data_3DE9
#
_model_server_result.job_id            bvzcgNSaz-Ehsy196QxuvQ 
_model_server_result.datetime_utc      '2024-11-28 15:17:22' 
_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          3de9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":150}' 
#
_entry.id    3DE9 
#
_exptl.entry_id    3DE9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          3 
_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         120 
_cell.entry_id            3DE9 
_cell.length_a            51.042 
_cell.length_b            51.042 
_cell.length_c            121.971 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DE9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -25.521 -44.203669 0 
3 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 25.521 -44.203669 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_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 N ALA 1 A ALA 1 1_555 D NI NI . A NI 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc2 A O ALA 1 A ALA 1 1_555 D NI NI . A NI 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc3 A SD MET 7 A MET 7 1_555 E FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc4 A NE2 HIS 59 A HIS 59 1_555 B NI NI . A NI 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc5 A NE2 HIS 63 A HIS 63 1_555 B NI NI . A NI 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc6 A NE2 HIS 73 A HIS 73 1_555 C NI NI . A NI 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc7 A NE2 HIS 77 A HIS 77 1_555 C NI NI . A NI 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc8 A NE2 HIS 102 A HIS 102 1_555 E FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
#
_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                     3DE9 
_atom_sites.fract_transf_matrix[1][1]    0.019592 
_atom_sites.fract_transf_matrix[1][2]    0.011311 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022623 
_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]    0.008199 
_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 NI A 1 107 1 NI NI . 
C 2 NI A 1 108 2 NI NI . 
D 2 NI A 1 109 3 NI NI . 
E 3 HEM A 1 150 150 HEM HEM . 
F 4 HOH A 1 151 1 HOH HOH . 
F 4 HOH A 2 152 2 HOH HOH . 
F 4 HOH A 3 153 3 HOH HOH . 
F 4 HOH A 4 154 4 HOH HOH . 
F 4 HOH A 5 155 5 HOH HOH . 
F 4 HOH A 6 156 6 HOH HOH . 
F 4 HOH A 7 157 7 HOH HOH . 
F 4 HOH A 8 158 8 HOH HOH . 
F 4 HOH A 9 159 9 HOH HOH . 
F 4 HOH A 10 160 10 HOH HOH . 
F 4 HOH A 11 161 11 HOH HOH . 
F 4 HOH A 12 162 12 HOH HOH . 
F 4 HOH A 13 163 13 HOH HOH . 
F 4 HOH A 14 164 14 HOH HOH . 
F 4 HOH A 15 165 15 HOH HOH . 
F 4 HOH A 16 166 16 HOH HOH . 
F 4 HOH A 17 167 17 HOH HOH . 
F 4 HOH A 18 168 18 HOH HOH . 
F 4 HOH A 19 169 19 HOH HOH . 
F 4 HOH A 20 170 20 HOH HOH . 
F 4 HOH A 21 171 21 HOH HOH . 
F 4 HOH A 22 172 22 HOH HOH . 
F 4 HOH A 23 173 23 HOH HOH . 
F 4 HOH A 24 174 24 HOH HOH . 
F 4 HOH A 25 175 25 HOH HOH . 
F 4 HOH A 26 176 26 HOH HOH . 
F 4 HOH A 27 177 27 HOH HOH . 
F 4 HOH A 28 178 28 HOH HOH . 
F 4 HOH A 29 179 29 HOH HOH . 
F 4 HOH A 30 180 30 HOH HOH . 
F 4 HOH A 31 181 31 HOH HOH . 
F 4 HOH A 32 182 32 HOH HOH . 
F 4 HOH A 33 183 33 HOH HOH . 
F 4 HOH A 34 184 34 HOH HOH . 
F 4 HOH A 35 185 35 HOH HOH . 
F 4 HOH A 36 186 36 HOH HOH . 
F 4 HOH A 37 187 37 HOH HOH . 
F 4 HOH A 38 188 38 HOH HOH . 
F 4 HOH A 39 189 39 HOH HOH . 
F 4 HOH A 40 190 40 HOH HOH . 
F 4 HOH A 41 191 41 HOH HOH . 
F 4 HOH A 42 192 42 HOH HOH . 
F 4 HOH A 43 193 43 HOH HOH . 
F 4 HOH A 44 194 44 HOH HOH . 
F 4 HOH A 45 195 45 HOH HOH . 
F 4 HOH A 46 196 46 HOH HOH . 
F 4 HOH A 47 197 47 HOH HOH . 
F 4 HOH A 48 198 48 HOH HOH . 
F 4 HOH A 49 199 49 HOH HOH . 
F 4 HOH A 50 200 50 HOH HOH . 
F 4 HOH A 51 201 51 HOH HOH . 
F 4 HOH A 52 202 52 HOH HOH . 
F 4 HOH A 53 203 53 HOH HOH . 
F 4 HOH A 54 204 54 HOH HOH . 
F 4 HOH A 55 205 55 HOH HOH . 
