data_8HDD
#
_model_server_result.job_id            SnY5GMZtb53tvi_Opx2GfA 
_model_server_result.datetime_utc      '2024-12-04 12:34:57' 
_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          8hdd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":501}' 
#
_entry.id    8HDD 
#
_exptl.entry_id    8HDD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_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            8HDD 
_cell.length_a            204.015 
_cell.length_b            71.797 
_cell.length_c            114.221 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8HDD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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                      6 
_struct_asym.id                             F 
_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
disulf ? disulf1 A SG CYS 213 A CYS 213 1_555 C SG CYS 105 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
covale ? covale1 A NE2 HIS 105 A HIS 105 1_555 D C8M FAD . A FAD 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.69 ? 
covale ? covale2 B SG CYS 334 B CYS 334 1_555 F CAB HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
covale ? covale3 B SG CYS 337 B CYS 337 1_555 F CAC HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc1 A SG CYS 212 A CYS 212 1_555 E FE1 F3S . A F3S 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc2 A SG CYS 218 A CYS 218 1_555 E FE4 F3S . A F3S 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc3 A SG CYS 222 A CYS 222 1_555 E FE3 F3S . A F3S 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc4 B NE2 HIS 338 B HIS 338 1_555 F FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc5 B SD MET 386 B MET 386 1_555 F FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? 
#
_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 229 n n 
CHA C4D HEM doub 230 n n 
CHA HHA HEM sing 231 n n 
CHB C4A HEM sing 232 n n 
CHB C1B HEM doub 233 n n 
CHB HHB HEM sing 234 n n 
CHC C4B HEM sing 235 n n 
CHC C1C HEM doub 236 n n 
CHC HHC HEM sing 237 n n 
CHD C4C HEM doub 238 n n 
CHD C1D HEM sing 239 n n 
CHD HHD HEM sing 240 n n 
C1A C2A HEM doub 241 n y 
C1A NA HEM sing 242 n y 
C2A C3A HEM sing 243 n y 
C2A CAA HEM sing 244 n n 
C3A C4A HEM doub 245 n y 
C3A CMA HEM sing 246 n n 
C4A NA HEM sing 247 n y 
CMA HMA HEM sing 248 n n 
CMA HMAA HEM sing 249 n n 
CMA HMAB HEM sing 250 n n 
CAA CBA HEM sing 251 n n 
CAA HAA HEM sing 252 n n 
CAA HAAA HEM sing 253 n n 
CBA CGA HEM sing 254 n n 
CBA HBA HEM sing 255 n n 
CBA HBAA HEM sing 256 n n 
CGA O1A HEM doub 257 n n 
CGA O2A HEM sing 258 n n 
C1B C2B HEM sing 259 n n 
C1B NB HEM sing 260 n n 
C2B C3B HEM doub 261 n n 
C2B CMB HEM sing 262 n n 
C3B C4B HEM sing 263 n n 
C3B CAB HEM sing 264 n n 
C4B NB HEM doub 265 n n 
CMB HMB HEM sing 266 n n 
CMB HMBA HEM sing 267 n n 
CMB HMBB HEM sing 268 n n 
CAB CBB HEM doub 269 n n 
CAB HAB HEM sing 270 n n 
CBB HBB HEM sing 271 n n 
CBB HBBA HEM sing 272 n n 
C1C C2C HEM sing 273 n y 
C1C NC HEM sing 274 n y 
C2C C3C HEM doub 275 n y 
C2C CMC HEM sing 276 n n 
C3C C4C HEM sing 277 n y 
C3C CAC HEM sing 278 n n 
C4C NC HEM sing 279 n y 
CMC HMC HEM sing 280 n n 
CMC HMCA HEM sing 281 n n 
CMC HMCB HEM sing 282 n n 
CAC CBC HEM doub 283 n n 
CAC HAC HEM sing 284 n n 
CBC HBC HEM sing 285 n n 
CBC HBCA HEM sing 286 n n 
C1D C2D HEM sing 287 n n 
C1D ND HEM doub 288 n n 
C2D C3D HEM doub 289 n n 
C2D CMD HEM sing 290 n n 
C3D C4D HEM sing 291 n n 
C3D CAD HEM sing 292 n n 
C4D ND HEM sing 293 n n 
CMD HMD HEM sing 294 n n 
CMD HMDA HEM sing 295 n n 
CMD HMDB HEM sing 296 n n 
CAD CBD HEM sing 297 n n 
CAD HAD HEM sing 298 n n 
CAD HADA HEM sing 299 n n 
CBD CGD HEM sing 300 n n 
CBD HBD HEM sing 301 n n 
CBD HBDA HEM sing 302 n n 
CGD O1D HEM doub 303 n n 
CGD O2D HEM sing 304 n n 
O2A H2A HEM sing 305 n n 
O2D H2D HEM sing 306 n n 
FE NA HEM sing 307 n n 
FE NB HEM sing 308 n n 
FE NC HEM sing 309 n n 
FE ND HEM sing 310 n n 
#
_atom_sites.entry_id                     8HDD 
_atom_sites.fract_transf_matrix[1][1]    0.004902 
_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]    0.013928 
_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]    0.008755 
_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 1 701 701 FAD FAD . 
E 5 F3S A 1 702 702 F3S F3S . 
F 6 HEM B 1 501 1003 HEM HEM . 
