data_7XMD
#
_model_server_result.job_id            TQTxcpC5REBJ49a7WOX8KA 
_model_server_result.datetime_utc      '2025-02-27 01:15:11' 
_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          7xmd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":701}' 
#
_entry.id    7XMD 
#
_exptl.entry_id    7XMD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              838.854 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'HEME O' 
_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            7XMD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7XMD 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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 
_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    ? 
_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                      5 
_struct_asym.id                             E 
_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
metalc ? metalc1 A NE2 HIS 106 A HIS 106 1_555 F FE HEM . A HEM 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? 
metalc ? metalc2 A ND1 HIS 284 A HIS 284 1_555 G CU CU . A CU 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc3 A NE2 HIS 333 A HIS 333 1_555 G CU CU . A CU 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc4 A NE2 HIS 334 A HIS 334 1_555 G CU CU . A CU 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
metalc ? metalc5 A NE2 HIS 419 A HIS 419 1_555 E FE HEO . A HEO 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc6 A NE2 HIS 421 A HIS 421 1_555 F FE HEM . A HEM 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
#
_chem_comp.formula           'C49 H58 Fe N4 O5 2' 
_chem_comp.formula_weight    838.854 
_chem_comp.id                HEO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'HEME O' 
_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 HEO sing 211 n n 
FE NB HEO sing 212 n n 
FE NC HEO sing 213 n n 
FE ND HEO sing 214 n n 
CHA C1A HEO doub 215 n n 
CHA C4D HEO sing 216 n n 
CHA HHA HEO sing 217 n n 
CHB C4A HEO doub 218 n n 
CHB C1B HEO sing 219 n n 
CHB HHB HEO sing 220 n n 
CHC C4B HEO doub 221 n n 
CHC C1C HEO sing 222 n n 
CHC HHC HEO sing 223 n n 
CHD C4C HEO sing 224 n n 
CHD C1D HEO doub 225 n n 
CHD HHD HEO sing 226 n n 
NA C1A HEO sing 227 n n 
NA C4A HEO sing 228 n n 
C1A C2A HEO sing 229 n n 
C2A C3A HEO doub 230 n n 
C2A CAA HEO sing 231 n n 
C3A C4A HEO sing 232 n n 
C3A CMA HEO sing 233 n n 
CMA HA1 HEO sing 234 n n 
CMA HA2 HEO sing 235 n n 
CMA HA3 HEO sing 236 n n 
CAA CBA HEO sing 237 n n 
CAA HAA1 HEO sing 238 n n 
CAA HAA2 HEO sing 239 n n 
CBA CGA HEO sing 240 n n 
CBA HBA1 HEO sing 241 n n 
CBA HBA2 HEO sing 242 n n 
CGA O1A HEO doub 243 n n 
CGA O2A HEO sing 244 n n 
