data_6GD9 # _model_server_result.job_id REiEaHdereJkEPA-fwmEDw _model_server_result.datetime_utc '2024-11-26 23:21:14' _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 6gd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6GD9 # _exptl.entry_id 6GD9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _entity.pdbx_number_of_molecules 1 _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 6GD9 _cell.length_a 101.59 _cell.length_b 101.59 _cell.length_c 86.52 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GD9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 19 A CYS 14 1_555 B CAB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? covale ? covale2 A SG CYS 19 A CYS 14 1_555 B CBB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? covale ? covale3 A SG CYS 22 A CYS 17 1_555 B CAC HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.655 ? metalc ? metalc1 A NE2 HIS 23 A HIS 18 1_555 B FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc2 A SD MET 85 A MET 80 1_555 B FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? # _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 314 n n FE NB HEC sing 315 n n FE NC HEC sing 316 n n FE ND HEC sing 317 n n CHA C1A HEC doub 318 n n CHA C4D HEC sing 319 n n CHA HHA HEC sing 320 n n CHB C4A HEC doub 321 n n CHB C1B HEC sing 322 n n CHB HHB HEC sing 323 n n CHC C4B HEC doub 324 n n CHC C1C HEC sing 325 n n CHC HHC HEC sing 326 n n CHD C4C HEC doub 327 n n CHD C1D HEC sing 328 n n CHD HHD HEC sing 329 n n NA C1A HEC sing 330 n y NA C4A HEC sing 331 n y C1A C2A HEC sing 332 n y C2A C3A HEC doub 333 n y C2A CAA HEC sing 334 n n C3A C4A HEC sing 335 n y C3A CMA HEC sing 336 n n CMA HMA1 HEC sing 337 n n CMA HMA2 HEC sing 338 n n CMA HMA3 HEC sing 339 n n CAA CBA HEC sing 340 n n CAA HAA1 HEC sing 341 n n CAA HAA2 HEC sing 342 n n CBA CGA HEC sing 343 n n CBA HBA1 HEC sing 344 n n CBA HBA2 HEC sing 345 n n CGA O1A HEC doub 346 n n CGA O2A HEC sing 347 n n O2A H2A HEC sing 348 n n NB C1B HEC sing 349 n y NB C4B HEC sing 350 n y C1B C2B HEC doub 351 n y C2B C3B HEC sing 352 n y C2B CMB HEC sing 353 n n C3B C4B HEC sing 354 n y C3B CAB HEC doub 355 e n CMB HMB1 HEC sing 356 n n CMB HMB2 HEC sing 357 n n CMB HMB3 HEC sing 358 n n CAB CBB HEC sing 359 n n CAB HAB HEC sing 360 n n CBB HBB1 HEC sing 361 n n CBB HBB2 HEC sing 362 n n CBB HBB3 HEC sing 363 n n NC C1C HEC sing 364 n y NC C4C HEC sing 365 n y C1C C2C HEC doub 366 n y C2C C3C HEC sing 367 n y C2C CMC HEC sing 368 n n C3C C4C HEC sing 369 n y C3C CAC HEC doub 370 e n CMC HMC1 HEC sing 371 n n CMC HMC2 HEC sing 372 n n CMC HMC3 HEC sing 373 n n CAC CBC HEC sing 374 n n CAC HAC HEC sing 375 n n CBC HBC1 HEC sing 376 n n CBC HBC2 HEC sing 377 n n CBC HBC3 HEC sing 