data_3N6D
#
_model_server_result.job_id            Ffl5IVxjrNXF_EDPpSQ-Og 
_model_server_result.datetime_utc      '2024-11-13 15:26:03' 
_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          3n6d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":500}' 
#
_entry.id    3N6D 
#
_exptl.entry_id    3N6D 
_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    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            3N6D 
_cell.length_a            57.224 
_cell.length_b            106.669 
_cell.length_c            156.785 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3N6D 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,G,H,I,J,K,L,M 
_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 C N N 
? 2 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
metalc ? metalc1 A SG CYS 58 A CYS 96 1_555 G ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? 
metalc ? metalc2 A SG CYS 63 A CYS 101 1_555 G ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc3 A SG CYS 148 A CYS 186 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc4 G ZN ZN . A ZN 900 1_555 B SG CYS 58 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
#
_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 173 n n 
CHA C4D HEM doub 174 n n 
CHA HHA HEM sing 175 n n 
CHB C4A HEM sing 176 n n 
CHB C1B HEM doub 177 n n 
CHB HHB HEM sing 178 n n 
CHC C4B HEM sing 179 n n 
CHC C1C HEM doub 180 n n 
CHC HHC HEM sing 181 n n 
CHD C4C HEM doub 182 n n 
CHD C1D HEM sing 183 n n 
CHD HHD HEM sing 184 n n 
C1A C2A HEM doub 185 n y 
C1A NA HEM sing 186 n y 
C2A C3A HEM sing 187 n y 
C2A CAA HEM sing 188 n n 
C3A C4A HEM doub 189 n y 
C3A CMA HEM sing 190 n n 
C4A NA HEM sing 191 n y 
CMA HMA HEM sing 192 n n 
CMA HMAA HEM sing 193 n n 
CMA HMAB HEM sing 194 n n 
CAA CBA HEM sing 195 n n 
CAA HAA HEM sing 196 n n 
CAA HAAA HEM sing 197 n n 
CBA CGA HEM sing 198 n n 
CBA HBA HEM sing 199 n n 
CBA HBAA HEM sing 200 n n 
CGA O1A HEM doub 201 n n 
CGA O2A HEM sing 202 n n 
C1B C2B HEM sing 203 n n 
C1B NB HEM sing 204 n n 
C2B C3B HEM doub 205 n n 
C2B CMB HEM sing 206 n n 
C3B C4B HEM sing 207 n n 
C3B CAB HEM sing 208 n n 
C4B NB HEM doub 209 n n 
CMB HMB HEM sing 210 n n 
CMB HMBA HEM sing 211 n n 
CMB HMBB HEM sing 212 n n 
CAB CBB HEM doub 213 n n 
CAB HAB HEM sing 214 n n 
CBB HBB HEM sing 215 n n 
CBB HBBA HEM sing 216 n n 
C1C C2C HEM sing 217 n y 
C1C NC HEM sing 218 n y 
C2C C3C HEM doub 219 n y 
C2C CMC HEM sing 220 n n 
C3C C4C HEM sing 221 n y 
C3C CAC HEM sing 222 n n 
C4C NC HEM sing 223 n y 
CMC HMC HEM sing 224 n n 
CMC HMCA HEM sing 225 n n 
CMC HMCB HEM sing 226 n n 
CAC CBC HEM doub 227 n n 
CAC HAC HEM sing 228 n n 
CBC HBC HEM sing 229 n n 
CBC HBCA HEM sing 230 n n 
C1D C2D HEM sing 231 n n 
C1D ND HEM doub 232 n n 
C2D C3D HEM doub 233 n n 
C2D CMD HEM sing 234 n n 
C3D C4D HEM sing 235 n n 
C3D CAD HEM sing 236 n n 
C4D ND HEM sing 237 n n 
CMD HMD HEM sing 238 n n 
CMD HMDA HEM sing 239 n n 
CMD HMDB HEM sing 240 n n 
CAD CBD HEM sing 241 n n 
CAD HAD HEM sing 242 n n 
CAD HADA HEM sing 243 n n 
CBD CGD HEM sing 244 n n 
CBD HBD HEM sing 245 n n 
CBD HBDA HEM sing 246 n n 
CGD O1D HEM doub 247 n n 
CGD O2D HEM sing 248 n n 
O2A H2A HEM sing 249 n n 
O2D H2D HEM sing 250 n n 
FE NA HEM sing 251 n n 
FE NB HEM sing 252 n n 
FE NC HEM sing 253 n n 
FE ND HEM sing 254 n n 
#
_atom_sites.entry_id                     3N6D 
_atom_sites.fract_transf_matrix[1][1]    0.017475 
_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]    0.009375 
_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]    0.006378 
_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 HEM A 1 500 500 HEM HEM . 