O2A H2A HEO sing 245 n n 
NB C1B HEO doub 246 n n 
NB C4B HEO sing 247 n n 
C1B C2B HEO sing 248 n n 
C2B C3B HEO doub 249 n n 
C2B CMB HEO sing 250 n n 
C3B C4B HEO sing 251 n n 
C3B C11 HEO sing 252 n n 
CMB HMB1 HEO sing 253 n n 
CMB HMB2 HEO sing 254 n n 
CMB HMB3 HEO sing 255 n n 
NC C1C HEO sing 256 n y 
NC C4C HEO sing 257 n y 
C1C C2C HEO doub 258 n y 
C2C C3C HEO sing 259 n y 
C2C CMC HEO sing 260 n n 
C3C C4C HEO doub 261 n y 
C3C CAC HEO sing 262 n n 
CMC HMC1 HEO sing 263 n n 
CMC HMC2 HEO sing 264 n n 
CMC HMC3 HEO sing 265 n n 
CAC CBC HEO doub 266 n n 
CAC HAC HEO sing 267 n n 
CBC HBC1 HEO sing 268 n n 
CBC HBC2 HEO sing 269 n n 
ND C1D HEO sing 270 n n 
ND C4D HEO doub 271 n n 
C1D C2D HEO sing 272 n n 
C2D C3D HEO doub 273 n n 
C2D CMD HEO sing 274 n n 
C3D C4D HEO sing 275 n n 
C3D CAD HEO sing 276 n n 
CMD HMD1 HEO sing 277 n n 
CMD HMD2 HEO sing 278 n n 
CMD HMD3 HEO sing 279 n n 
CAD CBD HEO sing 280 n n 
CAD HAD1 HEO sing 281 n n 
CAD HAD2 HEO sing 282 n n 
CBD CGD HEO sing 283 n n 
CBD HBD1 HEO sing 284 n n 
CBD HBD2 HEO sing 285 n n 
CGD O1D HEO doub 286 n n 
CGD O2D HEO sing 287 n n 
O2D H2D HEO sing 288 n n 
C11 O11 HEO sing 289 n n 
C11 C12 HEO sing 290 n n 
C11 H11 HEO sing 291 n n 
O11 HO1 HEO sing 292 n n 
C12 C13 HEO sing 293 n n 
C12 H121 HEO sing 294 n n 
C12 H122 HEO sing 295 n n 
C13 C14 HEO sing 296 n n 
C13 H131 HEO sing 297 n n 
C13 H132 HEO sing 298 n n 
C14 C15 HEO doub 299 e n 
C14 H14 HEO sing 300 n n 
C15 C16 HEO sing 301 n n 
C15 C26 HEO sing 302 n n 
C16 C17 HEO sing 303 n n 
C16 H161 HEO sing 304 n n 
C16 H162 HEO sing 305 n n 
C17 C18 HEO sing 306 n n 
C17 H171 HEO sing 307 n n 
C17 H172 HEO sing 308 n n 
C18 C19 HEO doub 309 e n 
C18 H18 HEO sing 310 n n 
C19 C20 HEO sing 311 n n 
C19 C27 HEO sing 312 n n 
C20 C21 HEO sing 313 n n 
C20 H201 HEO sing 314 n n 
C20 H202 HEO sing 315 n n 
C21 C22 HEO sing 316 n n 
C21 H211 HEO sing 317 n n 
C21 H212 HEO sing 318 n n 
C22 C23 HEO doub 319 n n 
C22 H22 HEO sing 320 n n 
C23 C24 HEO sing 321 n n 
C23 C25 HEO sing 322 n n 
C24 H241 HEO sing 323 n n 
C24 H242 HEO sing 324 n n 
C24 H243 HEO sing 325 n n 
C25 H251 HEO sing 326 n n 
C25 H252 HEO sing 327 n n 
C25 H253 HEO sing 328 n n 
C26 H261 HEO sing 329 n n 
C26 H262 HEO sing 330 n n 
C26 H263 HEO sing 331 n n 
C27 H271 HEO sing 332 n n 
C27 H272 HEO sing 333 n n 
C27 H273 HEO sing 334 n n 
#
_atom_sites.entry_id                     7XMD 
_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
E 5 HEO A 1 701 1002 HEO HEO . 
F 6 HEM A 1 702 1001 HEM HEM . 
G 7 CU A 1 703 1003 CU CU . 
H 8 PEE A 1 704 1004 PEE PEE . 
I 9 JYR A 1 705 1006 JYR XN4 . 
J 10 UNX B 1 401 1005 UNX UNX . 
K 8 PEE C 1 301 301 PEE PEE . 
