data_3NMK
#
_model_server_result.job_id            w2vIX6F0tuBVjD-AEW_o2g 
_model_server_result.datetime_utc      '2024-11-15 13:54:36' 
_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":"K","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 . . . K 2 -35.741 57.577 -32.06 1 34.22 ? CHA HEM 150 C 1 
HETATM 2 C CHB HEM . . . K 2 -32.493 59.375 -35.183 1 32.19 ? CHB HEM 150 C 1 
HETATM 3 C CHC HEM . . . K 2 -30.595 54.942 -35.721 1 30.33 ? CHC HEM 150 C 1 
HETATM 4 C CHD HEM . . . K 2 -33.873 53.103 -32.656 1 27.85 ? CHD HEM 150 C 1 
HETATM 5 C C1A HEM . . . K 2 -35.089 58.437 -32.92 1 39 ? C1A HEM 150 C 1 
HETATM 6 C C2A HEM . . . K 2 -35.372 59.853 -33.102 1 40.41 ? C2A HEM 150 C 1 
HETATM 7 C C3A HEM . . . K 2 -34.468 60.346 -33.955 1 34.4 ? C3A HEM 150 C 1 
HETATM 8 C C4A HEM . . . K 2 -33.572 59.272 -34.335 1 31.82 ? C4A HEM 150 C 1 
HETATM 9 C CMA HEM . . . K 2 -34.426 61.792 -34.5 1 29.19 ? CMA HEM 150 C 1 
HETATM 10 C CAA HEM . . . K 2 -36.556 60.636 -32.488 1 48.39 ? CAA HEM 150 C 1 
HETATM 11 C CBA HEM . . . K 2 -36.59 60.452 -30.971 1 64.8 ? CBA HEM 150 C 1 
HETATM 12 C CGA HEM . . . K 2 -36.766 61.785 -30.273 1 74.49 ? CGA HEM 150 C 1 
HETATM 13 O O1A HEM . . . K 2 -36.011 62.068 -29.302 1 73.1 ? O1A HEM 150 C 1 
HETATM 14 O O2A HEM . . . K 2 -37.67 62.567 -30.678 1 79.34 ? O2A HEM 150 C 1 
HETATM 15 C C1B HEM . . . K 2 -31.709 58.333 -35.626 1 31.56 ? C1B HEM 150 C 1 
HETATM 16 C C2B HEM . . . K 2 -30.701 58.404 -36.667 1 29.8 ? C2B HEM 150 C 1 
HETATM 17 C C3B HEM . . . K 2 -30.171 57.186 -36.805 1 29.43 ? C3B HEM 150 C 1 
HETATM 18 C C4B HEM . . . K 2 -30.817 56.298 -35.855 1 31.68 ? C4B HEM 150 C 1 
HETATM 19 C CMB HEM . . . K 2 -30.281 59.679 -37.438 1 27.82 ? CMB HEM 150 C 1 
HETATM 20 C CAB HEM . . . K 2 -29.096 56.773 -37.834 1 31.63 ? CAB HEM 150 C 1 
HETATM 21 C CBB HEM . . . K 2 -27.997 57.518 -37.987 1 34.82 ? CBB HEM 150 C 1 
HETATM 22 C C1C HEM . . . K 2 -31.32 54.061 -34.943 1 26.27 ? C1C HEM 150 C 1 
HETATM 23 C C2C HEM . . . K 2 -31.094 52.629 -34.831 1 26.86 ? C2C HEM 150 C 1 
HETATM 24 C C3C HEM . . . K 2 -32.023 52.125 -34.014 1 26.95 ? C3C HEM 150 C 1 
HETATM 25 C C4C HEM . . . K 2 -32.849 53.218 -33.56 1 27.34 ? C4C HEM 150 C 1 
HETATM 26 C CMC HEM . . . K 2 -30.014 51.816 -35.575 1 19.04 ? CMC HEM 150 C 1 
HETATM 27 C CAC HEM . . . K 2 -32.235 50.636 -33.667 1 28.2 ? CAC HEM 150 C 1 
HETATM 28 C CBC HEM . . . K 2 -31.215 49.781 -33.808 1 28.98 ? CBC HEM 150 C 1 
HETATM 29 C C1D HEM . . . K 2 -34.63 54.133 -32.154 1 24.81 ? C1D HEM 150 C 1 
HETATM 30 C C2D HEM . . . K 2 -35.66 53.975 -31.15 1 27.48 ? C2D HEM 150 C 1 
HETATM 31 C C3D HEM . . . K 2 -36.249 55.373 -30.965 1 30.7 ? C3D HEM 150 C 1 
HETATM 32 C C4D HEM . . . K 2 -35.502 56.234 -31.866 1 29.46 ? C4D HEM 150 C 1 
HETATM 33 C CMD HEM . . . K 2 -36.071 52.686 -30.404 1 19.45 ? CMD HEM 150 C 1 
HETATM 34 C CAD HEM . . . K 2 -37.358 55.757 -29.966 1 30.76 ? CAD HEM 150 C 1 
HETATM 35 C CBD HEM . . . K 2 -36.718 56.434 -28.761 1 41.32 ? CBD HEM 150 C 1 
HETATM 36 C CGD HEM . . . K 2 -37.689 56.442 -27.613 1 46.47 ? CGD HEM 150 C 1 
HETATM 37 O O1D HEM . . . K 2 -38.915 56.492 -27.875 1 51.42 ? O1D HEM 150 C 1 
HETATM 38 O O2D HEM . . . K 2 -37.246 56.307 -26.442 1 54.83 ? O2D HEM 150 C 1 
HETATM 39 N NA HEM . . . K 2 -33.99 58.117 -33.699 1 34.61 ? NA HEM 150 C 1 
HETATM 40 N NB HEM . . . K 2 -31.73 57.041 -35.129 1 31.52 ? NB HEM 150 C 1 
HETATM 41 N NC HEM . . . K 2 -32.375 54.39 -34.116 1 24.33 ? NC HEM 150 C 1 
HETATM 42 N ND HEM . . . K 2 -34.592 55.456 -32.575 1 26.25 ? ND HEM 150 C 1 
HETATM 43 FE FE HEM . . . K 2 -33.187 56.226 -33.907 1 27.16 ? FE HEM 150 C 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#