1 HETATM 5 C CHD HEC . . . H 5 -7.177 -24.086 90.98 1 39.56 ? CHD HEC 404 A 1 HETATM 6 N NA HEC . . . H 5 -5.996 -21.3 86.857 1 37.91 ? NA HEC 404 A 1 HETATM 7 C C1A HEC . . . H 5 -6.705 -20.167 87.208 1 38.31 ? C1A HEC 404 A 1 HETATM 8 C C2A HEC . . . H 5 -6.451 -19.157 86.196 1 32.97 ? C2A HEC 404 A 1 HETATM 9 C C3A HEC . . . H 5 -5.621 -19.681 85.288 1 29.51 ? C3A HEC 404 A 1 HETATM 10 C C4A HEC . . . H 5 -5.316 -21.041 85.682 1 30.7 ? C4A HEC 404 A 1 HETATM 11 C CMA HEC . . . H 5 -5.08 -18.964 84.034 1 29.85 ? CMA HEC 404 A 1 HETATM 12 C CAA HEC . . . H 5 -7.034 -17.726 86.171 1 25.99 ? CAA HEC 404 A 1 HETATM 13 C CBA HEC . . . H 5 -8.249 -17.69 85.249 1 24.32 ? CBA HEC 404 A 1 HETATM 14 C CGA HEC . . . H 5 -8.944 -16.362 85.376 1 25.74 ? CGA HEC 404 A 1 HETATM 15 O O1A HEC . . . H 5 -8.464 -15.515 86.169 1 36.69 ? O1A HEC 404 A 1 HETATM 16 O O2A HEC . . . H 5 -9.975 -16.15 84.689 1 24.79 ? O2A HEC 404 A 1 HETATM 17 N NB HEC . . . H 5 -4.786 -23.896 86.451 1 28.13 ? NB HEC 404 A 1 HETATM 18 C C1B HEC . . . H 5 -4.092 -23.144 85.525 1 27.36 ? C1B HEC 404 A 1 HETATM 19 C C2B HEC . . . H 5 -2.869 -23.846 85.188 1 34.01 ? C2B HEC 404 A 1 HETATM 20 C C3B HEC . . . H 5 -2.84 -24.991 85.89 1 33.38 ? C3B HEC 404 A 1 HETATM 21 C C4B HEC . . . H 5 -4.043 -25.035 86.691 1 33.6 ? C4B HEC 404 A 1 HETATM 22 C CMB HEC . . . H 5 -1.828 -23.319 84.179 1 42.66 ? CMB HEC 404 A 1 HETATM 23 C CAB HEC . . . H 5 -1.77 -26.111 85.933 1 34.35 ? CAB HEC 404 A 1 HETATM 24 C CBB HEC . . . H 5 -0.601 -26.091 85.279 1 40.73 ? CBB HEC 404 A 1 HETATM 25 N NC HEC . . . H 5 -5.867 -24.781 89.034 1 39.32 ? NC HEC 404 A 1 HETATM 26 C C1C HEC . . . H 5 -5.05 -25.854 88.743 1 37.69 ? C1C HEC 404 A 1 HETATM 27 C C2C HEC . . . H 5 -5.004 -26.727 89.896 1 39.43 ? C2C HEC 404 A 1 HETATM 28 C C3C HEC . . . H 5 -5.782 -26.186 90.852 1 46.78 ? C3C HEC 404 A 1 HETATM 29 C C4C HEC . . . H 5 -6.331 -24.95 90.321 1 41.76 ? C4C HEC 404 A 1 HETATM 30 C CMC HEC . . . H 5 -4.184 -28.036 89.945 1 39.09 ? CMC HEC 404 A 1 HETATM 31 C CAC HEC . . . H 5 -6.072 -26.691 92.289 1 48.65 ? CAC HEC 404 A 1 HETATM 32 C CBC HEC . . . H 5 -5.548 -27.796 92.839 1 40.67 ? CBC HEC 404 A 1 HETATM 33 N ND HEC . . . H 5 -7.083 -22.191 89.413 1 32.23 ? ND HEC 404 A 1 HETATM 34 C C1D HEC . . . H 5 -7.564 -22.841 90.534 1 40.23 ? C1D HEC 404 A 1 HETATM 35 C C2D HEC . . . H 5 -8.549 -21.982 91.157 1 45.96 ? C2D HEC 404 A 1 HETATM 36 C C3D HEC . . . H 5 -8.641 -20.863 90.433 1 41.89 ? C3D HEC 404 A 1 HETATM 37 C C4D HEC . . . H 5 -7.722 -20.97 89.312 1 35.3 ? C4D HEC 404 A 1 HETATM 38 C CMD HEC . . . H 5 -9.346 -22.3 92.441 1 37.76 ? CMD HEC 404 A 1 HETATM 39 C CAD HEC . . . H 5 -9.578 -19.674 90.739 1 40.82 ? CAD HEC 404 A 1 HETATM 40 C CBD HEC . . . H 5 -8.737 -18.428 90.992 1 43.77 ? CBD HEC 404 A 1 HETATM 41 C CGD HEC . . . H 5 -9.585 -17.199 90.815 1 46.48 ? CGD HEC 404 A 1 HETATM 42 O O1D HEC . . . H 5 -10.812 -17.267 91.088 1 41.43 ? O1D HEC 404 A 1 HETATM 43 O O2D HEC . . . H 5 -9.022 -16.15 90.405 1 48.39 ? O2D HEC 404 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #