data_8XCM
#
_model_server_result.job_id            HjlV2w_cqvEdk_YVtFTERQ 
_model_server_result.datetime_utc      '2025-08-04 11:02:37' 
_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          8xcm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":501}' 
#
_entry.id    8XCM 
#
_exptl.entry_id    8XCM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              618.503 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'HEME C' 
_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            8XCM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XCM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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
? 6 F N N 
? 6 G N N 
? 6 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 C CB CYS 52 C CYS 52 1_555 H CBB HEC . C HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? 
covale ? covale2 C SG CYS 55 C CYS 55 1_555 H CBC HEC . C HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? 
covale ? covale3 C N TYR 115 C TYR 115 1_555 H O2D HEC . C HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale4 C SG CYS 201 C CYS 201 1_555 G CAB HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
covale ? covale5 C SG CYS 204 C CYS 204 1_555 G CBC HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? 
covale ? covale6 C CB CYS 343 C CYS 343 1_555 F CAB HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? 
covale ? covale7 C SG CYS 343 C CYS 343 1_555 F CAB HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? 
covale ? covale8 C SG CYS 346 C CYS 346 1_555 F CBC HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
covale ? covale9 C CG ASP 375 C ASP 375 1_555 G O1D HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? 
covale ? covale10 C CG1 ILE 393 C ILE 393 1_555 F O2D HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? 
metalc ? metalc1 A SG CYS 216 A CYS 216 1_555 E FE4 F3S . A F3S 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc2 A SG CYS 222 A CYS 222 1_555 E FE3 F3S . A F3S 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc3 A SG CYS 226 A CYS 226 1_555 E FE1 F3S . A F3S 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc4 C NE2 HIS 56 C HIS 56 1_555 H FE HEC . C HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc5 C NE2 HIS 205 C HIS 205 1_555 G FE HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc6 C NE2 HIS 347 C HIS 347 1_555 F FE HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
#
_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 229 n n 
FE NB HEC sing 230 n n 
FE NC HEC sing 231 n n 
FE ND HEC sing 232 n n 
CHA C1A HEC doub 233 n n 
CHA C4D HEC sing 234 n n 
CHA HHA HEC sing 235 n n 
CHB C4A HEC doub 236 n n 
CHB C1B HEC sing 237 n n 
CHB HHB HEC sing 238 n n 
CHC C4B HEC doub 239 n n 
CHC C1C HEC sing 240 n n 
CHC HHC HEC sing 241 n n 
CHD C4C HEC doub 242 n n 
CHD C1D HEC sing 243 n n 
