data_3DDR
#
_model_server_result.job_id            N1e8pBGDmT7H9CUMDcOw_g 
_model_server_result.datetime_utc      '2024-12-12 02:44:31' 
_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          3ddr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":200}' 
#
_entry.id    3DDR 
#
_exptl.entry_id    3DDR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          5 
_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            3DDR 
_cell.length_a            157.41 
_cell.length_b            162.72 
_cell.length_c            597.01 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DDR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        22 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'F 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_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,E,F,M,O 1 1 
B,D,G,H,I,J,K,L,N,P,Q 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
? 5 M N N 
? 5 N 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 538 A CYS 538 1_555 A SG CYS 546 A CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf2 A SG CYS 715 A CYS 715 1_555 A SG CYS 750 A CYS 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 B SG CYS 538 B CYS 538 1_555 B SG CYS 546 B CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 B SG CYS 715 B CYS 715 1_555 B SG CYS 750 B CYS 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc1 C OH TYR 93 C TYR 75 1_555 M FE HEM . C HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc2 D OH TYR 93 D TYR 75 1_555 N FE HEM . D HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
#
_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 142 n n 
CHA C4D HEM doub 143 n n 
CHA HHA HEM sing 144 n n 
CHB C4A HEM sing 145 n n 
CHB C1B HEM doub 146 n n 
CHB HHB HEM sing 147 n n 
CHC C4B HEM sing 148 n n 
CHC C1C HEM doub 149 n n 
CHC HHC HEM sing 150 n n 
CHD C4C HEM doub 151 n n 
CHD C1D HEM sing 152 n n 
CHD HHD HEM sing 153 n n 
C1A C2A HEM doub 154 n y 
C1A NA HEM sing 155 n y 
C2A C3A HEM sing 156 n y 
C2A CAA HEM sing 157 n n 
C3A C4A HEM doub 158 n y 
C3A CMA HEM sing 159 n n 
C4A NA HEM sing 160 n y 
CMA HMA HEM sing 161 n n 
CMA HMAA HEM sing 162 n n 
CMA HMAB HEM sing 163 n n 
CAA CBA HEM sing 164 n n 
CAA HAA HEM sing 165 n n 
CAA HAAA HEM sing 166 n n 
CBA CGA HEM sing 167 n n 
CBA HBA HEM sing 168 n n 
CBA HBAA HEM sing 169 n n 
CGA O1A HEM doub 170 n n 
CGA O2A HEM sing 171 n n 
C1B C2B HEM sing 172 n n 
C1B NB HEM sing 173 n n 
C2B C3B HEM doub 174 n n 
C2B CMB HEM sing 175 n n 
C3B C4B HEM sing 176 n n 
C3B CAB HEM sing 177 n n 
C4B NB HEM doub 178 n n 
CMB HMB HEM sing 179 n n 
CMB HMBA HEM sing 180 n n 
CMB HMBB HEM sing 181 n n 
CAB CBB HEM doub 182 n n 
CAB HAB HEM sing 183 n n 
CBB HBB HEM sing 184 n n 
CBB HBBA HEM sing 185 n n 
C1C C2C HEM sing 186 n y 
C1C NC HEM sing 187 n y 
C2C C3C HEM doub 188 n y 
C2C CMC HEM sing 189 n n 
C3C C4C HEM sing 190 n y 
C3C CAC HEM sing 191 n n 
C4C NC HEM sing 192 n y 
CMC HMC HEM sing 193 n n 
CMC HMCA HEM sing 194 n n 
CMC HMCB HEM sing 195 n n 
CAC CBC HEM doub 196 n n 
CAC HAC HEM sing 197 n n 
CBC HBC HEM sing 198 n n 
CBC HBCA HEM sing 199 n n 
C1D C2D HEM sing 200 n n 
C1D ND HEM doub 201 n n 
C2D C3D HEM doub 202 n n 
C2D CMD HEM sing 203 n n 
C3D C4D HEM sing 204 n n 
C3D CAD HEM sing 205 n n 
C4D ND HEM sing 206 n n 
CMD HMD HEM sing 207 n n 
CMD HMDA HEM sing 208 n n 
CMD HMDB HEM sing 209 n n 
CAD CBD HEM sing 210 n n 
CAD HAD HEM sing 211 n n 
CAD HADA HEM sing 212 n n 
CBD CGD HEM sing 213 n n 
CBD HBD HEM sing 214 n n 
CBD HBDA HEM sing 215 n n 
CGD O1D HEM doub 216 n n 
CGD O2D HEM sing 217 n n 
O2A H2A HEM sing 218 n n 
O2D H2D HEM sing 219 n n 
FE NA HEM sing 220 n n 
FE NB HEM sing 221 n n 
FE NC HEM sing 222 n n 
FE ND HEM sing 223 n n 
#
_atom_sites.entry_id                     3DDR 
_atom_sites.fract_transf_matrix[1][1]    0.006353 
_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]    0.006146 
_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]    0.001675 
_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 3 NA A 1 866 1 NA NA . 