#
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 HEO . . . E 5 173.846 192.579 187.866 1 69.79 ? FE HEO 701 A 1 
HETATM 2 C CHA HEO . . . E 5 172.962 193.237 184.755 1 69.79 ? CHA HEO 701 A 1 
HETATM 3 C CHB HEO . . . E 5 170.592 193.104 188.958 1 69.79 ? CHB HEO 701 A 1 
HETATM 4 C CHC HEO . . . E 5 174.572 191.26 191.064 1 69.79 ? CHC HEO 701 A 1 
HETATM 5 C CHD HEO . . . E 5 177.056 191.951 186.993 1 69.79 ? CHD HEO 701 A 1 
HETATM 6 N NA HEO . . . E 5 172.11 193.063 187.038 1 69.79 ? NA HEO 701 A 1 
HETATM 7 C C1A HEO . . . E 5 171.968 193.345 185.697 1 69.79 ? C1A HEO 701 A 1 
HETATM 8 C C2A HEO . . . E 5 170.629 193.766 185.465 1 69.79 ? C2A HEO 701 A 1 
HETATM 9 C C3A HEO . . . E 5 169.996 193.721 186.653 1 69.79 ? C3A HEO 701 A 1 
HETATM 10 C C4A HEO . . . E 5 170.898 193.277 187.63 1 69.79 ? C4A HEO 701 A 1 
HETATM 11 C CMA HEO . . . E 5 168.556 194.085 186.869 1 69.79 ? CMA HEO 701 A 1 
HETATM 12 C CAA HEO . . . E 5 169.89 194.234 184.23 1 69.79 ? CAA HEO 701 A 1 
HETATM 13 C CBA HEO . . . E 5 170.494 193.939 182.86 1 69.79 ? CBA HEO 701 A 1 
HETATM 14 C CGA HEO . . . E 5 170.057 195.02 181.907 1 69.79 ? CGA HEO 701 A 1 
HETATM 15 O O1A HEO . . . E 5 170.638 195.147 180.805 1 69.79 ? O1A HEO 701 A 1 
HETATM 16 O O2A HEO . . . E 5 169.116 195.789 182.217 1 69.79 ? O2A HEO 701 A 1 
HETATM 17 N NB HEO . . . E 5 172.795 192.257 189.66 1 69.79 ? NB HEO 701 A 1 
HETATM 18 C C1B HEO . . . E 5 171.501 192.537 189.848 1 69.79 ? C1B HEO 701 A 1 
HETATM 19 C C2B HEO . . . E 5 171.106 192.172 191.158 1 69.79 ? C2B HEO 701 A 1 
HETATM 20 C C3B HEO . . . E 5 172.194 191.658 191.777 1 69.79 ? C3B HEO 701 A 1 
HETATM 21 C C4B HEO . . . E 5 173.287 191.711 190.784 1 69.79 ? C4B HEO 701 A 1 
HETATM 22 C CMB HEO . . . E 5 169.737 192.331 191.756 1 69.79 ? CMB HEO 701 A 1 
HETATM 23 N NC HEO . . . E 5 175.522 191.854 188.888 1 69.79 ? NC HEO 701 A 1 
HETATM 24 C C1C HEO . . . E 5 175.549 191.214 190.092 1 69.79 ? C1C HEO 701 A 1 
HETATM 25 C C2C HEO . . . E 5 176.707 190.448 190.199 1 69.79 ? C2C HEO 701 A 1 
HETATM 26 C C3C HEO . . . E 5 177.438 190.642 189.045 1 69.79 ? C3C HEO 701 A 1 
HETATM 27 C C4C HEO . . . E 5 176.679 191.527 188.232 1 69.79 ? C4C HEO 701 A 1 
HETATM 28 C CMC HEO . . . E 5 177.059 189.592 191.39 1 69.79 ? CMC HEO 701 A 1 
HETATM 29 C CAC HEO . . . E 5 178.741 190.012 188.73 1 69.79 ? CAC HEO 701 A 1 
HETATM 30 C CBC HEO . . . E 5 179.773 190.107 189.571 1 69.79 ? CBC HEO 701 A 1 
