data_8D9M
#
_model_server_result.job_id            NE04mXX98zLqgqdHEx5L_Q 
_model_server_result.datetime_utc      '2024-11-09 02:48:13' 
_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          8d9m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":607}' 
#
_entry.id    8D9M 
#
_exptl.entry_id    8D9M 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? heptameric 7 'representative helical assembly' 1 
? monomeric 1 'helical asymmetric unit' 2 
? monomeric 1 'helical asymmetric unit, std helical frame' 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I 1 (1-7) 
A,B,C,D,E,F,G,H,I 2 4 
A,B,C,D,E,F,G,H,I 3 H 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
1 'helical symmetry operation' ? ? -0.416281 -0.909236 0 0.909236 -0.416281 0 0 0 1 0 0 -174.3 
2 'helical symmetry operation' ? ? 0.724172 0.68962 0 -0.68962 0.724172 0 0 0 1 0 0 -116.2 
3 'helical symmetry operation' ? ? -0.928486 -0.371368 0 0.371368 -0.928486 0 0 0 1 0 0 -58.1 
4 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
5 'helical symmetry operation' ? ? -0.928486 0.371368 0 -0.371368 -0.928486 0 0 0 1 0 0 58.1 
6 'helical symmetry operation' ? ? 0.724172 -0.68962 0 0.68962 0.724172 0 0 0 1 0 0 116.2 
7 'helical symmetry operation' ? ? -0.416281 0.909236 0 -0.909236 -0.416281 0 0 0 1 0 0 174.3 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 B N N 
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I 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 A SG CYS 92 A CYS 92 1_555 B CAC HEC . A HEC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
covale ? covale2 A SG CYS 114 A CYS 114 1_555 C CAC HEC . A HEC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? 
covale ? covale3 A SG CYS 134 A CYS 134 1_555 E CAC HEC . A HEC 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
covale ? covale4 A SG CYS 178 A CYS 178 1_555 H CAB HEC . A HEC 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? 
covale ? covale5 A SG CYS 181 A CYS 181 1_555 H CAC HEC . A HEC 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? 
covale ? covale6 A SG CYS 229 A CYS 229 1_555 F CAB HEC . A HEC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? 
covale ? covale7 A SG CYS 232 A CYS 232 1_555 F CAC HEC . A HEC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? 
metalc ? metalc1 A NE2 HIS 54 A HIS 54 1_555 D FE HEC . A HEC 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc2 A NE2 HIS 64 A HIS 64 1_555 C FE HEC . A HEC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc3 A NE2 HIS 65 A HIS 65 1_555 B FE HEC . A HEC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc4 A NE2 HIS 93 A HIS 93 1_555 B FE HEC . A HEC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc5 A NE2 HIS 115 A HIS 115 1_555 C FE HEC . A HEC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc6 A NE2 HIS 120 A HIS 120 1_555 D FE HEC . A HEC 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc7 A NE2 HIS 121 A HIS 121 1_555 E FE HEC . A HEC 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc8 A NE2 HIS 135 A HIS 135 1_555 E FE HEC . A HEC 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc9 A NE2 HIS 182 A HIS 182 1_555 H FE HEC . A HEC 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc10 A NE2 HIS 206 A HIS 206 1_555 F FE HEC . A