#
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 . . . E 3 -0.339 -8.192 -6.799 1 35.82 ? CHA HEM 150 A 1 
HETATM 2 C CHB HEM . . . E 3 1.445 -8.834 -2.34 1 34.73 ? CHB HEM 150 A 1 
HETATM 3 C CHC HEM . . . E 3 1.729 -13.6 -3.375 1 27.66 ? CHC HEM 150 A 1 
HETATM 4 C CHD HEM . . . E 3 0.025 -12.949 -7.865 1 31.57 ? CHD HEM 150 A 1 
HETATM 5 C C1A HEM . . . E 3 0.112 -7.932 -5.519 1 36.3 ? C1A HEM 150 A 1 
HETATM 6 C C2A HEM . . . E 3 0.132 -6.652 -4.875 1 39.53 ? C2A HEM 150 A 1 
HETATM 7 C C3A HEM . . . E 3 0.618 -6.815 -3.633 1 38.83 ? C3A HEM 150 A 1 
HETATM 8 C C4A HEM . . . E 3 0.943 -8.209 -3.461 1 37.92 ? C4A HEM 150 A 1 
HETATM 9 C CMA HEM . . . E 3 0.824 -5.735 -2.547 1 38.01 ? CMA HEM 150 A 1 
HETATM 10 C CAA HEM . . . E 3 -0.371 -5.324 -5.517 1 41.34 ? CAA HEM 150 A 1 
HETATM 11 C CBA HEM . . . E 3 -1.779 -5.086 -4.939 1 44.92 ? CBA HEM 150 A 1 
HETATM 12 C CGA HEM . . . E 3 -2.348 -3.745 -5.341 1 49.79 ? CGA HEM 150 A 1 
HETATM 13 O O1A HEM . . . E 3 -3.085 -3.716 -6.376 1 51.06 ? O1A HEM 150 A 1 
HETATM 14 O O2A HEM . . . E 3 -2.064 -2.72 -4.629 1 52.93 ? O2A HEM 150 A 1 
HETATM 15 C C1B HEM . . . E 3 1.723 -10.191 -2.252 1 33.38 ? C1B HEM 150 A 1 
HETATM 16 C C2B HEM . . . E 3 2.389 -10.822 -1.164 1 31.34 ? C2B HEM 150 A 1 
HETATM 17 C C3B HEM . . . E 3 2.475 -12.124 -1.446 1 28.93 ? C3B HEM 150 A 1 
HETATM 18 C C4B HEM . . . E 3 1.854 -12.367 -2.746 1 29.34 ? C4B HEM 150 A 1 
HETATM 19 C CMB HEM . . . E 3 2.944 -10.109 0.11 1 30.98 ? CMB HEM 150 A 1 
HETATM 20 C CAB HEM . . . E 3 3.172 -13.166 -0.535 1 27.46 ? CAB HEM 150 A 1 
HETATM 21 C CBB HEM . . . E 3 2.741 -13.263 0.735 1 24.71 ? CBB HEM 150 A 1 
HETATM 22 C C1C HEM . . . E 3 1.328 -13.874 -4.638 1 27.78 ? C1C HEM 150 A 1 
HETATM 23 C C2C HEM . . . E 3 1.345 -15.133 -5.333 1 24.2 ? C2C HEM 150 A 1 
HETATM 24 C C3C HEM . . . E 3 0.847 -14.939 -6.579 1 24.53 ? C3C HEM 150 A 1 
HETATM 25 C C4C HEM . . . E 3 0.532 -13.552 -6.727 1 27.71 ? C4C HEM 150 A 1 
HETATM 26 C CMC HEM . . . E 3 1.845 -16.461 -4.759 1 28.22 ? CMC HEM 150 A 1 
HETATM 27 C CAC HEM . . . E 3 0.718 -15.939 -7.757 1 26.52 ? CAC HEM 150 A 1 
HETATM 28 C CBC HEM . . . E 3 0.438 -17.219 -7.494 1 21.97 ? CBC HEM 150 A 1 
HETATM 29 C C1D HEM . . . E 3 -0.257 -11.613 -7.999 1 32.99 ? C1D HEM 150 A 1 
HETATM 30 C C2D HEM . . . E 3 -0.859 -10.979 -9.155 1 34.27 ? C2D HEM 150 A 1 
HETATM 31 C C3D HEM . . . E 3 -0.986 -9.51 -8.803 1 35.38 ? C3D HEM 150 A 1 
HETATM 32 C C4D HEM . . . E 3 -0.415 -9.384 -7.478 1 35.56 ? C4D HEM 150 A 1 
HETATM 33 C CMD HEM . . . E 3 -1.298 -11.593 -10.49 1 35.88 ? CMD HEM 150 A 1 
HETATM 34 C CAD HEM . . . E 3 -1.538 -8.392 -9.724 1 36.11 ? CAD HEM 150 A 1 
HETATM 35 C CBD HEM . . . E 3 -3.043 -8.528 -9.927 1 37.35 ? CBD HEM 150 A 1 
HETATM 36 C CGD HEM . . . E 3 -3.565 -7.435 -10.795 1 38.67 ? CGD HEM 150 A 1 
HETATM 37 O O1D HEM . . . E 3 -4.686 -6.977 -10.483 1 42.53 ? O1D HEM 150 A 1 
HETATM 38 O O2D HEM . . . E 3 -2.877 -7.012 -11.773 1 43.65 ? O2D HEM 150 A 1 
HETATM 39 N NA HEM . . . E 3 0.614 -8.83 -4.634 1 36.81 ? NA HEM 150 A 1 
HETATM 40 N NB HEM . . . E 3 1.44 -11.161 -3.188 1 31.15 ? NB HEM 150 A 1 
HETATM 41 N NC HEM . . . E 3 0.819 -12.933 -5.531 1 31 ? NC HEM 150 A 1 
HETATM 42 N ND HEM . . . E 3 -0.034 -10.647 -7.031 1 33.51 ? ND HEM 150 A 1 
HETATM 43 FE FE HEM . . . E 3 0.65 -10.827 -5.017 1 32.95 ? FE HEM 150 A 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           396 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           43 
#