data_1LM3
#
_model_server_result.job_id            QiAN6Lw5hHTT6MieM3L7Uw 
_model_server_result.datetime_utc      '2025-09-08 15:50:41' 
_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          1lm3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":200}' 
#
_entry.id    1LM3 
#
_exptl.entry_id    1LM3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          3 
_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            1LM3 
_cell.length_a            42.098 
_cell.length_b            48.995 
_cell.length_c            114.419 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1LM3 
_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,G,H,I 
_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
? 3 D N N 
? 3 G 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 B MET 7 1_555 D FE HEM . B HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? 
metalc ? metalc2 A OG1 THR 9 B THR 9 1_555 C MG MG . B MG 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.109 ? 
metalc ? metalc3 A NE2 HIS 102 B HIS 102 1_555 D FE HEM . B HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc4 B SD MET 7 D MET 7 1_555 G FE HEM . D HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc5 B OD1 ASP 74 D ASP 74 1_555 E MG MG . D MG 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? 
metalc ? metalc6 B NE2 HIS 102 D HIS 102 1_555 G FE HEM . D HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
#
_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 116 n n 
CHA C4D HEM doub 117 n n 
CHA HHA HEM sing 118 n n 
CHB C4A HEM sing 119 n n 
CHB C1B HEM doub 120 n n 
CHB HHB HEM sing 121 n n 
CHC C4B HEM sing 122 n n 
CHC C1C HEM doub 123 n n 
CHC HHC HEM sing 124 n n 
CHD C4C HEM doub 125 n n 
CHD C1D HEM sing 126 n n 
CHD HHD HEM sing 127 n n 
C1A C2A HEM doub 128 n y 
C1A NA HEM sing 129 n y 
C2A C3A HEM sing 130 n y 
C2A CAA HEM sing 131 n n 
C3A C4A HEM doub 132 n y 
C3A CMA HEM sing 133 n n 
C4A NA HEM sing 134 n y 
CMA HMA HEM sing 135 n n 
CMA HMAA HEM sing 136 n n 
CMA HMAB HEM sing 137 n n 
CAA CBA HEM sing 138 n n 
CAA HAA HEM sing 139 n n 
CAA HAAA HEM sing 140 n n 
CBA CGA HEM sing 141 n n 
CBA HBA HEM sing 142 n n 
CBA HBAA HEM sing 143 n n 
CGA O1A HEM doub 144 n n 
CGA O2A HEM sing 145 n n 
C1B C2B HEM sing 146 n n 
C1B NB HEM sing 147 n n 
C2B C3B HEM doub 148 n n 
C2B CMB HEM sing 149 n n 
C3B C4B HEM sing 150 n n 
C3B CAB HEM sing 151 n n 
C4B NB HEM doub 152 n n 
CMB HMB HEM sing 153 n n 
CMB HMBA HEM sing 154 n n 
CMB HMBB HEM sing 155 n n 
CAB CBB HEM doub 156 n n 
CAB HAB HEM sing 157 n n 
CBB HBB HEM sing 158 n n 
CBB HBBA HEM sing 159 n n 
C1C C2C HEM sing 160 n y 
C1C NC HEM sing 161 n y 
C2C C3C HEM doub 162 n y 
C2C CMC HEM sing 163 n n 
C3C C4C HEM sing 164 n y 
C3C CAC HEM sing 165 n n 
C4C NC HEM sing 166 n y 
CMC HMC HEM sing 167 n n 
CMC HMCA HEM sing 168 n n 
CMC HMCB HEM sing 169 n n 
CAC CBC HEM doub 170 n n 
CAC HAC HEM sing 171 n n 
CBC HBC HEM sing 172 n n 
CBC HBCA HEM sing 173 n n 
C1D C2D HEM sing 174 n n 
C1D ND HEM doub 175 n n 
C2D C3D HEM doub 176 n n 
C2D CMD HEM sing 177 n n 
C3D C4D HEM sing 178 n n 
C3D CAD HEM sing 179 n n 
C4D ND HEM sing 180 n n 
CMD HMD HEM sing 181 n n 
CMD HMDA HEM sing 182 n n 
CMD HMDB HEM sing 183 n n 
CAD CBD HEM sing 184 n n 
CAD HAD HEM sing 185 n n 
CAD HADA HEM sing 186 n n 
CBD CGD HEM sing 187 n n 
CBD HBD HEM sing 188 n n 
CBD HBDA HEM sing 189 n n 
CGD O1D HEM doub 190 n n 
CGD O2D HEM sing 191 n n 
O2A H2A HEM sing 192 n n 
O2D H2D HEM sing 193 n n 
FE NA HEM sing 194 n n 
FE NB HEM sing 195 n n 
FE NC HEM sing 196 n n 
FE ND HEM sing 197 n n 
#
_atom_sites.entry_id                     1LM3 
_atom_sites.fract_transf_matrix[1][1]    0.023754 
_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]    0.02041 
_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]    0.00874 
_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 MG B 1 107 25 MG MG . 