HEC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc11 A NE2 HIS 207 A HIS 207 1_555 G FE HEC . A HEC 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc12 A NE2 HIS 218 A HIS 218 1_555 G FE HEC . A HEC 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc13 A NE2 HIS 233 A HIS 233 1_555 F FE HEC . A HEC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc14 A NE2 HIS 239 A HIS 239 1_555 I FE HEC . A HEC 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc15 A NE2 HIS 265 A HIS 265 1_555 H FE HEC . A HEC 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc16 A NE2 HIS 276 A HIS 276 1_555 I FE HEC . A HEC 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
#
_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 129 n n 
FE NB HEC sing 130 n n 
FE NC HEC sing 131 n n 
FE ND HEC sing 132 n n 
CHA C1A HEC doub 133 n n 
CHA C4D HEC sing 134 n n 
CHA HHA HEC sing 135 n n 
CHB C4A HEC doub 136 n n 
CHB C1B HEC sing 137 n n 
CHB HHB HEC sing 138 n n 
CHC C4B HEC doub 139 n n 
CHC C1C HEC sing 140 n n 
CHC HHC HEC sing 141 n n 
CHD C4C HEC doub 142 n n 
CHD C1D HEC sing 143 n n 
CHD HHD HEC sing 144 n n 
NA C1A HEC sing 145 n y 
NA C4A HEC sing 146 n y 
C1A C2A HEC sing 147 n y 
C2A C3A HEC doub 148 n y 
C2A CAA HEC sing 149 n n 
C3A C4A HEC sing 150 n y 
C3A CMA HEC sing 151 n n 
CMA HMA1 HEC sing 152 n n 
CMA HMA2 HEC sing 153 n n 
CMA HMA3 HEC sing 154 n n 
CAA CBA HEC sing 155 n n 
CAA HAA1 HEC sing 156 n n 
CAA HAA2 HEC sing 157 n n 
CBA CGA HEC sing 158 n n 
CBA HBA1 HEC sing 159 n n 
CBA HBA2 HEC sing 160 n n 
CGA O1A HEC doub 161 n n 
CGA O2A HEC sing 162 n n 
O2A H2A HEC sing 163 n n 
NB C1B HEC sing 164 n y 
NB C4B HEC sing 165 n y 
C1B C2B HEC doub 166 n y 
C2B C3B HEC sing 167 n y 
C2B CMB HEC sing 168 n n 
C3B C4B HEC sing 169 n y 
C3B CAB HEC doub 170 e n 
CMB HMB1 HEC sing 171 n n 
CMB HMB2 HEC sing 172 n n 
CMB HMB3 HEC sing 173 n n 
CAB CBB HEC sing 174 n n 
CAB HAB HEC sing 175 n n 
CBB HBB1 HEC sing 176 n n 
CBB HBB2 HEC sing 177 n n 
CBB HBB3 HEC sing 178 n n 
NC C1C HEC sing 179 n y 
NC C4C HEC sing 180 n y 
C1C C2C HEC doub 181 n y 
C2C C3C HEC sing 182 n y 
C2C CMC HEC sing 183 n n 
C3C C4C HEC sing 184 n y 
C3C CAC HEC doub 185 e n 
CMC HMC1 HEC sing 186 n n 
CMC HMC2 HEC sing 187 n n 
CMC HMC3 HEC sing 188 n n 
CAC CBC HEC sing 189 n n 
CAC HAC HEC sing 190 n n 
CBC HBC1 HEC sing 191 n n 
CBC HBC2 HEC sing 192 n n 
CBC HBC3 HEC sing 193 n n 
ND C1D HEC sing 194 n y 
ND C4D HEC sing 195 n y 
C1D C2D HEC doub 196 n y 
C2D C3D HEC sing 197 n y 
C2D CMD HEC sing 198 n n 
C3D C4D HEC doub 199 n y 
C3D CAD HEC sing 200 n n 
CMD HMD1 HEC sing 201 n n 
CMD HMD2 HEC sing 202 n n 
CMD HMD3 HEC sing 203 n n 
CAD CBD HEC sing 204 n n 
CAD HAD1 HEC sing 205 n n 
CAD HAD2 HEC sing 206 n n 
CBD CGD HEC sing 207 n n 
CBD HBD1 HEC sing 208 n n 
CBD HBD2 HEC sing 209 n n 
CGD O1D HEC doub 210 n n 
CGD O2D HEC sing 211 n n 
O2D H2D HEC sing 212 n n 
#
_atom_sites.entry_id                     8D9M 
_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
B 2 HEC A 1 601 601 HEC HEC . 
C 2 HEC A 1 602 602 HEC HEC . 
D 2 HEC A 1 603 603 HEC HEC . 
E 2 HEC A 1 604 604 HEC HEC . 
F 2 HEC A 1 605 605 HEC HEC . 
G 2 HEC A 1 606 606 HEC HEC . 
H 2 HEC A 1 607 607 HEC HEC . 
I 2 HEC A 1 608 608 HEC HEC . 
