data_3M15
#
_model_server_result.job_id            oKTA3GSo4xcbE8y9jRFY5A 
_model_server_result.datetime_utc      '2024-11-06 15:27:30' 
_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          3m15 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":150}' 
#
_entry.id    3M15 
#
_exptl.entry_id    3M15 
_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    3 
_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            3M15 
_cell.length_a            50.879 
_cell.length_b            74.819 
_cell.length_c            81.358 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3M15 
_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    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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 D N N 
? 2 F 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 SD MET 7 A MET 7 1_555 D FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc2 A NE2 HIS 59 A HIS 59 1_555 G ZN ZN . B ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? 
metalc ? metalc3 A NE2 HIS 73 A HIS 73 1_555 E ZN ZN . A ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc4 A NE2 HIS 77 A HIS 77 1_555 E ZN ZN . A ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? 
metalc ? metalc5 A NE2 HIS 102 A HIS 102 1_555 D FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc6 E ZN ZN . A ZN 107 1_555 B NE2 HIS 59 B HIS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc7 E ZN ZN . A ZN 107 1_555 C NE2 HIS 59 C HIS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc8 B SD MET 7 B MET 7 1_555 F FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? 
metalc ? metalc9 B NE2 HIS 73 B HIS 73 1_555 G ZN ZN . B ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc10 B NE2 HIS 77 B HIS 77 1_555 G ZN ZN . B ZN 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.866 ? 
metalc ? metalc11 B NE2 HIS 102 B HIS 102 1_555 F FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc12 G ZN ZN . B ZN 107 1_555 C NE2 HIS 77 C HIS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc13 C SD MET 7 C MET 7 1_555 H FE HEM . C HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc14 C NE2 HIS 102 C HIS 102 1_555 H FE HEM . C HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
#
_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                     3M15 
_atom_sites.fract_transf_matrix[1][1]    0.019654 
_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]    0.013366 
_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]    0.012291 
_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
D 2 HEM A 1 150 150 HEM HEM . 
E 3 ZN A 1 107 2 ZN ZN . 
F 2 HEM B 1 150 150 HEM HEM . 
G 3 ZN B 1 107 1 ZN ZN . 
H 2 HEM C 1 150 150 HEM HEM . 
I 4 HOH A 1 108 1 HOH HOH . 
I 4 HOH A 2 109 4 HOH HOH . 
I 4 HOH A 3 110 9 HOH HOH . 
I 4 HOH A 4 111 11 HOH HOH . 
I 4 HOH A 5 112 12 HOH HOH . 
I 4 HOH A 6 113 13 HOH HOH . 
I 4 HOH A 7 114 14 HOH HOH . 
I 4 HOH A 8 115 15 HOH HOH . 
I 4 HOH A 9 116 16 HOH HOH . 
I 4 HOH A 10 117 18 HOH HOH . 
I 4 HOH A 11 118 20 HOH HOH . 
I 4 HOH A 12 119 17 HOH HOH . 
J 4 HOH B 1 108 5 HOH HOH . 
J 4 HOH B 2 109 7 HOH HOH . 
K 4 HOH C 1 107 2 HOH HOH . 
K 4 HOH C 2 108 3 HOH HOH . 
K 4 HOH C 3 109 6 HOH HOH . 
K 4 HOH C 4 110 8 HOH HOH . 
K 4 HOH C 5 111 10 HOH HOH . 
