data_1DUK
#
_model_server_result.job_id            ePCi5N8XTQk-vPf7d89viA 
_model_server_result.datetime_utc      '2024-11-22 09:13:14' 
_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          1duk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":155}' 
#
_entry.id    1DUK 
#
_exptl.entry_id    1DUK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    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            1DUK 
_cell.length_a            40.132 
_cell.length_b            49.071 
_cell.length_c            79.339 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1DUK 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_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                      2 
_struct_asym.id                             B 
_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 93 A HIS 93 1_555 B FE HEM . A HEM 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
metalc ? metalc2 B FE HEM . A HEM 155 1_555 C O HOH . A HOH 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? 
#
_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 116 n n 
CHA C4D HEM doub 117 n n 
CHA HHA HEM sing 118 n n 
CHB C4A HEM sing 119 n n 
CHB C1B HEM doub 120 n n 
CHB HHB HEM sing 121 n n 
CHC C4B HEM sing 122 n n 
CHC C1C HEM doub 123 n n 
CHC HHC HEM sing 124 n n 
CHD C4C HEM doub 125 n n 
CHD C1D HEM sing 126 n n 
CHD HHD HEM sing 127 n n 
C1A C2A HEM doub 128 n y 
C1A NA HEM sing 129 n y 
C2A C3A HEM sing 130 n y 
C2A CAA HEM sing 131 n n 
C3A C4A HEM doub 132 n y 
C3A CMA HEM sing 133 n n 
C4A NA HEM sing 134 n y 
CMA HMA HEM sing 135 n n 
CMA HMAA HEM sing 136 n n 
CMA HMAB HEM sing 137 n n 
CAA CBA HEM sing 138 n n 
CAA HAA HEM sing 139 n n 
CAA HAAA HEM sing 140 n n 
CBA CGA HEM sing 141 n n 
CBA HBA HEM sing 142 n n 
CBA HBAA HEM sing 143 n n 
CGA O1A HEM doub 144 n n 
CGA O2A HEM sing 145 n n 
C1B C2B HEM sing 146 n n 
C1B NB HEM sing 147 n n 
C2B C3B HEM doub 148 n n 
C2B CMB HEM sing 149 n n 
C3B C4B HEM sing 150 n n 
C3B CAB HEM sing 151 n n 
C4B NB HEM doub 152 n n 
CMB HMB HEM sing 153 n n 
CMB HMBA HEM sing 154 n n 
CMB HMBB HEM sing 155 n n 
CAB CBB HEM doub 156 n n 
CAB HAB HEM sing 157 n n 
CBB HBB HEM sing 158 n n 
CBB HBBA HEM sing 159 n n 
C1C C2C HEM sing 160 n y 
C1C NC HEM sing 161 n y 
C2C C3C HEM doub 162 n y 
C2C CMC HEM sing 163 n n 
C3C C4C HEM sing 164 n y 
C3C CAC HEM sing 165 n n 
C4C NC HEM sing 166 n y 
CMC HMC HEM sing 167 n n 
CMC HMCA HEM sing 168 n n 
CMC HMCB HEM sing 169 n n 
CAC CBC HEM doub 170 n n 
CAC HAC HEM sing 171 n n 
CBC HBC HEM sing 172 n n 
CBC HBCA HEM sing 173 n n 
C1D C2D HEM sing 174 n n 
C1D ND HEM doub 175 n n 
C2D C3D HEM doub 176 n n 
C2D CMD HEM sing 177 n n 
C3D C4D HEM sing 178 n n 
C3D CAD HEM sing 179 n n 
C4D ND HEM sing 180 n n 
CMD HMD HEM sing 181 n n 
CMD HMDA HEM sing 182 n n 
CMD HMDB HEM sing 183 n n 
CAD CBD HEM sing 184 n n 
CAD HAD HEM sing 185 n n 
CAD HADA HEM sing 186 n n 
CBD CGD HEM sing 187 n n 
CBD HBD HEM sing 188 n n 
CBD HBDA HEM sing 189 n n 
CGD O1D HEM doub 190 n n 
CGD O2D HEM sing 191 n n 
O2A H2A HEM sing 192 n n 
O2D H2D HEM sing 193 n n 
FE NA HEM sing 194 n n 
FE NB HEM sing 195 n n 
FE NC HEM sing 196 n n 
FE ND HEM sing 197 n n 
#
_atom_sites.entry_id                     1DUK 
_atom_sites.fract_transf_matrix[1][1]    0.024918 
_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]    0.020379 
_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]    0.012604 
_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 HEM A 1 155 0 HEM HEM . 
C 3 HOH A 1 156 0 HOH WAT . 
C 3 HOH A 2 157 0 HOH WAT . 
C 3 HOH A 3 158 0 HOH WAT . 
C 3 HOH A 4 159 0 HOH WAT . 
C 3 HOH A 5 160 0 HOH WAT . 
C 3 HOH A 6 161 0 HOH WAT . 
C 3 HOH A 7 162 0 HOH WAT . 
C 3 HOH A 8 163 0 HOH WAT . 
C 3 HOH A 9 164 0 HOH WAT . 
C 3 HOH A 10 165 0 HOH WAT . 
C 3 HOH A 11 166 0 HOH WAT . 
C 3 HOH A 12 167 0 HOH WAT . 
