data_7DI8
#
_model_server_result.job_id            cCD28jvQNfI4-n4ATOlOJw 
_model_server_result.datetime_utc      '2024-11-15 16:27:00' 
_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          7di8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":601}' 
#
_entry.id    7DI8 
#
_exptl.entry_id    7DI8 
_exptl.method      'ELECTRON CRYSTALLOGRAPHY' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    4 
_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            7DI8 
_cell.length_a            69.98 
_cell.length_b            174.02 
_cell.length_c            199.45 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7DI8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,L 
_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
? 2 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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
metalc ? metalc1 A OH TYR 358 A TYR 357 1_555 E FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc2 B OH TYR 358 B TYR 357 1_555 G FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
metalc ? metalc3 C OH TYR 358 C TYR 357 1_555 I FE HEM . C HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc4 D OH TYR 358 D TYR 357 1_555 K FE HEM . D HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
#
_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 129 n n 
CHA C4D HEM doub 130 n n 
CHA HHA HEM sing 131 n n 
CHB C4A HEM sing 132 n n 
CHB C1B HEM doub 133 n n 
CHB HHB HEM sing 134 n n 
CHC C4B HEM sing 135 n n 
CHC C1C HEM doub 136 n n 
CHC HHC HEM sing 137 n n 
CHD C4C HEM doub 138 n n 
CHD C1D HEM sing 139 n n 
CHD HHD HEM sing 140 n n 
C1A C2A HEM doub 141 n y 
C1A NA HEM sing 142 n y 
C2A C3A HEM sing 143 n y 
C2A CAA HEM sing 144 n n 
C3A C4A HEM doub 145 n y 
C3A CMA HEM sing 146 n n 
C4A NA HEM sing 147 n y 
CMA HMA HEM sing 148 n n 
CMA HMAA HEM sing 149 n n 
CMA HMAB HEM sing 150 n n 
CAA CBA HEM sing 151 n n 
CAA HAA HEM sing 152 n n 
CAA HAAA HEM sing 153 n n 
CBA CGA HEM sing 154 n n 
CBA HBA HEM sing 155 n n 
CBA HBAA HEM sing 156 n n 
CGA O1A HEM doub 157 n n 
CGA O2A HEM sing 158 n n 
C1B C2B HEM sing 159 n n 
C1B NB HEM sing 160 n n 
C2B C3B HEM doub 161 n n 
C2B CMB HEM sing 162 n n 
C3B C4B HEM sing 163 n n 
C3B CAB HEM sing 164 n n 
C4B NB HEM doub 165 n n 
CMB HMB HEM sing 166 n n 
CMB HMBA HEM sing 167 n n 
CMB HMBB HEM sing 168 n n 
CAB CBB HEM doub 169 n n 
CAB HAB HEM sing 170 n n 
CBB HBB HEM sing 171 n n 
CBB HBBA HEM sing 172 n n 
C1C C2C HEM sing 173 n y 
C1C NC HEM sing 174 n y 
C2C C3C HEM doub 175 n y 
C2C CMC HEM sing 176 n n 
C3C C4C HEM sing 177 n y 
C3C CAC HEM sing 178 n n 
C4C NC HEM sing 179 n y 
CMC HMC HEM sing 180 n n 
CMC HMCA HEM sing 181 n n 
CMC HMCB HEM sing 182 n n 
CAC CBC HEM doub 183 n n 
CAC HAC HEM sing 184 n n 
CBC HBC HEM sing 185 n n 
CBC HBCA HEM sing 186 n n 
C1D C2D HEM sing 187 n n 
C1D ND HEM doub 188 n n 
C2D C3D HEM doub 189 n n 
C2D CMD HEM sing 190 n n 
C3D C4D HEM sing 191 n n 
C3D CAD HEM sing 192 n n 
C4D ND HEM sing 193 n n 
CMD HMD HEM sing 194 n n 
CMD HMDA HEM sing 195 n n 
CMD HMDB HEM sing 196 n n 
CAD CBD HEM sing 197 n n 
CAD HAD HEM sing 198 n n 
CAD HADA HEM sing 199 n n 
CBD CGD HEM sing 200 n n 
CBD HBD HEM sing 201 n n 
CBD HBDA HEM sing 202 n n 
CGD O1D HEM doub 203 n n 
CGD O2D HEM sing 204 n n 
O2A H2A HEM sing 205 n n 
O2D H2D HEM sing 206 n n 
FE NA HEM sing 207 n n 
FE NB HEM sing 208 n n 
FE NC HEM sing 209 n n 
FE ND HEM sing 210 n n 
#
_atom_sites.entry_id                     7DI8 
_atom_sites.fract_transf_matrix[1][1]    0.01429 
_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]    0.005746 
_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]    0.005014 
_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 2 HEM A 1 601 527 HEM HEM . 
F 3 NDP A 1 602 528 NDP NDP . 
G 2 HEM B 1 601 527 HEM HEM . 
H 3 NDP B 1 602 528 NDP NDP . 
I 2 HEM C 1 601 527 HEM HEM . 
J 3 NDP C 1 602 528 NDP NDP . 