F 4 GOL A 1 867 2 GOL GOL . 
G 3 NA B 1 866 2 NA NA . 
H 4 GOL B 1 867 1 GOL GOL . 
I 4 GOL B 1 868 3 GOL GOL . 
J 4 GOL B 1 869 4 GOL GOL . 
K 4 GOL B 1 870 5 GOL GOL . 
L 4 GOL B 1 871 6 GOL GOL . 
M 5 HEM C 1 200 200 HEM HEM . 
N 5 HEM D 1 200 200 HEM HEM . 
O 6 HOH A 1 868 1 HOH HOH . 
O 6 HOH A 2 869 3 HOH HOH . 
O 6 HOH A 3 870 4 HOH HOH . 
O 6 HOH A 4 871 6 HOH HOH . 
O 6 HOH A 5 872 9 HOH HOH . 
O 6 HOH A 6 873 11 HOH HOH . 
P 6 HOH B 1 872 5 HOH HOH . 
P 6 HOH B 2 873 7 HOH HOH . 
P 6 HOH B 3 874 8 HOH HOH . 
P 6 HOH B 4 875 10 HOH HOH . 
P 6 HOH B 5 876 12 HOH HOH . 
P 6 HOH B 6 877 13 HOH HOH . 
Q 6 HOH D 1 201 2 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 . . . N 5 92.415 8.636 177.88 0.91 95.15 ? CHA HEM 200 D 1 
HETATM 2 C CHB HEM . . . N 5 92.37 10.605 173.466 0.91 134.06 ? CHB HEM 200 D 1 
HETATM 3 C CHC HEM . . . N 5 96.623 12.788 174.343 0.91 93.55 ? CHC HEM 200 D 1 
HETATM 4 C CHD HEM . . . N 5 96.699 10.866 178.782 0.91 93.17 ? CHD HEM 200 D 1 
HETATM 5 C C1A HEM . . . N 5 92.004 8.97 176.607 0.91 126.7 ? C1A HEM 200 D 1 
HETATM 6 C C2A HEM . . . N 5 90.782 8.558 175.927 0.91 129.43 ? C2A HEM 200 D 1 
HETATM 7 C C3A HEM . . . N 5 90.785 9.105 174.718 0.91 136.01 ? C3A HEM 200 D 1 
HETATM 8 C C4A HEM . . . N 5 91.996 9.884 174.576 0.91 128.49 ? C4A HEM 200 D 1 
HETATM 9 C CMA HEM . . . N 5 89.67 8.934 173.665 0.91 162.07 ? CMA HEM 200 D 1 
HETATM 10 C CAA HEM . . . N 5 89.641 7.658 176.448 0.91 126.69 ? CAA HEM 200 D 1 
HETATM 11 C CBA HEM . . . N 5 90.145 6.272 176.83 0.91 160.95 ? CBA HEM 200 D 1 
HETATM 12 C CGA HEM . . . N 5 89.039 5.555 177.562 0.91 177.7 ? CGA HEM 200 D 1 
HETATM 13 O O1A HEM . . . N 5 87.892 6.087 177.592 0.91 127.72 ? O1A HEM 200 D 1 
HETATM 14 O O2A HEM . . . N 5 89.307 4.455 178.116 0.91 199.94 ? O2A HEM 200 D 1 
HETATM 15 C C1B HEM . . . N 5 93.515 11.357 173.324 0.91 131.43 ? C1B HEM 200 D 1 
HETATM 16 C C2B HEM . . . N 5 93.878 12.11 172.14 0.91 128.95 ? C2B HEM 200 D 1 
HETATM 17 C C3B HEM . . . N 5 95.04 12.709 172.379 0.91 115.42 ? C3B HEM 200 D 1 
HETATM 18 C C4B HEM . . . N 5 95.469 12.364 173.724 0.91 105.71 ? C4B HEM 200 D 1 
HETATM 19 C CMB HEM . . . N 5 93.066 12.225 170.83 0.91 106.21 ? CMB HEM 200 D 1 