378 n n ND C1D HEC sing 379 n y ND C4D HEC sing 380 n y C1D C2D HEC doub 381 n y C2D C3D HEC sing 382 n y C2D CMD HEC sing 383 n n C3D C4D HEC doub 384 n y C3D CAD HEC sing 385 n n CMD HMD1 HEC sing 386 n n CMD HMD2 HEC sing 387 n n CMD HMD3 HEC sing 388 n n CAD CBD HEC sing 389 n n CAD HAD1 HEC sing 390 n n CAD HAD2 HEC sing 391 n n CBD CGD HEC sing 392 n n CBD HBD1 HEC sing 393 n n CBD HBD2 HEC sing 394 n n CGD O1D HEC doub 395 n n CGD O2D HEC sing 396 n n O2D H2D HEC sing 397 n n # _atom_sites.entry_id 6GD9 _atom_sites.fract_transf_matrix[1][1] 0.009843 _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] 0.009843 _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] 0.011558 _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 B 2 HEC A 1 201 118 HEC HEM . C 3 EVB A 1 202 1 EVB SC8 . D 3 EVB A 1 203 2 EVB SC8 . E 3 EVB A 1 204 3 EVB SC8 . F 4 EPE A 1 205 1 EPE EPE . G 4 EPE A 1 206 2 EPE EPE . H 4 EPE A 1 207 3 EPE EPE . I 4 EPE A 1 208 4 EPE EPE . J 5 SO4 A 1 209 1 SO4 SO4 . K 5 SO4 A 1 210 3 SO4 SO4 . L 5 SO4 A 1 211 4 SO4 SO4 . M 6 HOH A 1 301 37 HOH HOH . M 6 HOH A 2 302 16 HOH HOH . M 6 HOH A 3 303 7 HOH HOH . M 6 HOH A 4 304 21 HOH HOH . M 6 HOH A 5 305 12 HOH HOH . M 6 HOH A 6 306 30 HOH HOH . M 6 HOH A 7 307 17 HOH HOH . M 6 HOH A 8 308 2 HOH HOH . M 6 HOH A 9 309 27 HOH HOH . M 6 HOH A 10 310 18 HOH HOH . M 6 HOH A 11 311 34 HOH HOH . M 6 HOH A 12 312 14 HOH HOH . M 6 HOH A 13 313 29 HOH HOH . M 6 HOH A 14 314 9 HOH HOH . M 6 HOH A 15 315 11 HOH HOH . M 6 HOH A 16 316 3 HOH HOH . M 6 HOH A 17 317 15 HOH HOH . M 6 HOH A 18 318 36 HOH HOH . M 6 HOH A 19 319 28 HOH HOH . M 6 HOH A 20 320 6 HOH HOH . M 6 HOH A 21 321 1 HOH HOH . M 6 HOH A 22 322 8 HOH HOH . M 6 HOH A 23 323 10 HOH HOH . M 6 HOH A 24 324 13 HOH HOH . M 6 HOH A 25 325 5 HOH HOH . M 6 HOH A 26 326 4 HOH HOH . M 6 HOH A 27 327 35 HOH HOH . M 6 HOH A 28 328 25 HOH HOH . M 6 HOH A 29 329 33 HOH HOH . M 6 HOH A 30 330 19 HOH HOH . M 6 HOH A 31 331 22 HOH HOH . M 6 HOH A 32 332 20 HOH HOH . M 6 HOH A 33 333 23 HOH HOH . M 6 HOH A 34 334 24 HOH HOH . M 6 HOH A 35 335 32 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 FE FE HEC . . . B 2 -34.569 -2.719 2.345 1 31.68 ? FE HEC 201 A 1 HETATM 2 C CHA HEC . . . B 2 -35.77 -0.649 0.026 1 31.8 ? CHA HEC 201 A 1 HETATM 3 C CHB HEC . . . B 2 -32.824 -4.499 -0.067 1 31.66 ? CHB HEC 201 A 1 HETATM 4 C CHC HEC . . . B 2 -32.898 -4.596 4.802 1 32.32 ? CHC HEC 201 A 1 HETATM 5 C CHD HEC . . . B 2 -36.573 -1.47 4.753 1 32.18 ? CHD HEC 201 A 1 HETATM 6 N NA HEC . . . B 2 -34.363 -2.639 0.372 1 31.8 ? NA HEC 201 A 1 HETATM 7 C C1A HEC . . . B 2 -34.913 -1.639 -0.397 1 31.57 ? C1A HEC 201 A 1 HETATM 8 C C2A HEC . . . B 2 -34.496 -1.829 -1.732 1 31.27 ? C2A HEC 201 A 