K 2 HEM D 1 601 527 HEM HEM . 
L 3 NDP D 1 602 528 NDP NDP . 
#
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 . . . K 2 80.023 59.727 150.762 1 12.88 ? CHA HEM 601 D 1 
HETATM 2 C CHB HEM . . . K 2 77.061 56.057 149.595 1 12.88 ? CHB HEM 601 D 1 
HETATM 3 C CHC HEM . . . K 2 80.076 52.952 151.729 1 12.9 ? CHC HEM 601 D 1 
HETATM 4 C CHD HEM . . . K 2 83.196 56.576 152.637 1 12.9 ? CHD HEM 601 D 1 
HETATM 5 C C1A HEM . . . K 2 78.985 58.998 150.223 1 12.88 ? C1A HEM 601 D 1 
HETATM 6 C C2A HEM . . . K 2 77.921 59.523 149.391 1 12.88 ? C2A HEM 601 D 1 
HETATM 7 C C3A HEM . . . K 2 77.11 58.513 149.075 1 12.88 ? C3A HEM 601 D 1 
HETATM 8 C C4A HEM . . . K 2 77.623 57.309 149.692 1 12.88 ? C4A HEM 601 D 1 
HETATM 9 C CMA HEM . . . K 2 75.847 58.605 148.193 1 12.88 ? CMA HEM 601 D 1 
HETATM 10 C CAA HEM . . . K 2 77.761 60.995 148.95 1 12.87 ? CAA HEM 601 D 1 
HETATM 11 C CBA HEM . . . K 2 78.919 61.427 148.058 1 12.88 ? CBA HEM 601 D 1 
HETATM 12 C CGA HEM . . . K 2 78.738 62.886 147.743 1 12.87 ? CGA HEM 601 D 1 
HETATM 13 O O1A HEM . . . K 2 79.55 63.44 146.96 1 12.87 ? O1A HEM 601 D 1 
HETATM 14 O O2A HEM . . . K 2 77.774 63.492 148.276 1 12.87 ? O2A HEM 601 D 1 
HETATM 15 C C1B HEM . . . K 2 77.643 54.883 150.003 1 12.89 ? C1B HEM 601 D 1 
HETATM 16 C C2B HEM . . . K 2 77.18 53.554 149.671 1 12.9 ? C2B HEM 601 D 1 
HETATM 17 C C3B HEM . . . K 2 78.005 52.671 150.27 1 13.11 ? C3B HEM 601 D 1 
HETATM 18 C C4B HEM . . . K 2 79.022 53.44 150.979 1 13.11 ? C4B HEM 601 D 1 
HETATM 19 C CMB HEM . . . K 2 75.924 53.331 148.796 1 12.89 ? CMB HEM 601 D 1 
HETATM 20 C CAB HEM . . . K 2 77.981 51.119 150.248 1 13.12 ? CAB HEM 601 D 1 
HETATM 21 C CBB HEM . . . K 2 77.289 50.381 149.373 1 12.91 ? CBB HEM 601 D 1 
HETATM 22 C C1C HEM . . . K 2 81.234 53.635 152.058 1 12.9 ? C1C HEM 601 D 1 
HETATM 23 C C2C HEM . . . K 2 82.513 53.039 152.388 1 12.91 ? C2C HEM 601 D 1 
HETATM 24 C C3C HEM . . . K 2 83.38 54.045 152.647 1 12.91 ? C3C HEM 601 D 1 
HETATM 25 C C4C HEM . . . K 2 82.67 55.303 152.474 1 12.9 ? C4C HEM 601 D 1 
HETATM 26 C CMC HEM . . . K 2 82.707 51.504 152.422 1 12.92 ? CMC HEM 601 D 1 
HETATM 27 C CAC HEM . . . K 2 84.876 54.021 153.045 1 12.91 ? CAC HEM 601 D 1 
HETATM 28 C CBC HEM . . . K 2 85.65 52.937 153.012 1 12.92 ? CBC HEM 601 D 1 
HETATM 29 C C1D HEM . . . K 2 82.622 57.765 152.221 1 12.89 ? C1D HEM 601 D 1 
HETATM 30 C C2D HEM . . . K 2 83.183 59.109 152.315 1 12.89 ? C2D HEM 601 D 1 
HETATM 31 C C3D HEM . . . K 2 82.297 59.963 151.791 1 13.09 ? C3D HEM 601 D 1 
HETATM 32 C C4D HEM . . . K 2 81.149 59.204 151.351 1 13.09 ? C4D HEM 601 D 1 
HETATM 33 C CMD HEM . . . K 2 84.555 59.506 152.906 1 12.89 ? CMD HEM 601 D 1 
HETATM 34 C CAD HEM . . . K 2 82.44 61.497 151.671 1 12.88 ? CAD HEM 601 D 1 
HETATM 35 C CBD HEM . . . K 2 83.047 61.888 150.329 1 13.08 ? CBD HEM 601 D 1 
HETATM 36 C CGD HEM . . . K 2 83.16 63.388 150.289 1 12.87 ? CGD HEM 601 D 1 
HETATM 37 O O1D HEM . . . K 2 83.393 63.988 151.369 1 12.87 ? O1D HEM 601 D 1 