CHD HHD HEC sing 244 n n 
NA C1A HEC sing 245 n y 
NA C4A HEC sing 246 n y 
C1A C2A HEC sing 247 n y 
C2A C3A HEC doub 248 n y 
C2A CAA HEC sing 249 n n 
C3A C4A HEC sing 250 n y 
C3A CMA HEC sing 251 n n 
CMA HMA1 HEC sing 252 n n 
CMA HMA2 HEC sing 253 n n 
CMA HMA3 HEC sing 254 n n 
CAA CBA HEC sing 255 n n 
CAA HAA1 HEC sing 256 n n 
CAA HAA2 HEC sing 257 n n 
CBA CGA HEC sing 258 n n 
CBA HBA1 HEC sing 259 n n 
CBA HBA2 HEC sing 260 n n 
CGA O1A HEC doub 261 n n 
CGA O2A HEC sing 262 n n 
O2A H2A HEC sing 263 n n 
NB C1B HEC sing 264 n y 
NB C4B HEC sing 265 n y 
C1B C2B HEC doub 266 n y 
C2B C3B HEC sing 267 n y 
C2B CMB HEC sing 268 n n 
C3B C4B HEC sing 269 n y 
C3B CAB HEC doub 270 e n 
CMB HMB1 HEC sing 271 n n 
CMB HMB2 HEC sing 272 n n 
CMB HMB3 HEC sing 273 n n 
CAB CBB HEC sing 274 n n 
CAB HAB HEC sing 275 n n 
CBB HBB1 HEC sing 276 n n 
CBB HBB2 HEC sing 277 n n 
CBB HBB3 HEC sing 278 n n 
NC C1C HEC sing 279 n y 
NC C4C HEC sing 280 n y 
C1C C2C HEC doub 281 n y 
C2C C3C HEC sing 282 n y 
C2C CMC HEC sing 283 n n 
C3C C4C HEC sing 284 n y 
C3C CAC HEC doub 285 e n 
CMC HMC1 HEC sing 286 n n 
CMC HMC2 HEC sing 287 n n 
CMC HMC3 HEC sing 288 n n 
CAC CBC HEC sing 289 n n 
CAC HAC HEC sing 290 n n 
CBC HBC1 HEC sing 291 n n 
CBC HBC2 HEC sing 292 n n 
CBC HBC3 HEC sing 293 n n 
ND C1D HEC sing 294 n y 
ND C4D HEC sing 295 n y 
C1D C2D HEC doub 296 n y 
C2D C3D HEC sing 297 n y 
C2D CMD HEC sing 298 n n 
C3D C4D HEC doub 299 n y 
C3D CAD HEC sing 300 n n 
CMD HMD1 HEC sing 301 n n 
CMD HMD2 HEC sing 302 n n 
CMD HMD3 HEC sing 303 n n 
CAD CBD HEC sing 304 n n 
CAD HAD1 HEC sing 305 n n 
CAD HAD2 HEC sing 306 n n 
CBD CGD HEC sing 307 n n 
CBD HBD1 HEC sing 308 n n 
CBD HBD2 HEC sing 309 n n 
CGD O1D HEC doub 310 n n 
CGD O2D HEC sing 311 n n 
O2D H2D HEC sing 312 n n 
#
_atom_sites.entry_id                     8XCM 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
D 4 FAD A 1 601 601 FAD FAD . 
E 5 F3S A 1 602 602 F3S F3S . 
F 6 HEC C 1 501 501 HEC HEC . 
G 6 HEC C 1 502 502 HEC HEC . 
H 6 HEC C 1 503 503 HEC HEC . 
I 7 U10 C 1 504 504 U10 U10 . 
#
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 . . . F 6 110.436 114.221 100.193 1 137.72 ? FE HEC 501 C 1 
HETATM 2 C CHA HEC . . . F 6 109.772 111.298 98.585 1 116.59 ? CHA HEC 501 C 1 
HETATM 3 C CHB HEC . . . F 6 108.394 113.259 102.761 1 118.74 ? CHB HEC 501 C 1 
HETATM 4 C CHC HEC . . . F 6 111.48 116.916 102.014 1 117.38 ? CHC HEC 501 C 1 
HETATM 5 C CHD HEC . . . F 6 111.992 115.434 97.447 1 115.46 ? CHD HEC 501 C 1 
HETATM 6 N NA HEC . . . F 6 109.31 112.616 100.59 1 121.55 ? NA HEC 501 C 1 
HETATM 7 C C1A HEC . . . F 6 109.179 111.486 99.81 1 116.44 ? C1A HEC 501 C 1 
HETATM 8 C C2A HEC . . . F 6 108.302 110.548 100.459 1 114.07 ? C2A HEC 501 C 1 
HETATM 9 C C3A HEC . . . F 6 107.922 111.09 101.617 1 117.06 ? C3A HEC 501 C 1 