D 3 H4B A 1 600 600 H4B H4B . 
E 4 CAD A 1 950 950 CAD CAD . 
F 5 XFN A 1 800 800 XFN XFN . 
G 6 ZN A 1 900 900 ZN ZN . 
H 2 HEM B 1 500 500 HEM HEM . 
I 3 H4B B 1 600 600 H4B H4B . 
J 4 CAD B 1 950 950 CAD CAD . 
K 5 XFN B 1 800 800 XFN XFN . 
L 7 HOH A 1 1001 1001 HOH HOH . 
L 7 HOH A 2 1002 1002 HOH HOH . 
L 7 HOH A 3 1003 1003 HOH HOH . 
L 7 HOH A 4 1004 1004 HOH HOH . 
L 7 HOH A 5 1005 1005 HOH HOH . 
L 7 HOH A 6 1006 1006 HOH HOH . 
L 7 HOH A 7 1007 1007 HOH HOH . 
L 7 HOH A 8 1008 1008 HOH HOH . 
L 7 HOH A 9 1009 1009 HOH HOH . 
L 7 HOH A 10 1010 1010 HOH HOH . 
L 7 HOH A 11 1011 1011 HOH HOH . 
L 7 HOH A 12 1012 1012 HOH HOH . 
L 7 HOH A 13 1013 1013 HOH HOH . 
M 7 HOH B 1 1014 1014 HOH HOH . 
M 7 HOH B 2 1015 1015 HOH HOH . 
M 7 HOH B 3 1016 1016 HOH HOH . 
M 7 HOH B 4 1017 1017 HOH HOH . 
M 7 HOH B 5 1018 1018 HOH HOH . 
M 7 HOH B 6 1019 1019 HOH HOH . 
M 7 HOH B 7 1020 1020 HOH HOH . 
M 7 HOH B 8 1021 1021 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 . . . H 2 4.426 7.883 64.188 1 33.35 ? CHA HEM 500 B 1 
HETATM 2 C CHB HEM . . . H 2 2.837 12.35 64.834 1 32.63 ? CHB HEM 500 B 1 
HETATM 3 C CHC HEM . . . H 2 3.835 12.002 69.499 1 32.83 ? CHC HEM 500 B 1 
HETATM 4 C CHD HEM . . . H 2 6.003 7.825 68.735 1 32.94 ? CHD HEM 500 B 1 
HETATM 5 C C1A HEM . . . H 2 3.736 9.019 64.042 1 35.67 ? C1A HEM 500 B 1 
HETATM 6 C C2A HEM . . . H 2 2.825 9.295 62.96 1 39.22 ? C2A HEM 500 B 1 
HETATM 7 C C3A HEM . . . H 2 2.394 10.542 63.131 1 38.27 ? C3A HEM 500 B 1 
HETATM 8 C C4A HEM . . . H 2 3.015 11.094 64.328 1 35.85 ? C4A HEM 500 B 1 
HETATM 9 C CMA HEM . . . H 2 1.403 11.272 62.227 1 39.17 ? CMA HEM 500 B 1 
HETATM 10 C CAA HEM . . . H 2 2.503 8.34 61.8 1 45.15 ? CAA HEM 500 B 1 
HETATM 11 C CBA HEM . . . H 2 1.328 7.386 61.96 1 54.14 ? CBA HEM 500 B 1 
HETATM 12 C CGA HEM . . . H 2 0.526 7.374 60.669 1 58.19 ? CGA HEM 500 B 1 
HETATM 13 O O1A HEM . . . H 2 0.955 8.113 59.727 1 58.92 ? O1A HEM 500 B 1 
HETATM 14 O O2A HEM . . . H 2 -0.525 6.653 60.586 1 59.54 ? O2A HEM 500 B 1 
HETATM 15 C C1B HEM . . . H 2 2.977 12.662 66.153 1 33.31 ? C1B HEM 500 B 1 
HETATM 16 C C2B HEM . . . H 2 2.591 13.904 66.792 1 34.96 ? C2B HEM 500 B 1 