#
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 2 -4.244 -7.971 -11.767 1 124.41 ? FE HEC 607 A 1 
HETATM 2 C CHA HEC . . . H 2 -1.731 -8.341 -9.483 1 124.41 ? CHA HEC 607 A 1 
HETATM 3 C CHB HEC . . . H 2 -4.459 -4.639 -10.976 1 124.41 ? CHB HEC 607 A 1 
HETATM 4 C CHC HEC . . . H 2 -6.696 -7.528 -14.138 1 124.41 ? CHC HEC 607 A 1 
HETATM 5 C CHD HEC . . . H 2 -4.022 -11.274 -12.618 1 124.41 ? CHD HEC 607 A 1 
HETATM 6 N NA HEC . . . H 2 -3.28 -6.73 -10.504 1 124.41 ? NA HEC 607 A 1 
HETATM 7 C C1A HEC . . . H 2 -2.291 -7.097 -9.618 1 124.41 ? C1A HEC 607 A 1 
HETATM 8 C C2A HEC . . . H 2 -1.924 -5.945 -8.832 1 124.41 ? C2A HEC 607 A 1 
HETATM 9 C C3A HEC . . . H 2 -2.67 -4.921 -9.235 1 124.41 ? C3A HEC 607 A 1 
HETATM 10 C C4A HEC . . . H 2 -3.535 -5.392 -10.295 1 124.41 ? C4A HEC 607 A 1 
HETATM 11 C CMA HEC . . . H 2 -2.623 -3.487 -8.669 1 124.41 ? CMA HEC 607 A 1 
HETATM 12 C CAA HEC . . . H 2 -0.862 -5.943 -7.714 1 124.41 ? CAA HEC 607 A 1 
HETATM 13 C CBA HEC . . . H 2 -1.599 -6.164 -6.395 1 124.41 ? CBA HEC 607 A 1 
HETATM 14 C CGA HEC . . . H 2 -0.966 -7.251 -5.565 1 124.41 ? CGA HEC 607 A 1 
HETATM 15 O O1A HEC . . . H 2 -1.462 -7.497 -4.436 1 124.41 ? O1A HEC 607 A 1 
HETATM 16 O O2A HEC . . . H 2 0.027 -7.872 -6.023 1 124.41 ? O2A HEC 607 A 1 
HETATM 17 N NB HEC . . . H 2 -5.363 -6.39 -12.439 1 124.41 ? NB HEC 607 A 1 
HETATM 18 C C1B HEC . . . H 2 -5.3 -5.097 -11.962 1 124.41 ? C1B HEC 607 A 1 
HETATM 19 C C2B HEC . . . H 2 -6.269 -4.298 -12.681 1 124.41 ? C2B HEC 607 A 1 
HETATM 20 C C3B HEC . . . H 2 -6.902 -5.09 -13.551 1 124.41 ? C3B HEC 607 A 1 
HETATM 21 C C4B HEC . . . H 2 -6.334 -6.417 -13.42 1 124.41 ? C4B HEC 607 A 1 
HETATM 22 C CMB HEC . . . H 2 -6.518 -2.793 -12.441 1 124.41 ? CMB HEC 607 A 1 
HETATM 23 C CAB HEC . . . H 2 -8.008 -4.666 -14.545 1 124.41 ? CAB HEC 607 A 1 
HETATM 24 C CBB HEC . . . H 2 -7.35 -3.805 -15.643 1 124.41 ? CBB HEC 607 A 1 
HETATM 25 N NC HEC . . . H 2 -5.163 -9.153 -13.106 1 124.41 ? NC HEC 607 A 1 
HETATM 26 C C1C HEC . . . H 2 -6.156 -8.785 -13.992 1 124.41 ? C1C HEC 607 A 1 
HETATM 27 C C2C HEC . . . H 2 -6.525 -9.948 -14.767 1 124.41 ? C2C HEC 607 A 1 
HETATM 28 C C3C HEC . . . H 2 -5.803 -10.982 -14.331 1 124.41 ? C3C HEC 607 A 1 
HETATM 29 C C4C HEC . . . H 2 -4.93 -10.499 -13.292 1 124.41 ? C4C HEC 607 A 1 
HETATM 30 C CMC HEC . . . H 2 -7.627 -9.962 -15.846 1 124.41 ? CMC HEC 607 A 1 
HETATM 31 C CAC HEC . . . H 2 -5.84 -12.445 -14.818 1 124.41 ? CAC HEC 607 A 1 
HETATM 32 C CBC HEC . . . H 2 -5.345 -12.581 -16.272 1 124.41 ? CBC HEC 607 A 1 
HETATM 33 N ND HEC . . . H 2 -3.059 -9.558 -11.145 1 124.41 ? ND HEC 607 A 1 
HETATM 34 C C1D HEC . . . H 2 -3.153 -10.848 -11.648 1 124.41 ? C1D HEC 607 A 1 
HETATM 35 C C2D HEC . . . H 2 -2.186 -11.691 -10.988 1 124.41 ? C2D HEC 607 A 1 
HETATM 36 C C3D HEC . . . H 2 -1.467 -10.781 -9.992 1 124.41 ? C3D HEC 607 A 1 
HETATM 37 C C4D HEC . . . H 2 -2.071 -9.478 -10.172 1 124.41 ? C4D HEC 607 A 1 
HETATM 38 C CMD HEC . . . H 2 -1.938 -13.195 -11.228 1 124.41 ? CMD HEC 607 A 1 
HETATM 39 C CAD HEC . . . H 2 -0.32 -11.195 -9.044 1 124.41 ? CAD HEC 607 A 1 
HETATM 40 C CBD HEC . . . H 2 -0.608 -10.8 -7.602 1 124.41 ? CBD HEC 607 A 1 
HETATM 41 C CGD HEC . . . H 2 0.669 -10.879 -6.813 1 124.41 ? CGD HEC 607 A 1 
HETATM 42 O O1D HEC . . . H 2 1.728 -11.214 -7.403 1 124.41 ? O1D HEC 607 A 1 
HETATM 43 O O2D HEC . . . H 2 0.629 -10.608 -5.592 1 124.41 ? O2D HEC 607 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#