data_4NKZ
#
_model_server_result.job_id            9XdYZVQTFxETaVBKCXlbKA 
_model_server_result.datetime_utc      '2024-10-12 06:27:13' 
_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          4nkz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":600}' 
#
_entry.id    4NKZ 
#
_exptl.entry_id    4NKZ 
_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    4 
_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            4NKZ 
_cell.length_a            85.82 
_cell.length_b            151.093 
_cell.length_c            170.342 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NKZ 
_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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,M 1 1 
B,G,H,N 2 1 
C,I,J 3 1 
D,K,L,O 4 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 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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 424 A CYS 442 1_555 E FE HEM . A HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? 
metalc ? metalc2 B SG CYS 424 B CYS 442 1_555 G FE HEM . B HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? 
metalc ? metalc3 C SG CYS 424 C CYS 442 1_555 I FE HEM . C HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? 
metalc ? metalc4 D SG CYS 424 D CYS 442 1_555 K FE HEM . D HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? 
#
_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                     4NKZ 
_atom_sites.fract_transf_matrix[1][1]    0.011652 
_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]    0.006618 
_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]    0.005871 
_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 2 HEM A 1 600 600 HEM HEM . 
F 3 LZZ A 1 601 601 LZZ LZZ . 
G 2 HEM B 1 600 600 HEM HEM . 
H 3 LZZ B 1 601 601 LZZ LZZ . 
I 2 HEM C 1 600 600 HEM HEM . 
J 3 LZZ C 1 601 601 LZZ LZZ . 
K 2 HEM D 1 600 600 HEM HEM . 
L 3 LZZ D 1 601 601 LZZ LZZ . 
M 4 HOH A 1 701 3 HOH HOH . 
M 4 HOH A 2 702 8 HOH HOH . 
N 4 HOH B 1 701 2 HOH HOH . 
N 4 HOH B 2 702 4 HOH HOH . 
N 4 HOH B 3 703 5 HOH HOH . 
N 4 HOH B 4 704 9 HOH HOH . 
N 4 HOH B 5 705 10 HOH HOH . 
O 4 HOH D 1 701 7 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 . . . E 2 28.036 -10.758 202.493 1 51.53 ? CHA HEM 600 A 1 
HETATM 2 C CHB HEM . . . E 2 26.469 -10.235 207.032 1 55.07 ? CHB HEM 600 A 1 
HETATM 3 C CHC HEM . . . E 2 30.501 -7.769 208.151 1 50.31 ? CHC HEM 600 A 1 
HETATM 4 C CHD HEM . . . E 2 32.19 -8.496 203.667 1 52.22 ? CHD HEM 600 A 1 
HETATM 5 C C1A HEM . . . E 2 27.26 -10.783 203.61 1 60.33 ? C1A HEM 600 A 1 
HETATM 6 C C2A HEM . . . E 2 25.936 -11.333 203.642 1 63.95 ? C2A HEM 600 A 1 
