data_4PK6
#
_model_server_result.job_id            2JiMBe4GIk-AV8xkxsjQuw 
_model_server_result.datetime_utc      '2024-11-15 00:42:58' 
_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          4pk6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":501}' 
#
_entry.id    4PK6 
#
_exptl.entry_id    4PK6 
_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            4PK6 
_cell.length_a            84.08 
_cell.length_b            91.12 
_cell.length_c            135.69 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PK6 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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 
#
_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 E 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 328 A CYS 308 1_555 B SG CYS 328 B CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
metalc ? metalc1 A NE2 HIS 366 A HIS 346 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc2 C FE HEM . A HEM 501 1_555 D N12 PKL . A PKL 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc3 B NE2 HIS 366 B HIS 346 1_555 E FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc4 E FE HEM . B HEM 501 1_555 F N12 PKL . B PKL 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
#
_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                     4PK6 
_atom_sites.fract_transf_matrix[1][1]    0.011893 
_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]    0.010975 
_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]    0.00737 
_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 1 501 404 HEM HEM . 
D 3 PKL A 1 502 1 PKL UNL . 
E 2 HEM B 1 501 404 HEM HEM . 
F 3 PKL B 1 502 2 PKL UNL . 
#
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 2 21.179 -2.659 21.575 1 67.66 ? CHA HEM 501 B 1 
HETATM 2 C CHB HEM . . . E 2 22.794 -6.961 23.047 1 68.83 ? CHB HEM 501 B 1 
HETATM 3 C CHC HEM . . . E 2 24.198 -7.955 18.491 1 71.1 ? CHC HEM 501 B 1 
HETATM 4 C CHD HEM . . . E 2 22.232 -3.811 16.988 1 67.79 ? CHD HEM 501 B 1 
HETATM 5 C C1A HEM . . . E 2 21.534 -3.741 22.329 1 65.59 ? C1A HEM 501 B 1 
HETATM 6 C C2A HEM . . . E 2 21.404 -3.783 23.733 1 64.65 ? C2A HEM 501 B 1 
HETATM 7 C C3A HEM . . . E 2 21.859 -4.99 24.143 1 64.7 ? C3A HEM 501 B 1 
HETATM 8 C C4A HEM . . . E 2 22.262 -5.694 22.997 1 65.7 ? C4A HEM 501 B 1 
HETATM 9 C CMA HEM . . . E 2 21.908 -5.51 25.558 1 65.19 ? CMA HEM 501 B 1 
HETATM 10 C CAA HEM . . . E 2 20.85 -2.696 24.619 1 63.16 ? CAA HEM 501 B 1 
HETATM 11 C CBA HEM . . . E 2 22.023 -1.956 25.264 1 63.19 ? CBA HEM 501 B 1 
HETATM 12 C CGA HEM . . . E 2 22.376 -0.758 24.429 1 63.47 ? CGA HEM 501 B 1 
HETATM 13 O O1A HEM . . . E 2 23.053 -0.882 23.385 1 62.41 ? O1A HEM 501 B 1 
HETATM 14 O O2A HEM . . . E 2 21.984 0.37 24.793 1 66 ? O2A HEM 501 B 1 
HETATM 15 C C1B HEM . . . E 2 23.307 -7.599 21.923 1 70.06 ? C1B HEM 501 B 1 
HETATM 16 C C2B HEM . . . E 2 23.875 -8.899 21.982 1 69.9 ? C2B HEM 501 B 1 
HETATM 17 C C3B HEM . . . E 2 24.278 -9.205 20.713 1 70.84 ? C3B HEM 501 B 1 
HETATM 18 C C4B HEM . . . E 2 23.931 -8.03 19.869 1 70.47 ? C4B HEM 501 B 1 
HETATM 19 C CMB HEM . . . E 2 24 -9.76 23.215 1 69.66 ? CMB HEM 501 B 1 
HETATM 20 C CAB HEM . . . E 2 24.927 -10.452 20.265 1 71.86 ? CAB HEM 501 B 1 
HETATM 21 C CBB HEM . . . E 2 24.215 -11.365 19.609 1 70.14 ? CBB HEM 501 B 1 
HETATM 22 C C1C HEM . . . E 2 23.801 -6.919 17.645 1 69.28 ? C1C HEM 501 B 1 
HETATM 23 C C2C HEM . . . E 2 24.081 -6.789 16.269 1 69.9 ? C2C HEM 501 B 1 
HETATM 24 C C3C HEM . . . E 2 23.514 -5.597 15.838 1 67.8 ? C3C HEM 501 B 1 
HETATM 25 C C4C HEM . . . E 2 22.891 -5.006 16.971 1 67.8 ? C4C HEM 501 B 1 
HETATM 26 C CMC HEM . . . E 2 24.838 -7.775 15.411 1 72.01 ? CMC HEM 501 B 1 
HETATM 27 C CAC HEM . . . E 2 23.535 -5.052 14.467 1 66.13 ? CAC HEM 501 B 1 
HETATM 28 C CBC HEM . . . E 2 24.308 -4.011 14.17 1 63.61 ? CBC HEM 501 B 1 
HETATM 29 C C1D HEM . . . E 2 21.792 -3.213 18.169 1 67.81 ? C1D HEM 501 B 1 
HETATM 30 C C2D HEM . . . E 2 21.125 -1.913 18.1 1 67.09 ? C2D HEM 501 B 1 
HETATM 31 C C3D HEM . . . E 2 20.822 -1.578 19.36 1 66.95 ? C3D HEM 501 B 1 
HETATM 32 C C4D HEM . . . E 2 21.315 -2.684 20.202 1 68.09 ? C4D HEM 501 B 1 
HETATM 33 C CMD HEM . . . E 2 20.842 -1.115 16.854 1 68.88 ? CMD HEM 501 B 1 
HETATM 34 C CAD HEM . . . E 2 20.123 -0.312 19.795 1 66.81 ? CAD HEM 501 B 1 
HETATM 35 C CBD HEM . . . E 2 18.678 -0.605 20.226 1 65.13 ? CBD HEM 501 B 1 
HETATM 36 C CGD HEM . . . E 2 17.745 -0.829 19.057 1 65.47 ? CGD HEM 501 B 1 
HETATM 37 O O1D HEM . . . E 2 16.754 -1.587 19.182 1 64.9 ? O1D HEM 501 B 1 
HETATM 38 O O2D HEM . . . E 2 17.935 -0.258 17.96 1 65.58 ? O2D HEM 501 B 1 
HETATM 39 N NA HEM . . . E 2 22.111 -4.904 21.884 1 64.94 ? NA HEM 501 B 1 
HETATM 40 N NB HEM . . . E 2 23.372 -7.12 20.679 1 68.84 ? NB HEM 501 B 1 
HETATM 41 N NC HEM . . . E 2 23.149 -5.799 18.046 1 66.88 ? NC HEM 501 B 1 
HETATM 42 N ND HEM . . . E 2 21.902 -3.632 19.451 1 68.35 ? ND HEM 501 B 1 
HETATM 43 FE FE HEM . . . E 2 22.668 -5.27 19.993 1 64.78 ? FE HEM 501 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#