data_2D0U
#
_model_server_result.job_id            vNkT6SaaBpLWHc54tC-VtA 
_model_server_result.datetime_utc      '2024-11-22 23:17:35' 
_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          2d0u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":404}' 
#
_entry.id    2D0U 
#
_exptl.entry_id    2D0U 
_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    2 
_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            2D0U 
_cell.length_a            86.352 
_cell.length_b            97.089 
_cell.length_c            129.378 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2D0U 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F 1 1 
B,G,H,I,J 2 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
? 3 D N N 
? 3 H 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
disulf ? disulf1 A SG CYS 311 A CYS 308 1_555 B SG CYS 311 B CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc1 A NE2 HIS 349 A HIS 346 1_555 D FE HEM . A HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? 
metalc ? metalc2 D FE HEM . A HEM 404 1_555 C C CYN . A CYN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc3 B NE2 HIS 349 B HIS 346 1_555 H FE HEM . B HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc4 H FE HEM . B HEM 404 1_555 G C CYN . B CYN 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
#
_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 130 n n 
CHA C4D HEM doub 131 n n 
CHA HHA HEM sing 132 n n 
CHB C4A HEM sing 133 n n 
CHB C1B HEM doub 134 n n 
CHB HHB HEM sing 135 n n 
CHC C4B HEM sing 136 n n 
CHC C1C HEM doub 137 n n 
CHC HHC HEM sing 138 n n 
CHD C4C HEM doub 139 n n 
CHD C1D HEM sing 140 n n 
CHD HHD HEM sing 141 n n 
C1A C2A HEM doub 142 n y 
C1A NA HEM sing 143 n y 
C2A C3A HEM sing 144 n y 
C2A CAA HEM sing 145 n n 
C3A C4A HEM doub 146 n y 
C3A CMA HEM sing 147 n n 
C4A NA HEM sing 148 n y 
CMA HMA HEM sing 149 n n 
CMA HMAA HEM sing 150 n n 
CMA HMAB HEM sing 151 n n 
CAA CBA HEM sing 152 n n 
CAA HAA HEM sing 153 n n 
CAA HAAA HEM sing 154 n n 
CBA CGA HEM sing 155 n n 
CBA HBA HEM sing 156 n n 
CBA HBAA HEM sing 157 n n 
CGA O1A HEM doub 158 n n 
CGA O2A HEM sing 159 n n 
C1B C2B HEM sing 160 n n 
C1B NB HEM sing 161 n n 
C2B C3B HEM doub 162 n n 
C2B CMB HEM sing 163 n n 
C3B C4B HEM sing 164 n n 
C3B CAB HEM sing 165 n n 
C4B NB HEM doub 166 n n 
CMB HMB HEM sing 167 n n 
CMB HMBA HEM sing 168 n n 
CMB HMBB HEM sing 169 n n 
CAB CBB HEM doub 170 n n 
CAB HAB HEM sing 171 n n 
CBB HBB HEM sing 172 n n 
CBB HBBA HEM sing 173 n n 
C1C C2C HEM sing 174 n y 
C1C NC HEM sing 175 n y 
C2C C3C HEM doub 176 n y 
C2C CMC HEM sing 177 n n 
C3C C4C HEM sing 178 n y 
C3C CAC HEM sing 179 n n 
C4C NC HEM sing 180 n y 
CMC HMC HEM sing 181 n n 
CMC HMCA HEM sing 182 n n 
CMC HMCB HEM sing 183 n n 
CAC CBC HEM doub 184 n n 
CAC HAC HEM sing 185 n n 
CBC HBC HEM sing 186 n n 
CBC HBCA HEM sing 187 n n 
C1D C2D HEM sing 188 n n 
C1D ND HEM doub 189 n n 
C2D C3D HEM doub 190 n n 
C2D CMD HEM sing 191 n n 
C3D C4D HEM sing 192 n n 
C3D CAD HEM sing 193 n n 
C4D ND HEM sing 194 n n 
CMD HMD HEM sing 195 n n 
CMD HMDA HEM sing 196 n n 
CMD HMDB HEM sing 197 n n 
CAD CBD HEM sing 198 n n 
CAD HAD HEM sing 199 n n 
CAD HADA HEM sing 200 n n 
CBD CGD HEM sing 201 n n 
CBD HBD HEM sing 202 n n 
CBD HBDA HEM sing 203 n n 
CGD O1D HEM doub 204 n n 
CGD O2D HEM sing 205 n n 
O2A H2A HEM sing 206 n n 
O2D H2D HEM sing 207 n n 
FE NA HEM sing 208 n n 
FE NB HEM sing 209 n n 
FE NC HEM sing 210 n n 
FE ND HEM sing 211 n n 
#
_atom_sites.entry_id                     2D0U 
_atom_sites.fract_transf_matrix[1][1]    0.011581 
_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]    0.0103 
_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]    0.007729 
_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
C 2 CYN A 1 405 405 CYN CYN . 
D 3 HEM A 1 404 404 HEM HEM . 
E 4 NHE A 1 406 406 NHE NHE . 
F 4 NHE A 1 407 407 NHE NHE . 
G 2 CYN B 1 1405 405 CYN CYN . 
H 3 HEM B 1 404 404 HEM HEM . 
I 4 NHE B 1 1406 406 NHE NHE . 
J 4 NHE B 1 1407 407 NHE NHE . 