HETATM 7 C C3A HEM . . . E 2 25.474 -11.204 204.907 1 58.35 ? C3A HEM 600 A 1 
HETATM 8 C C4A HEM . . . E 2 26.514 -10.565 205.698 1 55.71 ? C4A HEM 600 A 1 
HETATM 9 C CMA HEM . . . E 2 24.097 -11.63 205.465 1 58.18 ? CMA HEM 600 A 1 
HETATM 10 C CAA HEM . . . E 2 25.307 -11.913 202.343 1 58.74 ? CAA HEM 600 A 1 
HETATM 11 C CBA HEM . . . E 2 24.106 -12.808 202.586 1 64.41 ? CBA HEM 600 A 1 
HETATM 12 C CGA HEM . . . E 2 23.867 -13.6 201.322 1 70.39 ? CGA HEM 600 A 1 
HETATM 13 O O1A HEM . . . E 2 23.706 -14.858 201.445 1 74.18 ? O1A HEM 600 A 1 
HETATM 14 O O2A HEM . . . E 2 23.874 -12.972 200.219 1 54.19 ? O2A HEM 600 A 1 
HETATM 15 C C1B HEM . . . E 2 27.419 -9.503 207.717 1 56.6 ? C1B HEM 600 A 1 
HETATM 16 C C2B HEM . . . E 2 27.311 -9.093 209.107 1 50.29 ? C2B HEM 600 A 1 
HETATM 17 C C3B HEM . . . E 2 28.425 -8.414 209.412 1 50.83 ? C3B HEM 600 A 1 
HETATM 18 C C4B HEM . . . E 2 29.269 -8.384 208.233 1 53.46 ? C4B HEM 600 A 1 
HETATM 19 C CMB HEM . . . E 2 26.067 -9.435 209.953 1 49.61 ? CMB HEM 600 A 1 
HETATM 20 C CAB HEM . . . E 2 28.885 -7.728 210.709 1 54.22 ? CAB HEM 600 A 1 
HETATM 21 C CBB HEM . . . E 2 28.232 -7.769 211.872 1 65.66 ? CBB HEM 600 A 1 
HETATM 22 C C1C HEM . . . E 2 31.351 -7.836 207.07 1 57.37 ? C1C HEM 600 A 1 
HETATM 23 C C2C HEM . . . E 2 32.756 -7.498 207.083 1 57.56 ? C2C HEM 600 A 1 
HETATM 24 C C3C HEM . . . E 2 33.256 -7.69 205.862 1 62.17 ? C3C HEM 600 A 1 
HETATM 25 C C4C HEM . . . E 2 32.159 -8.173 205.012 1 58.65 ? C4C HEM 600 A 1 
HETATM 26 C CMC HEM . . . E 2 33.513 -7.016 208.332 1 65.39 ? CMC HEM 600 A 1 
HETATM 27 C CAC HEM . . . E 2 34.745 -7.426 205.521 1 67.51 ? CAC HEM 600 A 1 
HETATM 28 C CBC HEM . . . E 2 35.28 -7.592 204.312 1 68.06 ? CBC HEM 600 A 1 
HETATM 29 C C1D HEM . . . E 2 31.205 -9.114 202.926 1 57.22 ? C1D HEM 600 A 1 
HETATM 30 C C2D HEM . . . E 2 31.271 -9.381 201.498 1 56.53 ? C2D HEM 600 A 1 
HETATM 31 C C3D HEM . . . E 2 29.972 -10.099 201.143 1 56.13 ? C3D HEM 600 A 1 
HETATM 32 C C4D HEM . . . E 2 29.261 -10.19 202.387 1 51.78 ? C4D HEM 600 A 1 
HETATM 33 C CMD HEM . . . E 2 32.391 -9.014 200.514 1 62.5 ? CMD HEM 600 A 1 
HETATM 34 C CAD HEM . . . E 2 29.483 -10.591 199.764 1 68.98 ? CAD HEM 600 A 1 
HETATM 35 C CBD HEM . . . E 2 30.175 -11.888 199.352 1 73.17 ? CBD HEM 600 A 1 
HETATM 36 C CGD HEM . . . E 2 29.49 -12.488 198.147 1 66.64 ? CGD HEM 600 A 1 
HETATM 37 O O1D HEM . . . E 2 30.019 -13.495 197.614 1 70.95 ? O1D HEM 600 A 1 
HETATM 38 O O2D HEM . . . E 2 28.419 -11.982 197.718 1 64.22 ? O2D HEM 600 A 1 
HETATM 39 N NA HEM . . . E 2 27.582 -10.321 204.862 1 59.65 ? NA HEM 600 A 1 
HETATM 40 N NB HEM . . . E 2 28.617 -9.04 207.206 1 51.62 ? NB HEM 600 A 1 