D 3 HEM B 1 200 200 HEM HEC . 
E 2 MG D 1 107 61 MG MG . 
F 2 MG D 1 108 70 MG MG . 
G 3 HEM D 1 200 200 HEM HEC . 
H 4 HOH B 1 201 1 HOH HOH . 
H 4 HOH B 2 202 2 HOH HOH . 
H 4 HOH B 3 203 3 HOH HOH . 
H 4 HOH B 4 204 4 HOH HOH . 
H 4 HOH B 5 205 13 HOH HOH . 
H 4 HOH B 6 206 14 HOH HOH . 
H 4 HOH B 7 207 15 HOH HOH . 
H 4 HOH B 8 208 16 HOH HOH . 
H 4 HOH B 9 209 17 HOH HOH . 
H 4 HOH B 10 210 18 HOH HOH . 
H 4 HOH B 11 211 19 HOH HOH . 
H 4 HOH B 12 212 20 HOH HOH . 
H 4 HOH B 13 213 21 HOH HOH . 
H 4 HOH B 14 214 22 HOH HOH . 
H 4 HOH B 15 215 23 HOH HOH . 
H 4 HOH B 16 216 26 HOH HOH . 
H 4 HOH B 17 217 27 HOH HOH . 
H 4 HOH B 18 218 28 HOH HOH . 
H 4 HOH B 19 219 29 HOH HOH . 
H 4 HOH B 20 220 30 HOH HOH . 
H 4 HOH B 21 221 36 HOH HOH . 
H 4 HOH B 22 222 37 HOH HOH . 
H 4 HOH B 23 223 38 HOH HOH . 
H 4 HOH B 24 224 39 HOH HOH . 
H 4 HOH B 25 225 40 HOH HOH . 
H 4 HOH B 26 226 41 HOH HOH . 
H 4 HOH B 27 227 43 HOH HOH . 
H 4 HOH B 28 228 45 HOH HOH . 
H 4 HOH B 29 229 46 HOH HOH . 
H 4 HOH B 30 230 47 HOH HOH . 
H 4 HOH B 31 231 64 HOH HOH . 
H 4 HOH B 32 232 65 HOH HOH . 
H 4 HOH B 33 233 67 HOH HOH . 
H 4 HOH B 34 234 68 HOH HOH . 
H 4 HOH B 35 235 69 HOH HOH . 
H 4 HOH B 36 236 71 HOH HOH . 
H 4 HOH B 37 237 74 HOH HOH . 
I 4 HOH D 1 201 5 HOH HOH . 
I 4 HOH D 2 202 6 HOH HOH . 
I 4 HOH D 3 203 7 HOH HOH . 
I 4 HOH D 4 204 8 HOH HOH . 
I 4 HOH D 5 205 9 HOH HOH . 
I 4 HOH D 6 206 10 HOH HOH . 
I 4 HOH D 7 207 11 HOH HOH . 
I 4 HOH D 8 208 12 HOH HOH . 
I 4 HOH D 9 209 24 HOH HOH . 
I 4 HOH D 10 210 31 HOH HOH . 
I 4 HOH D 11 211 32 HOH HOH . 
I 4 HOH D 12 212 33 HOH HOH . 
I 4 HOH D 13 213 42 HOH HOH . 
I 4 HOH D 14 214 48 HOH HOH . 
I 4 HOH D 15 215 50 HOH HOH . 
I 4 HOH D 16 216 51 HOH HOH . 
I 4 HOH D 17 217 52 HOH HOH . 
I 4 HOH D 18 218 54 HOH HOH . 
I 4 HOH D 19 219 55 HOH HOH . 
I 4 HOH D 20 220 56 HOH HOH . 
I 4 HOH D 21 221 57 HOH HOH . 
I 4 HOH D 22 222 59 HOH HOH . 
I 4 HOH D 23 223 60 HOH HOH . 
I 4 HOH D 24 224 62 HOH HOH . 
I 4 HOH D 25 225 63 HOH HOH . 
I 4 HOH D 26 226 72 HOH HOH . 