K 4 HOH C 6 112 19 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 20.889 -24.213 9.446 1 7.9 ? CHA HEM 150 C 1 
HETATM 2 C CHB HEM . . . H 2 22.61 -20.097 7.612 1 8.62 ? CHB HEM 150 C 1 
HETATM 3 C CHC HEM . . . H 2 20.553 -17.833 11.382 1 5.86 ? CHC HEM 150 C 1 
HETATM 4 C CHD HEM . . . H 2 19.003 -21.963 13.341 1 7.4 ? CHD HEM 150 C 1 
HETATM 5 C C1A HEM . . . H 2 21.561 -23.315 8.66 1 9.84 ? C1A HEM 150 C 1 
HETATM 6 C C2A HEM . . . H 2 22.35 -23.65 7.489 1 10.41 ? C2A HEM 150 C 1 
HETATM 7 C C3A HEM . . . H 2 22.834 -22.521 6.955 1 9.22 ? C3A HEM 150 C 1 
HETATM 8 C C4A HEM . . . H 2 22.352 -21.432 7.776 1 9.47 ? C4A HEM 150 C 1 
HETATM 9 C CMA HEM . . . H 2 23.737 -22.386 5.703 1 10.69 ? CMA HEM 150 C 1 
HETATM 10 C CAA HEM . . . H 2 22.549 -25.088 6.983 1 10.5 ? CAA HEM 150 C 1 
HETATM 11 C CBA HEM . . . H 2 21.389 -25.365 6.008 1 13.02 ? CBA HEM 150 C 1 
HETATM 12 C CGA HEM . . . H 2 21.538 -26.716 5.328 1 14.21 ? CGA HEM 150 C 1 
HETATM 13 O O1A HEM . . . H 2 20.498 -27.422 5.221 1 13.17 ? O1A HEM 150 C 1 
HETATM 14 O O2A HEM . . . H 2 22.691 -27.09 4.922 1 14.04 ? O2A HEM 150 C 1 
HETATM 15 C C1B HEM . . . H 2 22.162 -19.115 8.465 1 7.21 ? C1B HEM 150 C 1 
HETATM 16 C C2B HEM . . . H 2 22.329 -17.691 8.261 1 6.68 ? C2B HEM 150 C 1 
HETATM 17 C C3B HEM . . . H 2 21.765 -17.059 9.301 1 6.5 ? C3B HEM 150 C 1 
HETATM 18 C C4B HEM . . . H 2 21.226 -18.079 10.198 1 6.48 ? C4B HEM 150 C 1 
HETATM 19 C CMB HEM . . . H 2 23.014 -17.06 7.027 1 5.7 ? CMB HEM 150 C 1 
HETATM 20 C CAB HEM . . . H 2 21.668 -15.517 9.533 1 5.77 ? CAB HEM 150 C 1 
HETATM 21 C CBB HEM . . . H 2 21.716 -14.568 8.582 1 2.57 ? CBB HEM 150 C 1 
HETATM 22 C C1C HEM . . . H 2 19.94 -18.712 12.253 1 5.29 ? C1C HEM 150 C 1 
HETATM 23 C C2C HEM . . . H 2 19.236 -18.41 13.49 1 5.37 ? C2C HEM 150 C 1 
HETATM 24 C C3C HEM . . . H 2 18.8 -19.553 14.015 1 5.58 ? C3C HEM 150 C 1 
HETATM 25 C C4C HEM . . . H 2 19.229 -20.619 13.153 1 6.46 ? C4C HEM 150 C 1 
HETATM 26 C CMC HEM . . . H 2 19.007 -17.003 14.093 1 5.97 ? CMC HEM 150 C 1 
HETATM 27 C CAC HEM . . . H 2 17.994 -19.78 15.316 1 7.26 ? CAC HEM 150 C 1 
HETATM 28 C CBC HEM . . . H 2 17.508 -18.815 16.115 1 8.83 ? CBC HEM 150 C 1 
HETATM 29 C C1D HEM . . . H 2 19.406 -22.977 12.49 1 7.45 ? C1D HEM 150 C 1 
HETATM 30 C C2D HEM . . . H 2 19.268 -24.383 12.754 1 6.49 ? C2D HEM 150 C 1 
HETATM 31 C C3D HEM . . . H 2 19.841 -25.081 11.523 1 7.89 ? C3D HEM 150 C 1 
HETATM 32 C C4D HEM . . . H 2 20.291 -24.023 10.657 1 8.39 ? C4D HEM 150 C 1 
HETATM 33 C CMD HEM . . . H 2 18.669 -25.031 14.022 1 8.5 ? CMD HEM 150 C 1 
HETATM 34 C CAD HEM . . . H 2 19.952 -26.595 11.267 1 8.95 ? CAD HEM 150 C 1 
HETATM 35 C CBD HEM . . . H 2 18.986 -27.021 10.16 1 11.33 ? CBD HEM 150 C 1 
HETATM 36 C CGD HEM . . . H 2 19.238 -28.469 9.778 1 13.16 ? CGD HEM 150 C 1 
HETATM 37 O O1D HEM . . . H 2 18.28 -29.262 9.959 1 14.21 ? O1D HEM 150 C 1 
HETATM 38 O O2D HEM . . . H 2 20.367 -28.826 9.304 1 11.33 ? O2D HEM 150 C 1 
HETATM 39 N NA HEM . . . H 2 21.581 -21.948 8.799 1 9.82 ? NA HEM 150 C 1 
HETATM 40 N NB HEM . . . H 2 21.474 -19.314 9.635 1 6.4 ? NB HEM 150 C 1 
HETATM 41 N NC HEM . . . H 2 19.898 -20.07 12.083 1 6.97 ? NC HEM 150 C 1 
HETATM 42 N ND HEM . . . H 2 20.013 -22.806 11.252 1 8.55 ? ND HEM 150 C 1 
HETATM 43 FE FE HEM . . . H 2 20.736 -21.016 10.391 1 11.36 ? FE HEM 150 C 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#