data_3NMK
#
_model_server_result.job_id            Z6vXOfKG9DDaNnYofxd4WQ 
_model_server_result.datetime_utc      '2024-11-15 13:58:26' 
_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          3nmk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":150}' 
#
_entry.id    3NMK 
#
_exptl.entry_id    3NMK 
_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         120 
_cell.entry_id            3NMK 
_cell.length_a            99.467 
_cell.length_b            99.467 
_cell.length_c            109.544 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NMK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
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,O 1 1 
B,G,H,I,P 2 1 
C,J,K,L,Q 3 1 
D,M,N,R 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 K N N 
? 2 M 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 SD MET 7 A MET 7 1_555 E FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc2 A NE2 HIS 102 A HIS 102 1_555 E FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc3 F NAJ PXX . A PXX 151 1_555 J ZN ZN . C ZN 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc4 F NAK PXX . A PXX 151 1_555 J ZN ZN . C ZN 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc5 B SD MET 7 B MET 7 1_555 G FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc6 B NE2 HIS 102 B HIS 102 1_555 G FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc7 P O HOH . B HOH 113 1_555 I ZN ZN . B ZN 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? 
metalc ? metalc8 H NAK PXX . B PXX 151 1_555 I ZN ZN . B ZN 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc9 H NAJ PXX . B PXX 151 1_555 I ZN ZN . B ZN 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc10 I ZN ZN . B ZN 152 1_555 N NAJ PXX . D PXX 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc11 I ZN ZN . B ZN 152 1_555 N NAK PXX . D PXX 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc12 C SD MET 7 C MET 7 1_555 K FE HEM . C HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc13 C NE2 HIS 102 C HIS 102 1_555 K FE HEM . C HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc14 Q O HOH . C HOH 107 1_555 J ZN ZN . C ZN 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? 
metalc ? metalc15 L NAK PXX . C PXX 151 1_555 J ZN ZN . C ZN 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc16 L NAJ PXX . C PXX 151 1_555 J ZN ZN . C ZN 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc17 D SD MET 7 D MET 7 1_555 M FE HEM . D HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc18 D NE2 HIS 102 D HIS 102 1_555 M FE HEM . D HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? 
#
_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                     3NMK 
_atom_sites.fract_transf_matrix[1][1]    0.010054 
_atom_sites.fract_transf_matrix[1][2]    0.005804 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011609 
_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]    0.009129 
_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 1 150 150 HEM HEM . 
F 3 PXX A 1 151 151 PXX PXX . 
G 2 HEM B 1 150 150 HEM HEM . 
H 3 PXX B 1 151 151 PXX PXX . 
I 4 ZN B 1 152 152 ZN ZN . 
J 4 ZN C 1 152 152 ZN ZN . 
K 2 HEM C 1 150 150 HEM HEM . 
L 3 PXX C 1 151 151 PXX PXX . 
M 2 HEM D 1 150 150 HEM HEM . 
N 3 PXX D 1 151 151 PXX PXX . 
O 5 HOH A 1 108 7 HOH HOH . 
O 5 HOH A 2 109 25 HOH HOH . 
O 5 HOH A 3 110 29 HOH HOH . 
O 5 HOH A 4 112 17 HOH HOH . 
P 5 HOH B 1 107 8 HOH HOH . 
P 5 HOH B 2 108 9 HOH HOH . 
P 5 HOH B 3 109 11 HOH HOH . 
P 5 HOH B 4 110 27 HOH HOH . 
P 5 HOH B 5 111 32 HOH HOH . 
P 5 HOH B 6 112 34 HOH HOH . 
P 5 HOH B 7 113 2 HOH HOH . 
Q 5 HOH C 1 107 1 HOH HOH . 
Q 5 HOH C 2 108 5 HOH HOH . 
Q 5 HOH C 3 109 6 HOH HOH . 
Q 5 HOH C 4 110 12 HOH HOH . 
Q 5 HOH C 5 111 15 HOH HOH . 
Q 5 HOH C 6 112 4 HOH HOH . 
Q 5 HOH C 7 113 18 HOH HOH . 
Q 5 HOH C 8 114 20 HOH HOH . 
Q 5 HOH C 9 115 22 HOH HOH . 
Q 5 HOH C 10 116 24 HOH HOH . 
Q 5 HOH C 11 117 26 HOH HOH . 
Q 5 HOH C 12 118 33 HOH HOH . 
R 5 HOH D 1 108 3 HOH HOH . 
R 5 HOH D 2 109 10 HOH HOH . 
R 5 HOH D 3 110 13 HOH HOH . 
R 5 HOH D 4 111 14 HOH HOH . 
R 5 HOH D 5 112 16 HOH HOH . 
R 5 HOH D 6 113 19 HOH HOH . 
R 5 HOH D 7 114 21 HOH HOH . 
R 5 HOH D 8 115 23 HOH HOH . 