I 4 HOH D 27 227 73 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 . . . D 3 0.861 21.335 -2.445 1 52.81 ? CHA HEM 200 B 1 
HETATM 2 C CHB HEM . . . D 3 -2.573 21.253 0.874 1 50.74 ? CHB HEM 200 B 1 
HETATM 3 C CHC HEM . . . D 3 0.388 23.41 3.95 1 51.11 ? CHC HEM 200 B 1 
HETATM 4 C CHD HEM . . . D 3 3.83 23.457 0.638 1 50.89 ? CHD HEM 200 B 1 
HETATM 5 C C1A HEM . . . D 3 -0.347 21.121 -1.824 1 52.73 ? C1A HEM 200 B 1 
HETATM 6 C C2A HEM . . . D 3 -1.508 20.5 -2.459 1 54.39 ? C2A HEM 200 B 1 
HETATM 7 C C3A HEM . . . D 3 -2.469 20.476 -1.519 1 53.4 ? C3A HEM 200 B 1 
HETATM 8 C C4A HEM . . . D 3 -1.901 21.086 -0.313 1 52.16 ? C4A HEM 200 B 1 
HETATM 9 C CMA HEM . . . D 3 -3.877 19.917 -1.704 1 54.39 ? CMA HEM 200 B 1 
HETATM 10 C CAA HEM . . . D 3 -1.602 19.988 -3.912 1 58.1 ? CAA HEM 200 B 1 
HETATM 11 C CBA HEM . . . D 3 -0.827 18.695 -4.161 1 62.69 ? CBA HEM 200 B 1 
HETATM 12 C CGA HEM . . . D 3 -0.915 18.201 -5.619 1 65.05 ? CGA HEM 200 B 1 
HETATM 13 O O1A HEM . . . D 3 -1.577 18.848 -6.465 1 67.36 ? O1A HEM 200 B 1 
HETATM 14 O O2A HEM . . . D 3 -0.308 17.148 -5.92 1 66.55 ? O2A HEM 200 B 1 
HETATM 15 C C1B HEM . . . D 3 -2.07 21.832 2.031 1 49.75 ? C1B HEM 200 B 1 
HETATM 16 C C2B HEM . . . D 3 -2.829 21.995 3.262 1 49.86 ? C2B HEM 200 B 1 
HETATM 17 C C3B HEM . . . D 3 -1.961 22.627 4.129 1 50.53 ? C3B HEM 200 B 1 
HETATM 18 C C4B HEM . . . D 3 -0.716 22.816 3.415 1 50.2 ? C4B HEM 200 B 1 
HETATM 19 C CMB HEM . . . D 3 -4.293 21.56 3.525 1 51.23 ? CMB HEM 200 B 1 
HETATM 20 C CAB HEM . . . D 3 -2.278 23.048 5.581 1 51.4 ? CAB HEM 200 B 1 
HETATM 21 C CBB HEM . . . D 3 -2.217 21.92 6.607 1 52.72 ? CBB HEM 200 B 1 
HETATM 22 C C1C HEM . . . D 3 1.581 23.611 3.314 1 50.79 ? C1C HEM 200 B 1 
HETATM 23 C C2C HEM . . . D 3 2.711 24.252 3.948 1 51.08 ? C2C HEM 200 B 1 
HETATM 24 C C3C HEM . . . D 3 3.692 24.274 3.009 1 51.21 ? C3C HEM 200 B 1 
HETATM 25 C C4C HEM . . . D 3 3.137 23.634 1.818 1 50.28 ? C4C HEM 200 B 1 
HETATM 26 C CMC HEM . . . D 3 2.706 24.774 5.393 1 51.93 ? CMC HEM 200 B 1 
HETATM 27 C CAC HEM . . . D 3 5.07 24.959 3.078 1 50.75 ? CAC HEM 200 B 1 
HETATM 28 C CBC HEM . . . D 3 5.757 25.222 4.415 1 53.16 ? CBC HEM 200 B 1 
HETATM 29 C C1D HEM . . . D 3 3.329 22.877 -0.493 1 51.33 ? C1D HEM 200 B 1 
HETATM 30 C C2D HEM . . . D 3 4.095 22.717 -1.726 1 52.6 ? C2D HEM 200 B 1 
HETATM 31 C C3D HEM . . . D 3 3.24 22.111 -2.598 1 53.09 ? C3D HEM 200 B 1 
HETATM 32 C C4D HEM . . . D 3 1.992 21.92 -1.885 1 52.31 ? C4D HEM 200 B 1 
HETATM 33 C CMD HEM . . . D 3 5.547 23.147 -1.97 1 53.17 ? CMD HEM 200 B 1 
HETATM 34 C CAD HEM . . . D 3 3.513 21.694 -4.066 1 56 ? CAD HEM 200 B 1 
HETATM 35 C CBD HEM . . . D 3 4.02 20.263 -4.274 1 58.92 ? CBD HEM 200 B 1 
HETATM 36 C CGD HEM . . . D 3 4.369 19.916 -5.713 1 61.05 ? CGD HEM 200 B 1 
HETATM 37 O O1D HEM . . . D 3 4.163 18.758 -6.112 1 62.33 ? O1D HEM 200 B 1 
HETATM 38 O O2D HEM . . . D 3 4.862 20.793 -6.461 1 62.38 ? O2D HEM 200 B 1 
HETATM 39 N NA HEM . . . D 3 -0.602 21.479 -0.52 1 51.5 ? NA HEM 200 B 1 
HETATM 40 N NB HEM . . . D 3 -0.777 22.329 2.121 1 50.27 ? NB HEM 200 B 1 
HETATM 41 N NC HEM . . . D 3 1.838 23.237 2.015 1 50.75 ? NC HEM 200 B 1 
HETATM 42 N ND HEM . . . D 3 2.051 22.387 -0.598 1 50.95 ? ND HEM 200 B 1 
HETATM 43 FE FE HEM . . . D 3 0.608 22.342 0.751 1 51.12 ? FE HEM 200 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#