#
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 . . . F 6 -27.516 47.332 19.809 1 79.04 ? CHA HEM 501 B 1 
HETATM 2 C CHB HEM . . . F 6 -23.017 45.561 19.94 1 80.67 ? CHB HEM 501 B 1 
HETATM 3 C CHC HEM . . . F 6 -24.073 42.64 16.172 1 73.84 ? CHC HEM 501 B 1 
HETATM 4 C CHD HEM . . . F 6 -28.434 44.719 15.834 1 73.06 ? CHD HEM 501 B 1 
HETATM 5 C C1A HEM . . . F 6 -26.216 47.07 20.16 1 79.03 ? C1A HEM 501 B 1 
HETATM 6 C C2A HEM . . . F 6 -25.562 47.672 21.25 1 78.51 ? C2A HEM 501 B 1 
HETATM 7 C C3A HEM . . . F 6 -24.298 47.184 21.293 1 79.24 ? C3A HEM 501 B 1 
HETATM 8 C C4A HEM . . . F 6 -24.159 46.278 20.223 1 80.97 ? C4A HEM 501 B 1 
HETATM 9 C CMA HEM . . . F 6 -23.239 47.549 22.301 1 79.92 ? CMA HEM 501 B 1 
HETATM 10 C CAA HEM . . . F 6 -26.159 48.676 22.2 1 78.97 ? CAA HEM 501 B 1 
HETATM 11 C CBA HEM . . . F 6 -27.323 48.041 22.965 1 78.96 ? CBA HEM 501 B 1 
HETATM 12 C CGA HEM . . . F 6 -27.134 48.273 24.443 1 78.59 ? CGA HEM 501 B 1 
HETATM 13 O O1A HEM . . . F 6 -26.323 47.57 25.086 1 78.84 ? O1A HEM 501 B 1 
HETATM 14 O O2A HEM . . . F 6 -27.775 49.167 25.038 1 76.69 ? O2A HEM 501 B 1 
HETATM 15 C C1B HEM . . . F 6 -22.964 44.606 18.918 1 78.69 ? C1B HEM 501 B 1 
HETATM 16 C C2B HEM . . . F 6 -21.804 43.812 18.714 1 77.32 ? C2B HEM 501 B 1 
HETATM 17 C C3B HEM . . . F 6 -22.063 42.981 17.668 1 77.71 ? C3B HEM 501 B 1 
HETATM 18 C C4B HEM . . . F 6 -23.45 43.293 17.235 1 76.31 ? C4B HEM 501 B 1 
HETATM 19 C CMB HEM . . . F 6 -20.521 43.882 19.504 1 76.7 ? CMB HEM 501 B 1 
HETATM 20 C CAB HEM . . . F 6 -21.147 41.969 17.105 1 73.87 ? CAB HEM 501 B 1 
HETATM 21 C CBB HEM . . . F 6 -19.942 41.786 17.642 1 73.42 ? CBB HEM 501 B 1 
HETATM 22 C C1C HEM . . . F 6 -25.351 42.959 15.74 1 72.15 ? C1C HEM 501 B 1 
HETATM 23 C C2C HEM . . . F 6 -26.007 42.392 14.636 1 70.05 ? C2C HEM 501 B 1 
HETATM 24 C C3C HEM . . . F 6 -27.248 42.988 14.545 1 69.89 ? C3C HEM 501 B 1 
HETATM 25 C C4C HEM . . . F 6 -27.339 43.933 15.599 1 72.28 ? C4C HEM 501 B 1 
HETATM 26 C CMC HEM . . . F 6 -25.464 41.326 13.721 1 73.54 ? CMC HEM 501 B 1 
HETATM 27 C CAC HEM . . . F 6 -28.296 42.718 13.547 1 71.11 ? CAC HEM 501 B 1 
HETATM 28 C CBC HEM . . . F 6 -28.103 41.832 12.58 1 72.42 ? CBC HEM 501 B 1 
HETATM 29 C C1D HEM . . . F 6 -28.504 45.588 16.918 1 73.71 ? C1D HEM 501 B 1 
HETATM 30 C C2D HEM . . . F 6 -29.731 46.342 17.208 1 73.34 ? C2D HEM 501 B 1 
HETATM 31 C C3D HEM . . . F 6 -29.479 47.064 18.316 1 76.82 ? C3D HEM 501 B 1 
HETATM 32 C C4D HEM . . . F 6 -28.099 46.742 18.698 1 78.54 ? C4D HEM 501 B 1 
HETATM 33 C CMD HEM . . . F 6 -31.01 46.308 16.412 1 71.64 ? CMD HEM 501 B 1 
HETATM 34 C CAD HEM . . . F 6 -30.396 48.022 19.042 1 76.06 ? CAD HEM 501 B 1 
HETATM 35 C CBD HEM . . . F 6 -31.855 47.859 18.607 1 74.73 ? CBD HEM 501 B 1 
HETATM 36 C CGD HEM . . . F 6 -32.386 49.172 18.08 1 71 ? CGD HEM 501 B 1 
HETATM 37 O O1D HEM . . . F 6 -31.7 50.211 18.185 1 69.63 ? O1D HEM 501 B 1 
HETATM 38 O O2D HEM . . . F 6 -33.514 49.234 17.54 1 65.94 ? O2D HEM 501 B 1 
HETATM 39 N NA HEM . . . F 6 -25.341 46.218 19.534 1 78.95 ? NA HEM 501 B 1 
HETATM 40 N NB HEM . . . F 6 -23.917 44.274 18.03 1 77.26 ? NB HEM 501 B 1 
HETATM 41 N NC HEM . . . F 6 -26.172 43.891 16.308 1 73.08 ? NC HEM 501 B 1 
HETATM 42 N ND HEM . . . F 6 -27.563 45.86 17.836 1 76.72 ? ND HEM 501 B 1 
HETATM 43 FE FE HEM . . . F 6 -25.83 45.158 17.929 1 80.58 ? FE HEM 501 B 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#