HETATM 17 C C3B HEM . . . H 2 2.873 13.805 68.078 1 36.72 ? C3B HEM 500 B 1 
HETATM 18 C C4B HEM . . . H 2 3.449 12.499 68.298 1 34.39 ? C4B HEM 500 B 1 
HETATM 19 C CMB HEM . . . H 2 1.963 15.143 66.13 1 36.11 ? CMB HEM 500 B 1 
HETATM 20 C CAB HEM . . . H 2 2.62 14.893 69.159 1 41.69 ? CAB HEM 500 B 1 
HETATM 21 C CBB HEM . . . H 2 3.164 14.79 70.39 1 45.23 ? CBB HEM 500 B 1 
HETATM 22 C C1C HEM . . . H 2 4.45 10.807 69.665 1 32.44 ? C1C HEM 500 B 1 
HETATM 23 C C2C HEM . . . H 2 4.857 10.29 70.952 1 34.4 ? C2C HEM 500 B 1 
HETATM 24 C C3C HEM . . . H 2 5.475 9.137 70.743 1 33.36 ? C3C HEM 500 B 1 
HETATM 25 C C4C HEM . . . H 2 5.45 8.917 69.323 1 32.28 ? C4C HEM 500 B 1 
HETATM 26 C CMC HEM . . . H 2 4.629 10.985 72.319 1 36.13 ? CMC HEM 500 B 1 
HETATM 27 C CAC HEM . . . H 2 6.109 8.186 71.791 1 32.76 ? CAC HEM 500 B 1 
HETATM 28 C CBC HEM . . . H 2 6.868 8.638 72.787 1 31.94 ? CBC HEM 500 B 1 
HETATM 29 C C1D HEM . . . H 2 5.734 7.435 67.47 1 32.55 ? C1D HEM 500 B 1 
HETATM 30 C C2D HEM . . . H 2 6.061 6.137 66.964 1 33.45 ? C2D HEM 500 B 1 
HETATM 31 C C3D HEM . . . H 2 5.558 6.137 65.513 1 34.52 ? C3D HEM 500 B 1 
HETATM 32 C C4D HEM . . . H 2 4.992 7.469 65.344 1 33.34 ? C4D HEM 500 B 1 
HETATM 33 C CMD HEM . . . H 2 6.764 5.022 67.763 1 36.22 ? CMD HEM 500 B 1 
HETATM 34 C CAD HEM . . . H 2 5.633 5.047 64.415 1 35.03 ? CAD HEM 500 B 1 
HETATM 35 C CBD HEM . . . H 2 5.526 3.612 64.898 1 39.93 ? CBD HEM 500 B 1 
HETATM 36 C CGD HEM . . . H 2 4.386 2.958 64.144 1 44.82 ? CGD HEM 500 B 1 
HETATM 37 O O1D HEM . . . H 2 4.642 2.383 63.019 1 43.46 ? O1D HEM 500 B 1 
HETATM 38 O O2D HEM . . . H 2 3.221 3.041 64.695 1 46.51 ? O2D HEM 500 B 1 
HETATM 39 N NA HEM . . . H 2 3.857 10.12 64.868 1 34.75 ? NA HEM 500 B 1 
HETATM 40 N NB HEM . . . H 2 3.547 11.844 67.1 1 32.76 ? NB HEM 500 B 1 
HETATM 41 N NC HEM . . . H 2 4.832 9.953 68.679 1 30.2 ? NC HEM 500 B 1 
HETATM 42 N ND HEM . . . H 2 5.126 8.216 66.501 1 31.89 ? ND HEM 500 B 1 
HETATM 43 FE FE HEM . . . H 2 4.404 10.041 66.806 1 30.76 ? FE HEM 500 B 1 
#
_model_server_stats.io_time_ms              70 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#