HETATM 20 C CAB HEM . . . N 5 95.768 13.625 171.377 0.91 125.19 ? CAB HEM 200 D 1 
HETATM 21 C CBB HEM . . . N 5 96.646 14.525 171.826 0.91 156.15 ? CBB HEM 200 D 1 
HETATM 22 C C1C HEM . . . N 5 97.021 12.463 175.617 0.91 115.67 ? C1C HEM 200 D 1 
HETATM 23 C C2C HEM . . . N 5 98.233 12.909 176.276 0.91 118.23 ? C2C HEM 200 D 1 
HETATM 24 C C3C HEM . . . N 5 98.25 12.38 177.498 0.91 108.12 ? C3C HEM 200 D 1 
HETATM 25 C C4C HEM . . . N 5 97.055 11.578 177.67 0.91 97.29 ? C4C HEM 200 D 1 
HETATM 26 C CMC HEM . . . N 5 99.325 13.827 175.683 0.91 108.47 ? CMC HEM 200 D 1 
HETATM 27 C CAC HEM . . . N 5 99.368 12.592 178.531 0.91 99.35 ? CAC HEM 200 D 1 
HETATM 28 C CBC HEM . . . N 5 99.378 11.844 179.634 0.91 125.94 ? CBC HEM 200 D 1 
HETATM 29 C C1D HEM . . . N 5 95.572 10.093 178.959 0.91 93.15 ? C1D HEM 200 D 1 
HETATM 30 C C2D HEM . . . N 5 95.26 9.351 180.171 0.91 98.71 ? C2D HEM 200 D 1 
HETATM 31 C C3D HEM . . . N 5 93.927 8.653 179.882 0.91 93.06 ? C3D HEM 200 D 1 
HETATM 32 C C4D HEM . . . N 5 93.563 9.045 178.538 0.91 106.56 ? C4D HEM 200 D 1 
HETATM 33 C CMD HEM . . . N 5 96.101 9.264 181.472 0.91 92.88 ? CMD HEM 200 D 1 
HETATM 34 C CAD HEM . . . N 5 93.138 7.712 180.813 0.91 96.35 ? CAD HEM 200 D 1 
HETATM 35 C CBD HEM . . . N 5 92.771 6.507 179.944 0.91 145.19 ? CBD HEM 200 D 1 
HETATM 36 C CGD HEM . . . N 5 92.466 5.269 180.745 0.91 162.54 ? CGD HEM 200 D 1 
HETATM 37 O O1D HEM . . . N 5 92.092 4.244 180.112 0.91 152.58 ? O1D HEM 200 D 1 
HETATM 38 O O2D HEM . . . N 5 92.595 5.304 181.998 0.91 148.69 ? O2D HEM 200 D 1 
HETATM 39 N NA HEM . . . N 5 92.716 9.778 175.747 0.91 124.89 ? NA HEM 200 D 1 
HETATM 40 N NB HEM . . . N 5 94.515 11.524 174.271 0.91 124.14 ? NB HEM 200 D 1 
HETATM 41 N NC HEM . . . N 5 96.326 11.653 176.5 0.91 93.38 ? NC HEM 200 D 1 
HETATM 42 N ND HEM . . . N 5 94.549 9.894 178.043 0.91 93.27 ? ND HEM 200 D 1 
HETATM 43 FE FE HEM . . . N 5 94.497 10.716 176.223 0.91 114.99 ? FE HEM 200 D 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           137 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           400 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           43 
#