#
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 . . . B 2 -5.808 33.659 -9.24 1 13.65 ? CHA HEM 155 A 1 
HETATM 2 C CHB HEM . . . B 2 -4.406 31.323 -5.244 1 5 ? CHB HEM 155 A 1 
HETATM 3 C CHC HEM . . . B 2 -4.65 27.203 -7.624 1 10.21 ? CHC HEM 155 A 1 
HETATM 4 C CHD HEM . . . B 2 -6.031 29.465 -11.606 1 5 ? CHD HEM 155 A 1 
HETATM 5 C C1A HEM . . . B 2 -5.377 33.351 -7.978 1 5.82 ? C1A HEM 155 A 1 
HETATM 6 C C2A HEM . . . B 2 -5.161 34.321 -6.894 1 18.32 ? C2A HEM 155 A 1 
HETATM 7 C C3A HEM . . . B 2 -4.753 33.649 -5.807 1 11.92 ? C3A HEM 155 A 1 
HETATM 8 C C4A HEM . . . B 2 -4.757 32.265 -6.161 1 5 ? C4A HEM 155 A 1 
HETATM 9 C CMA HEM . . . B 2 -4.408 34.144 -4.381 1 14.42 ? CMA HEM 155 A 1 
HETATM 10 C CAA HEM . . . B 2 -5.416 35.832 -7.029 1 25.08 ? CAA HEM 155 A 1 
HETATM 11 C CBA HEM . . . B 2 -6.865 36.359 -7.235 1 75 ? CBA HEM 155 A 1 
HETATM 12 C CGA HEM . . . B 2 -7.972 35.361 -7.467 1 60.52 ? CGA HEM 155 A 1 
HETATM 13 O O1A HEM . . . B 2 -8.476 35.324 -8.633 1 26.65 ? O1A HEM 155 A 1 
HETATM 14 O O2A HEM . . . B 2 -8.348 34.704 -6.449 1 22.13 ? O2A HEM 155 A 1 
HETATM 15 C C1B HEM . . . B 2 -4.409 29.998 -5.547 1 5 ? C1B HEM 155 A 1 
HETATM 16 C C2B HEM . . . B 2 -4.165 28.998 -4.559 1 5 ? C2B HEM 155 A 1 
HETATM 17 C C3B HEM . . . B 2 -4.218 27.868 -5.23 1 5 ? C3B HEM 155 A 1 
HETATM 18 C C4B HEM . . . B 2 -4.474 28.143 -6.651 1 5 ? C4B HEM 155 A 1 
HETATM 19 C CMB HEM . . . B 2 -3.689 29.267 -3.1 1 5.3 ? CMB HEM 155 A 1 
HETATM 20 C CAB HEM . . . B 2 -3.902 26.486 -4.641 1 24.03 ? CAB HEM 155 A 1 
HETATM 21 C CBB HEM . . . B 2 -2.817 26.378 -3.848 1 11.14 ? CBB HEM 155 A 1 
HETATM 22 C C1C HEM . . . B 2 -4.979 27.468 -8.901 1 32.96 ? C1C HEM 155 A 1 
HETATM 23 C C2C HEM . . . B 2 -4.944 26.484 -9.942 1 12.34 ? C2C HEM 155 A 1 
HETATM 24 C C3C HEM . . . B 2 -5.386 27.079 -11.042 1 10.78 ? C3C HEM 155 A 1 
HETATM 25 C C4C HEM . . . B 2 -5.635 28.474 -10.713 1 11.09 ? C4C HEM 155 A 1 
HETATM 26 C CMC HEM . . . B 2 -4.543 25.018 -9.653 1 8.67 ? CMC HEM 155 A 1 
HETATM 27 C CAC HEM . . . B 2 -5.553 26.552 -12.484 1 10.16 ? CAC HEM 155 A 1 
HETATM 28 C CBC HEM . . . B 2 -5.04 25.373 -12.809 1 14.67 ? CBC HEM 155 A 1 
HETATM 29 C C1D HEM . . . B 2 -5.981 30.791 -11.28 1 5 ? C1D HEM 155 A 1 
HETATM 30 C C2D HEM . . . B 2 -6.198 31.839 -12.237 1 19.76 ? C2D HEM 155 A 1 
HETATM 31 C C3D HEM . . . B 2 -6.233 32.977 -11.545 1 6.81 ? C3D HEM 155 A 1 
HETATM 32 C C4D HEM . . . B 2 -5.933 32.703 -10.183 1 5 ? C4D HEM 155 A 1 
HETATM 33 C CMD HEM . . . B 2 -6.455 31.601 -13.75 1 10.01 ? CMD HEM 155 A 1 
HETATM 34 C CAD HEM . . . B 2 -6.293 34.399 -12.069 1 19.88 ? CAD HEM 155 A 1 
HETATM 35 C CBD HEM . . . B 2 -4.979 34.797 -12.803 1 19.51 ? CBD HEM 155 A 1 
HETATM 36 C CGD HEM . . . B 2 -4.764 36.244 -13.14 1 40.13 ? CGD HEM 155 A 1 
HETATM 37 O O1D HEM . . . B 2 -4.829 36.476 -14.367 1 59.48 ? O1D HEM 155 A 1 
HETATM 38 O O2D HEM . . . B 2 -4.601 37.079 -12.185 1 75 ? O2D HEM 155 A 1 
HETATM 39 N NA HEM . . . B 2 -5.121 32.041 -7.512 1 5 ? NA HEM 155 A 1 
HETATM 40 N NB HEM . . . B 2 -4.646 29.468 -6.847 1 5 ? NB HEM 155 A 1 
HETATM 41 N NC HEM . . . B 2 -5.432 28.687 -9.373 1 19.54 ? NC HEM 155 A 1 
HETATM 42 N ND HEM . . . B 2 -5.769 31.347 -9.99 1 5 ? ND HEM 155 A 1 
HETATM 43 FE FE HEM . . . B 2 -5.26 30.448 -8.491 1 15.4 ? FE HEM 155 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           404 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           43 
#