HETATM 10 C C4A HEC . . . F 6 108.548 112.384 101.716 1 120.64 ? C4A HEC 501 C 1 
HETATM 11 C CMA HEC . . . F 6 106.988 110.507 102.699 1 118.97 ? CMA HEC 501 C 1 
HETATM 12 C CAA HEC . . . F 6 107.954 109.187 99.839 1 117.18 ? CAA HEC 501 C 1 
HETATM 13 C CBA HEC . . . F 6 109.133 108.204 100 1 115.98 ? CBA HEC 501 C 1 
HETATM 14 C CGA HEC . . . F 6 108.855 106.817 99.479 1 124.21 ? CGA HEC 501 C 1 
HETATM 15 O O1A HEC . . . F 6 107.883 106.719 98.684 1 126.94 ? O1A HEC 501 C 1 
HETATM 16 O O2A HEC . . . F 6 109.495 105.901 100.056 1 121.35 ? O2A HEC 501 C 1 
HETATM 17 N NB HEC . . . F 6 110.008 114.945 102.015 1 127.38 ? NB HEC 501 C 1 
HETATM 18 C C1B HEC . . . F 6 109.138 114.395 102.935 1 123.36 ? C1B HEC 501 C 1 
HETATM 19 C C2B HEC . . . F 6 109.132 115.207 104.111 1 120.14 ? C2B HEC 501 C 1 
HETATM 20 C C3B HEC . . . F 6 109.982 116.217 103.889 1 119.43 ? C3B HEC 501 C 1 
HETATM 21 C C4B HEC . . . F 6 110.552 116.064 102.587 1 124.45 ? C4B HEC 501 C 1 
HETATM 22 C CMB HEC . . . F 6 108.258 114.901 105.35 1 113.36 ? CMB HEC 501 C 1 
HETATM 23 C CAB HEC . . . F 6 110.302 117.353 104.912 1 111.07 ? CAB HEC 501 C 1 
HETATM 24 C CBB HEC . . . F 6 111.209 116.784 105.825 1 107.71 ? CBB HEC 501 C 1 
HETATM 25 N NC HEC . . . F 6 111.513 115.855 99.798 1 122.61 ? NC HEC 501 C 1 
HETATM 26 C C1C HEC . . . F 6 111.853 116.842 100.692 1 116.19 ? C1C HEC 501 C 1 
HETATM 27 C C2C HEC . . . F 6 112.671 117.845 100.036 1 110.12 ? C2C HEC 501 C 1 
HETATM 28 C C3C HEC . . . F 6 112.807 117.436 98.769 1 119.35 ? C3C HEC 501 C 1 
HETATM 29 C C4C HEC . . . F 6 112.109 116.198 98.589 1 121 ? C4C HEC 501 C 1 
HETATM 30 C CMC HEC . . . F 6 113.218 119.1 100.746 1 108.17 ? CMC HEC 501 C 1 
HETATM 31 C CAC HEC . . . F 6 113.621 118.186 97.644 1 122.58 ? CAC HEC 501 C 1 
HETATM 32 C CBC HEC . . . F 6 112.999 119.282 97.132 1 122.26 ? CBC HEC 501 C 1 
HETATM 33 N ND HEC . . . F 6 110.8 113.5 98.363 1 121.95 ? ND HEC 501 C 1 
HETATM 34 C C1D HEC . . . F 6 111.47 114.156 97.345 1 114.64 ? C1D HEC 501 C 1 
HETATM 35 C C2D HEC . . . F 6 111.517 113.275 96.191 1 113.74 ? C2D HEC 501 C 1 
HETATM 36 C C3D HEC . . . F 6 110.906 112.129 96.515 1 118.84 ? C3D HEC 501 C 1 
HETATM 37 C C4D HEC . . . F 6 110.446 112.27 97.887 1 119.85 ? C4D HEC 501 C 1 
HETATM 38 C CMD HEC . . . F 6 112.202 113.717 94.874 1 115.46 ? CMD HEC 501 C 1 
HETATM 39 C CAD HEC . . . F 6 110.582 110.814 95.769 1 114.85 ? CAD HEC 501 C 1 
HETATM 40 C CBD HEC . . . F 6 111.382 110.153 94.655 1 104.75 ? CBD HEC 501 C 1 
HETATM 41 C CGD HEC . . . F 6 111.382 110.802 93.294 1 117.65 ? CGD HEC 501 C 1 
HETATM 42 O O1D HEC . . . F 6 110.221 111.018 92.835 1 121.3 ? O1D HEC 501 C 1 
HETATM 43 O O2D HEC . . . F 6 112.474 110.791 92.636 1 135.73 ? O2D HEC 501 C 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           226 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           43 
#