R 5 HOH D 9 116 31 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 . . . M 2 -12.42 30.111 -32.595 1 37.72 ? CHA HEM 150 D 1 
HETATM 2 C CHB HEM . . . M 2 -15.933 28.474 -35.504 1 34.83 ? CHB HEM 150 D 1 
HETATM 3 C CHC HEM . . . M 2 -18.137 32.77 -35.226 1 29.9 ? CHC HEM 150 D 1 
HETATM 4 C CHD HEM . . . M 2 -14.654 34.448 -32.295 1 28.64 ? CHD HEM 150 D 1 
HETATM 5 C C1A HEM . . . M 2 -13.185 29.299 -33.395 1 40.56 ? C1A HEM 150 D 1 
HETATM 6 C C2A HEM . . . M 2 -12.883 27.916 -33.709 1 42.85 ? C2A HEM 150 D 1 
HETATM 7 C C3A HEM . . . M 2 -13.867 27.452 -34.49 1 36.85 ? C3A HEM 150 D 1 
HETATM 8 C C4A HEM . . . M 2 -14.804 28.535 -34.719 1 36.62 ? C4A HEM 150 D 1 
HETATM 9 C CMA HEM . . . M 2 -13.98 26.033 -35.083 1 26.14 ? CMA HEM 150 D 1 
HETATM 10 C CAA HEM . . . M 2 -11.669 27.125 -33.165 1 42.47 ? CAA HEM 150 D 1 
HETATM 11 C CBA HEM . . . M 2 -11.954 26.718 -31.72 1 52.03 ? CBA HEM 150 D 1 
HETATM 12 C CGA HEM . . . M 2 -10.76 26.012 -31.124 1 59.38 ? CGA HEM 150 D 1 
HETATM 13 O O1A HEM . . . M 2 -10.918 24.86 -30.638 1 58.06 ? O1A HEM 150 D 1 
HETATM 14 O O2A HEM . . . M 2 -9.652 26.615 -31.1 1 61.79 ? O2A HEM 150 D 1 
HETATM 15 C C1B HEM . . . M 2 -16.796 29.515 -35.736 1 31.69 ? C1B HEM 150 D 1 
HETATM 16 C C2B HEM . . . M 2 -17.884 29.518 -36.688 1 33.4 ? C2B HEM 150 D 1 
HETATM 17 C C3B HEM . . . M 2 -18.48 30.704 -36.63 1 32.84 ? C3B HEM 150 D 1 
HETATM 18 C C4B HEM . . . M 2 -17.818 31.488 -35.603 1 33.71 ? C4B HEM 150 D 1 
HETATM 19 C CMB HEM . . . M 2 -18.27 28.37 -37.646 1 38.13 ? CMB HEM 150 D 1 
HETATM 20 C CAB HEM . . . M 2 -19.718 31.118 -37.456 1 29.91 ? CAB HEM 150 D 1 
HETATM 21 C CBB HEM . . . M 2 -20.909 30.574 -37.19 1 16.51 ? CBB HEM 150 D 1 
HETATM 22 C C1C HEM . . . M 2 -17.363 33.598 -34.449 1 29.39 ? C1C HEM 150 D 1 
HETATM 23 C C2C HEM . . . M 2 -17.642 34.991 -34.179 1 28.77 ? C2C HEM 150 D 1 
HETATM 24 C C3C HEM . . . M 2 -16.679 35.464 -33.379 1 28.76 ? C3C HEM 150 D 1 
HETATM 25 C C4C HEM . . . M 2 -15.76 34.378 -33.102 1 26.5 ? C4C HEM 150 D 1 
HETATM 26 C CMC HEM . . . M 2 -18.83 35.783 -34.757 1 21.03 ? CMC HEM 150 D 1 
HETATM 27 C CAC HEM . . . M 2 -16.538 36.936 -32.921 1 32.55 ? CAC HEM 150 D 1 
HETATM 28 C CBC HEM . . . M 2 -17.663 37.652 -32.742 1 22.11 ? CBC HEM 150 D 1 
HETATM 29 C C1D HEM . . . M 2 -13.732 33.447 -32.077 1 32.11 ? C1D HEM 150 D 1 
HETATM 30 C C2D HEM . . . M 2 -12.535 33.553 -31.254 1 32.15 ? C2D HEM 150 D 1 
HETATM 31 C C3D HEM . . . M 2 -11.855 32.191 -31.341 1 39.07 ? C3D HEM 150 D 1 
HETATM 32 C C4D HEM . . . M 2 -12.68 31.416 -32.245 1 38.36 ? C4D HEM 150 D 1 
HETATM 33 C CMD HEM . . . M 2 -12.055 34.741 -30.403 1 27.92 ? CMD HEM 150 D 1 
HETATM 34 C CAD HEM . . . M 2 -10.604 31.724 -30.559 1 44.98 ? CAD HEM 150 D 1 
HETATM 35 C CBD HEM . . . M 2 -11.051 30.931 -29.327 1 46.55 ? CBD HEM 150 D 1 
HETATM 36 C CGD HEM . . . M 2 -9.905 30.675 -28.378 1 47.34 ? CGD HEM 150 D 1 
HETATM 37 O O1D HEM . . . M 2 -8.788 31.212 -28.598 1 48.94 ? O1D HEM 150 D 1 
HETATM 38 O O2D HEM . . . M 2 -10.129 29.983 -27.353 1 49.28 ? O2D HEM 150 D 1 
HETATM 39 N NA HEM . . . M 2 -14.368 29.645 -34.021 1 36.29 ? NA HEM 150 D 1 
HETATM 40 N NB HEM . . . M 2 -16.813 30.718 -35.054 1 33.08 ? NB HEM 150 D 1 
HETATM 41 N NC HEM . . . M 2 -16.201 33.256 -33.782 1 30.21 ? NC HEM 150 D 1 
HETATM 42 N ND HEM . . . M 2 -13.754 32.195 -32.68 1 33.28 ? ND HEM 150 D 1 
HETATM 43 FE FE HEM . . . M 2 -15.318 31.463 -33.882 1 30.32 ? FE HEM 150 D 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#