HETATM 41 N NC HEM . . . E 2 31.012 -8.25 205.793 1 64.82 ? NC HEM 600 A 1 
HETATM 42 N ND HEM . . . E 2 29.991 -9.598 203.408 1 56.37 ? ND HEM 600 A 1 
HETATM 43 FE FE HEM . . . E 2 29.35 -9.496 205.395 1 56.53 ? FE HEM 600 A 1 
HETATM 44 H HHB HEM . . . E 2 25.661 -10.487 207.525 1 66.09 ? HHB HEM 600 A 1 
HETATM 45 H HHC HEM . . . E 2 30.858 -7.376 208.974 1 60.37 ? HHC HEM 600 A 1 
HETATM 46 H HHD HEM . . . E 2 33.009 -8.258 203.185 1 62.67 ? HHD HEM 600 A 1 
HETATM 47 H HMA HEM . . . E 2 23.388 -11.156 204.983 1 69.82 ? HMA HEM 600 A 1 
HETATM 48 H HMAA HEM . . . E 2 24.049 -11.41 206.418 1 69.82 ? HMAA HEM 600 A 1 
HETATM 49 H HMAB HEM . . . E 2 23.983 -12.597 205.347 1 69.82 ? HMAB HEM 600 A 1 
HETATM 50 H HAA HEM . . . E 2 25.984 -12.425 201.875 1 70.48 ? HAA HEM 600 A 1 
HETATM 51 H HAAA HEM . . . E 2 25.031 -11.174 201.778 1 70.48 ? HAAA HEM 600 A 1 
HETATM 52 H HBA HEM . . . E 2 23.327 -12.267 202.788 1 77.29 ? HBA HEM 600 A 1 
HETATM 53 H HBAA HEM . . . E 2 24.288 -13.412 203.324 1 77.29 ? HBAA HEM 600 A 1 
HETATM 54 H HMB HEM . . . E 2 25.28 -9.042 209.545 1 59.54 ? HMB HEM 600 A 1 
HETATM 55 H HMBA HEM . . . E 2 26.178 -9.08 210.849 1 59.54 ? HMBA HEM 600 A 1 
HETATM 56 H HMBB HEM . . . E 2 25.961 -10.398 209.998 1 59.54 ? HMBB HEM 600 A 1 
HETATM 57 H HAB HEM . . . E 2 29.706 -7.232 210.68 1 65.07 ? HAB HEM 600 A 1 
HETATM 58 H HBB HEM . . . E 2 28.589 -7.303 212.645 1 78.8 ? HBB HEM 600 A 1 
HETATM 59 H HBBA HEM . . . E 2 27.399 -8.259 211.944 1 78.8 ? HBBA HEM 600 A 1 
HETATM 60 H HMC HEM . . . E 2 33.108 -6.198 208.659 1 78.47 ? HMC HEM 600 A 1 
HETATM 61 H HMCA HEM . . . E 2 34.441 -6.85 208.104 1 78.47 ? HMCA HEM 600 A 1 
HETATM 62 H HMCB HEM . . . E 2 33.466 -7.698 209.021 1 78.47 ? HMCB HEM 600 A 1 
HETATM 63 H HAC HEM . . . E 2 35.319 -7.123 206.228 1 81.01 ? HAC HEM 600 A 1 
HETATM 64 H HBC HEM . . . E 2 36.222 -7.412 204.17 1 81.67 ? HBC HEM 600 A 1 
HETATM 65 H HBCA HEM . . . E 2 34.728 -7.897 203.575 1 81.67 ? HBCA HEM 600 A 1 
HETATM 66 H HMD HEM . . . E 2 32.153 -9.326 199.616 1 75.01 ? HMD HEM 600 A 1 
HETATM 67 H HMDA HEM . . . E 2 33.227 -9.441 200.797 1 75.01 ? HMDA HEM 600 A 1 
HETATM 68 H HMDB HEM . . . E 2 32.509 -8.042 200.502 1 75.01 ? HMDB HEM 600 A 1 
HETATM 69 H HAD HEM . . . E 2 29.669 -9.909 199.101 1 82.78 ? HAD HEM 600 A 1 
HETATM 70 H HADA HEM . . . E 2 28.526 -10.742 199.803 1 82.78 ? HADA HEM 600 A 1 
HETATM 71 H HBD HEM . . . E 2 30.139 -12.518 200.088 1 87.81 ? HBD HEM 600 A 1 
HETATM 72 H HBDA HEM . . . E 2 31.101 -11.702 199.134 1 87.81 ? HBDA HEM 600 A 1 
HETATM 73 H HHA HEM . . . E 2 27.675 -11.191 201.692 1 61.83 ? HHA HEM 600 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           73 
#