HETATM 31 N ND HEO . . . E 5 174.789 192.602 186.258 1 69.79 ? ND HEO 701 A 1 
HETATM 32 C C1D HEO . . . E 5 176.085 192.304 186.056 1 69.79 ? C1D HEO 701 A 1 
HETATM 33 C C2D HEO . . . E 5 176.406 192.397 184.629 1 69.79 ? C2D HEO 701 A 1 
HETATM 34 C C3D HEO . . . E 5 175.271 192.766 184.019 1 69.79 ? C3D HEO 701 A 1 
HETATM 35 C C4D HEO . . . E 5 174.253 192.867 185.064 1 69.79 ? C4D HEO 701 A 1 
HETATM 36 C CMD HEO . . . E 5 177.752 192.154 184 1 69.79 ? CMD HEO 701 A 1 
HETATM 37 C CAD HEO . . . E 5 175.053 192.98 182.547 1 69.79 ? CAD HEO 701 A 1 
HETATM 38 C CBD HEO . . . E 5 175.456 194.357 182.048 1 69.79 ? CBD HEO 701 A 1 
HETATM 39 C CGD HEO . . . E 5 175.551 194.287 180.544 1 69.79 ? CGD HEO 701 A 1 
HETATM 40 O O1D HEO . . . E 5 174.801 194.995 179.833 1 69.79 ? O1D HEO 701 A 1 
HETATM 41 O O2D HEO . . . E 5 176.377 193.514 180.005 1 69.79 ? O2D HEO 701 A 1 
HETATM 42 C C11 HEO . . . E 5 172.246 191.126 193.155 1 69.79 ? C11 HEO 701 A 1 
HETATM 43 O O11 HEO . . . E 5 172.797 189.807 193.136 1 69.79 ? O11 HEO 701 A 1 
HETATM 44 C C12 HEO . . . E 5 173.07 191.995 194.092 1 69.79 ? C12 HEO 701 A 1 
HETATM 45 C C13 HEO . . . E 5 173.023 191.396 195.495 1 69.79 ? C13 HEO 701 A 1 
HETATM 46 C C14 HEO . . . E 5 173.767 192.27 196.473 1 69.79 ? C14 HEO 701 A 1 
HETATM 47 C C15 HEO . . . E 5 173.117 193.165 197.228 1 69.79 ? C15 HEO 701 A 1 
HETATM 48 C C16 HEO . . . E 5 173.888 194.029 198.197 1 69.79 ? C16 HEO 701 A 1 
HETATM 49 C C17 HEO . . . E 5 174.198 193.212 199.444 1 69.79 ? C17 HEO 701 A 1 
HETATM 50 C C18 HEO . . . E 5 172.967 193.214 200.311 1 69.79 ? C18 HEO 701 A 1 
HETATM 51 C C19 HEO . . . E 5 172.771 194.105 201.292 1 69.79 ? C19 HEO 701 A 1 
HETATM 52 C C20 HEO . . . E 5 171.501 194.037 202.107 1 69.79 ? C20 HEO 701 A 1 
HETATM 53 C C21 HEO . . . E 5 170.628 192.908 201.572 1 69.79 ? C21 HEO 701 A 1 
HETATM 54 C C22 HEO . . . E 5 169.172 193.196 201.833 1 69.79 ? C22 HEO 701 A 1 
HETATM 55 C C23 HEO . . . E 5 168.275 193.033 200.854 1 69.79 ? C23 HEO 701 A 1 
HETATM 56 C C24 HEO . . . E 5 168.717 192.559 199.503 1 69.79 ? C24 HEO 701 A 1 
HETATM 57 C C25 HEO . . . E 5 166.826 193.319 201.108 1 69.79 ? C25 HEO 701 A 1 
HETATM 58 C C26 HEO . . . E 5 171.628 193.314 197.116 1 69.79 ? C26 HEO 701 A 1 
HETATM 59 C C27 HEO . . . E 5 173.794 195.161 201.589 1 69.79 ? C27 HEO 701 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           59 
#