1 HETATM 9 C C3A HEC . . . B 2 -33.68 -2.915 -1.759 1 31.3 ? C3A HEC 201 A 1 HETATM 10 C C4A HEC . . . B 2 -33.588 -3.415 -0.448 1 31.5 ? C4A HEC 201 A 1 HETATM 11 C CMA HEC . . . B 2 -32.991 -3.483 -2.974 1 31.41 ? CMA HEC 201 A 1 HETATM 12 C CAA HEC . . . B 2 -34.873 -0.994 -2.93 1 31.02 ? CAA HEC 201 A 1 HETATM 13 C CBA HEC . . . B 2 -36.069 -1.656 -3.618 1 30.99 ? CBA HEC 201 A 1 HETATM 14 C CGA HEC . . . B 2 -36.493 -0.89 -4.845 1 30.86 ? CGA HEC 201 A 1 HETATM 15 O O1A HEC . . . B 2 -37.476 -1.286 -5.514 1 30.35 ? O1A HEC 201 A 1 HETATM 16 O O2A HEC . . . B 2 -35.87 0.136 -5.203 1 30.94 ? O2A HEC 201 A 1 HETATM 17 N NB HEC . . . B 2 -33.13 -4.266 2.362 1 31.98 ? NB HEC 201 A 1 HETATM 18 C C1B HEC . . . B 2 -32.585 -4.831 1.275 1 31.86 ? C1B HEC 201 A 1 HETATM 19 C C2B HEC . . . B 2 -31.646 -5.835 1.662 1 31.95 ? C2B HEC 201 A 1 HETATM 20 C C3B HEC . . . B 2 -31.643 -5.891 3.031 1 32.52 ? C3B HEC 201 A 1 HETATM 21 C C4B HEC . . . B 2 -32.608 -4.843 3.458 1 32.37 ? C4B HEC 201 A 1 HETATM 22 C CMB HEC . . . B 2 -30.826 -6.688 0.725 1 32.2 ? CMB HEC 201 A 1 HETATM 23 C CAB HEC . . . B 2 -30.828 -6.722 3.964 1 33.51 ? CAB HEC 201 A 1 HETATM 24 C CBB HEC . . . B 2 -29.751 -7.43 3.614 1 34.21 ? CBB HEC 201 A 1 HETATM 25 N NC HEC . . . B 2 -34.707 -3 4.415 1 32.07 ? NC HEC 201 A 1 HETATM 26 C C1C HEC . . . B 2 -33.923 -3.765 5.231 1 32.21 ? C1C HEC 201 A 1 HETATM 27 C C2C HEC . . . B 2 -34.386 -3.666 6.556 1 32.24 ? C2C HEC 201 A 1 HETATM 28 C C3C HEC . . . B 2 -35.454 -2.775 6.558 1 32.7 ? C3C HEC 201 A 1 HETATM 29 C C4C HEC . . . B 2 -35.626 -2.354 5.195 1 32.05 ? C4C HEC 201 A 1 HETATM 30 C CMC HEC . . . B 2 -33.806 -4.384 7.749 1 31.91 ? CMC HEC 201 A 1 HETATM 31 C CAC HEC . . . B 2 -36.283 -2.316 7.711 1 33.75 ? CAC HEC 201 A 1 HETATM 32 C CBC HEC . . . B 2 -36.047 -2.57 8.999 1 33.55 ? CBC HEC 201 A 1 HETATM 33 N ND HEC . . . B 2 -35.873 -1.369 2.38 1 32.34 ? ND HEC 201 A 1 HETATM 34 C C1D HEC . . . B 2 -36.609 -0.993 3.439 1 32.58 ? C1D HEC 201 A 1 HETATM 35 C C2D HEC . . . B 2 -37.508 0.103 3.057 1 32.56 ? C2D HEC 201 A 1 HETATM 36 C C3D HEC . . . B 2 -37.295 0.342 1.751 1 32.72 ? C3D HEC 201 A 1 HETATM 37 C C4D HEC . . . B 2 -36.239 -0.596 1.335 1 32.32 ? C4D HEC 201 A 1 HETATM 38 C CMD HEC . . . B 2 -38.489 0.801 3.964 1 32.7 ? CMD HEC 201 A 1 HETATM 39 C CAD HEC . . . B 2 -37.983 1.391 0.912 1 33.42 ? CAD HEC 201 A 1 HETATM 40 C CBD HEC . . . B 2 -37.184 2.687 1.094 1 34.26 ? CBD HEC 201 A 1 HETATM 41 C CGD HEC . . . B 2 -37.754 3.856 0.324 1 34.93 ? CGD HEC 201 A 1 HETATM 42 O O1D HEC . . . B 2 -38.894 3.809 -0.192 1 35.76 ? O1D HEC 201 A 1 HETATM 43 O O2D HEC . . . B 2 -37.068 4.896 0.205 1 35.14 ? O2D HEC 201 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 43 #