HETATM 38 O O2D HEM . . . K 2 83.019 63.975 149.185 1 12.87 ? O2D HEM 601 D 1 
HETATM 39 N NA HEM . . . K 2 78.769 57.641 150.392 1 12.88 ? NA HEM 601 D 1 
HETATM 40 N NB HEM . . . K 2 78.763 54.782 150.8 1 12.89 ? NB HEM 601 D 1 
HETATM 41 N NC HEM . . . K 2 81.369 55.008 152.122 1 12.9 ? NC HEM 601 D 1 
HETATM 42 N ND HEM . . . K 2 81.378 57.872 151.629 1 12.89 ? ND HEM 601 D 1 
HETATM 43 FE FE HEM . . . K 2 79.957 56.365 151.538 1 12.89 ? FE HEM 601 D 1 
HETATM 44 H HHB HEM . . . K 2 76.132 56.009 149.287 1 15.64 ? HHB HEM 601 D 1 
HETATM 45 H HHC HEM . . . K 2 79.996 52.033 152.06 1 15.66 ? HHC HEM 601 D 1 
HETATM 46 H HHD HEM . . . K 2 84.06 56.64 153.094 1 15.66 ? HHD HEM 601 D 1 
HETATM 47 H HMA HEM . . . K 2 75.21 59.229 148.599 1 15.63 ? HMA HEM 601 D 1 
HETATM 48 H HMAA HEM . . . K 2 75.435 57.719 148.119 1 15.63 ? HMAA HEM 601 D 1 
HETATM 49 H HMAB HEM . . . K 2 76.095 58.925 147.3 1 15.63 ? HMAB HEM 601 D 1 
HETATM 50 H HAA HEM . . . K 2 77.737 61.562 149.737 1 15.63 ? HAA HEM 601 D 1 
HETATM 51 H HAAA HEM . . . K 2 76.928 61.092 148.462 1 15.63 ? HAAA HEM 601 D 1 
HETATM 52 H HBA HEM . . . K 2 78.911 60.91 147.237 1 15.63 ? HBA HEM 601 D 1 
HETATM 53 H HBAA HEM . . . K 2 79.76 61.292 148.522 1 15.63 ? HBAA HEM 601 D 1 
HETATM 54 H HMB HEM . . . K 2 75.153 53.732 149.227 1 15.65 ? HMB HEM 601 D 1 
HETATM 55 H HMBA HEM . . . K 2 75.773 52.379 148.684 1 15.65 ? HMBA HEM 601 D 1 
HETATM 56 H HMBB HEM . . . K 2 76.058 53.741 147.927 1 15.65 ? HMBB HEM 601 D 1 
HETATM 57 H HAB HEM . . . K 2 78.501 50.656 150.909 1 15.92 ? HAB HEM 601 D 1 
HETATM 58 H HBB HEM . . . K 2 77.32 49.413 149.424 1 15.67 ? HBB HEM 601 D 1 
HETATM 59 H HBBA HEM . . . K 2 76.752 50.814 148.69 1 15.67 ? HBBA HEM 601 D 1 
HETATM 60 H HMC HEM . . . K 2 82.108 51.117 153.079 1 15.68 ? HMC HEM 601 D 1 
HETATM 61 H HMCA HEM . . . K 2 83.624 51.3 152.661 1 15.68 ? HMCA HEM 601 D 1 
HETATM 62 H HMCB HEM . . . K 2 82.51 51.134 151.547 1 15.68 ? HMCB HEM 601 D 1 
HETATM 63 H HAC HEM . . . K 2 85.273 54.845 153.336 1 15.68 ? HAC HEM 601 D 1 
HETATM 64 H HBC HEM . . . K 2 86.58 52.998 153.281 1 15.69 ? HBC HEM 601 D 1 
HETATM 65 H HBCA HEM . . . K 2 85.283 52.088 152.723 1 15.69 ? HBCA HEM 601 D 1 
HETATM 66 H HMD HEM . . . K 2 84.595 59.236 153.847 1 15.64 ? HMD HEM 601 D 1 
HETATM 67 H HMDA HEM . . . K 2 84.671 60.477 152.84 1 15.64 ? HMDA HEM 601 D 1 
HETATM 68 H HMDB HEM . . . K 2 85.268 59.057 152.406 1 15.64 ? HMDB HEM 601 D 1 
HETATM 69 H HAD HEM . . . K 2 83.012 61.819 152.385 1 15.63 ? HAD HEM 601 D 1 
HETATM 70 H HADA HEM . . . K 2 81.564 61.905 151.756 1 15.63 ? HADA HEM 601 D 1 
HETATM 71 H HBD HEM . . . K 2 82.474 61.583 149.609 1 15.88 ? HBD HEM 601 D 1 
HETATM 72 H HBDA HEM . . . K 2 83.927 61.491 150.239 1 15.88 ? HBDA HEM 601 D 1 
HETATM 73 H HHA HEM . . . K 2 79.995 60.699 150.638 1 15.63 ? HHA HEM 601 D 1 
#
_model_server_stats.io_time_ms              45 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    44 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           73 
#