#
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 . . . D 3 66.158 51.592 20.589 1 21.88 ? CHA HEM 404 A 1 
HETATM 2 C CHB HEM . . . D 3 64.367 55.91 21.686 1 29.49 ? CHB HEM 404 A 1 
HETATM 3 C CHC HEM . . . D 3 63.425 56.797 16.981 1 27.17 ? CHC HEM 404 A 1 
HETATM 4 C CHD HEM . . . D 3 65.265 52.426 15.803 1 27.67 ? CHD HEM 404 A 1 
HETATM 5 C C1A HEM . . . D 3 65.713 52.701 21.331 1 25.72 ? C1A HEM 404 A 1 
HETATM 6 C C2A HEM . . . D 3 65.765 52.811 22.766 1 25.74 ? C2A HEM 404 A 1 
HETATM 7 C C3A HEM . . . D 3 65.261 54.022 23.062 1 26.17 ? C3A HEM 404 A 1 
HETATM 8 C C4A HEM . . . D 3 64.907 54.641 21.818 1 27.92 ? C4A HEM 404 A 1 
HETATM 9 C CMA HEM . . . D 3 65.081 54.634 24.457 1 23.34 ? CMA HEM 404 A 1 
HETATM 10 C CAA HEM . . . D 3 66.288 51.757 23.724 1 26.35 ? CAA HEM 404 A 1 
HETATM 11 C CBA HEM . . . D 3 65.481 50.556 24.177 1 24.05 ? CBA HEM 404 A 1 
HETATM 12 C CGA HEM . . . D 3 63.963 50.624 24.432 1 28.25 ? CGA HEM 404 A 1 
HETATM 13 O O1A HEM . . . D 3 63.168 50.074 23.618 1 37.43 ? O1A HEM 404 A 1 
HETATM 14 O O2A HEM . . . D 3 63.585 51.252 25.432 1 28.25 ? O2A HEM 404 A 1 
HETATM 15 C C1B HEM . . . D 3 63.983 56.531 20.484 1 31.41 ? C1B HEM 404 A 1 
HETATM 16 C C2B HEM . . . D 3 63.443 57.852 20.428 1 35.32 ? C2B HEM 404 A 1 
HETATM 17 C C3B HEM . . . D 3 63.158 58.144 19.096 1 31.52 ? C3B HEM 404 A 1 
HETATM 18 C C4B HEM . . . D 3 63.541 56.951 18.365 1 25.69 ? C4B HEM 404 A 1 
HETATM 19 C CMB HEM . . . D 3 63.229 58.774 21.654 1 50.22 ? CMB HEM 404 A 1 
HETATM 20 C CAB HEM . . . D 3 62.598 59.366 18.586 1 29.46 ? CAB HEM 404 A 1 
HETATM 21 C CBB HEM . . . D 3 61.413 60.012 19.019 1 32.45 ? CBB HEM 404 A 1 
HETATM 22 C C1C HEM . . . D 3 63.809 55.671 16.226 1 33.82 ? C1C HEM 404 A 1 
HETATM 23 C C2C HEM . . . D 3 63.617 55.567 14.803 1 39.97 ? C2C HEM 404 A 1 
HETATM 24 C C3C HEM . . . D 3 64.143 54.34 14.431 1 37.99 ? C3C HEM 404 A 1 
HETATM 25 C C4C HEM . . . D 3 64.618 53.728 15.689 1 32.18 ? C4C HEM 404 A 1 
HETATM 26 C CMC HEM . . . D 3 62.982 56.642 13.896 1 54.27 ? CMC HEM 404 A 1 
HETATM 27 C CAC HEM . . . D 3 64.159 53.816 13.131 1 39.11 ? CAC HEM 404 A 1 
HETATM 28 C CBC HEM . . . D 3 63.393 52.743 12.724 1 33.62 ? CBC HEM 404 A 1 
HETATM 29 C C1D HEM . . . D 3 65.714 51.806 17.043 1 25.37 ? C1D HEM 404 A 1 
HETATM 30 C C2D HEM . . . D 3 66.376 50.512 17.157 1 25.73 ? C2D HEM 404 A 1 
HETATM 31 C C3D HEM . . . D 3 66.625 50.269 18.49 1 22.43 ? C3D HEM 404 A 1 
HETATM 32 C C4D HEM . . . D 3 66.118 51.432 19.182 1 23.65 ? C4D HEM 404 A 1 
HETATM 33 C CMD HEM . . . D 3 66.724 49.576 16 1 28.1 ? CMD HEM 404 A 1 
HETATM 34 C CAD HEM . . . D 3 67.328 49.031 19.137 1 19.29 ? CAD HEM 404 A 1 
HETATM 35 C CBD HEM . . . D 3 68.834 48.894 19.332 1 15.01 ? CBD HEM 404 A 1 
HETATM 36 C CGD HEM . . . D 3 69.899 48.951 18.196 1 19.42 ? CGD HEM 404 A 1 
HETATM 37 O O1D HEM . . . D 3 70.74 49.852 18.241 1 25.09 ? O1D HEM 404 A 1 
HETATM 38 O O2D HEM . . . D 3 69.895 48.094 17.279 1 34.15 ? O2D HEM 404 A 1 
HETATM 39 N NA HEM . . . D 3 65.19 53.815 20.783 1 24.22 ? NA HEM 404 A 1 
HETATM 40 N NB HEM . . . D 3 64.057 55.974 19.234 1 22.98 ? NB HEM 404 A 1 
HETATM 41 N NC HEM . . . D 3 64.402 54.555 16.728 1 30.38 ? NC HEM 404 A 1 
HETATM 42 N ND HEM . . . D 3 65.564 52.364 18.287 1 23.41 ? ND HEM 404 A 1 
HETATM 43 FE FE HEM . . . D 3 64.921 54.111 18.792 1 22.55 ? FE HEM 404 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#