data_3LC4
#
_model_server_result.job_id            cb1k4PIXZpZGA5fdSfQNmQ 
_model_server_result.datetime_utc      '2024-12-03 19:27:33' 
_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          3lc4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    3LC4 
#
_exptl.entry_id    3LC4 
_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    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            3LC4 
_cell.length_a            70.779 
_cell.length_b            70.779 
_cell.length_c            224.629 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LC4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 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 C N N 
? 2 E 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 416 A CYS 437 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? 
metalc ? metalc2 C FE HEM . A HEM 500 1_555 D N15 LC4 . A LC4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? 
metalc ? metalc3 B SG CYS 416 B CYS 437 1_555 E FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc4 E FE HEM . B HEM 500 1_555 F N15 LC4 . B LC4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? 
#
_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                     3LC4 
_atom_sites.fract_transf_matrix[1][1]    0.014129 
_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]    0.014129 
_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]    0.004452 
_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 HEM A 1 500 500 HEM HEM . 
D 3 LC4 A 1 501 501 LC4 UNK . 
E 2 HEM B 1 500 500 HEM HEM . 
F 3 LC4 B 1 501 501 LC4 UNK . 
G 4 HOH A 1 1 1 HOH HOH . 
G 4 HOH A 2 2 2 HOH HOH . 
H 4 HOH B 1 3 3 HOH HOH . 
H 4 HOH B 2 4 4 HOH HOH . 
H 4 HOH B 3 5 5 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 . . . C 2 6.102 -6.249 5.745 1 25.08 ? CHA HEM 500 A 1 
HETATM 2 C CHB HEM . . . C 2 3.365 -2.341 6.494 1 23.62 ? CHB HEM 500 A 1 
HETATM 3 C CHC HEM . . . C 2 -0.24 -5.278 7.664 1 22.66 ? CHC HEM 500 A 1 
HETATM 4 C CHD HEM . . . C 2 2.388 -9.2 7.042 1 22.77 ? CHD HEM 500 A 1 
HETATM 5 C C1A HEM . . . C 2 5.705 -4.946 5.851 1 25.16 ? C1A HEM 500 A 1 
HETATM 6 C C2A HEM . . . C 2 6.52 -3.772 5.593 1 26.58 ? C2A HEM 500 A 1 
HETATM 7 C C3A HEM . . . C 2 5.749 -2.69 5.805 1 25.27 ? C3A HEM 500 A 1 
HETATM 8 C C4A HEM . . . C 2 4.433 -3.15 6.187 1 24.23 ? C4A HEM 500 A 1 
HETATM 9 C CMA HEM . . . C 2 6.159 -1.2 5.678 1 24.09 ? CMA HEM 500 A 1 
HETATM 10 C CAA HEM . . . C 2 8.015 -3.768 5.19 1 29.67 ? CAA HEM 500 A 1 
HETATM 11 C CBA HEM . . . C 2 8.225 -3.65 3.688 1 34.54 ? CBA HEM 500 A 1 
HETATM 12 C CGA HEM . . . C 2 9.704 -3.619 3.323 1 37.74 ? CGA HEM 500 A 1 
HETATM 13 O O1A HEM . . . C 2 10.045 -2.947 2.314 1 39.11 ? O1A HEM 500 A 1 
HETATM 14 O O2A HEM . . . C 2 10.559 -4.263 4.002 1 39.77 ? O2A HEM 500 A 1 
HETATM 15 C C1B HEM . . . C 2 2.132 -2.806 6.887 1 23.24 ? C1B HEM 500 A 1 
HETATM 16 C C2B HEM . . . C 2 0.948 -2.008 7.177 1 22.09 ? C2B HEM 500 A 1 
HETATM 17 C C3B HEM . . . C 2 -0.036 -2.858 7.509 1 21.61 ? C3B HEM 500 A 1 
HETATM 18 C C4B HEM . . . C 2 0.51 -4.181 7.423 1 22.45 ? C4B HEM 500 A 1 
HETATM 19 C CMB HEM . . . C 2 0.924 -0.47 7.094 1 22.39 ? CMB HEM 500 A 1 
HETATM 20 C CAB HEM . . . C 2 -1.514 -2.67 7.908 1 19.63 ? CAB HEM 500 A 1 
HETATM 21 C CBB HEM . . . C 2 -1.925 -1.632 8.623 1 20.82 ? CBB HEM 500 A 1 
HETATM 22 C C1C HEM . . . C 2 0.132 -6.569 7.535 1 22.46 ? C1C HEM 500 A 1 
HETATM 23 C C2C HEM . . . C 2 -0.77 -7.679 7.672 1 21.75 ? C2C HEM 500 A 1 
HETATM 24 C C3C HEM . . . C 2 -0.038 -8.769 7.531 1 22.18 ? C3C HEM 500 A 1 
HETATM 25 C C4C HEM . . . C 2 1.328 -8.382 7.28 1 22.53 ? C4C HEM 500 A 1 
HETATM 26 C CMC HEM . . . C 2 -2.288 -7.573 7.942 1 19.97 ? CMC HEM 500 A 1 
HETATM 27 C CAC HEM . . . C 2 -0.59 -10.187 7.573 1 23.47 ? CAC HEM 500 A 1 
HETATM 28 C CBC HEM . . . C 2 -1.891 -10.278 7.302 1 25.55 ? CBC HEM 500 A 1 
HETATM 29 C C1D HEM . . . C 2 3.627 -8.752 6.649 1 24.98 ? C1D HEM 500 A 1 
HETATM 30 C C2D HEM . . . C 2 4.748 -9.624 6.46 1 26.77 ? C2D HEM 500 A 1 
HETATM 31 C C3D HEM . . . C 2 5.911 -8.731 6.055 1 27.59 ? C3D HEM 500 A 1 
HETATM 32 C C4D HEM . . . C 2 5.376 -7.382 6.052 1 25.92 ? C4D HEM 500 A 1 
HETATM 33 C CMD HEM . . . C 2 4.742 -11.155 6.641 1 28.99 ? CMD HEM 500 A 1 
HETATM 34 C CAD HEM . . . C 2 7.346 -9.198 5.726 1 31.57 ? CAD HEM 500 A 1 
HETATM 35 C CBD HEM . . . C 2 7.769 -8.675 4.353 1 35.72 ? CBD HEM 500 A 1 
HETATM 36 C CGD HEM . . . C 2 8.816 -9.593 3.794 1 37.8 ? CGD HEM 500 A 1 
HETATM 37 O O1D HEM . . . C 2 8.406 -10.591 3.162 1 39.55 ? O1D HEM 500 A 1 
HETATM 38 O O2D HEM . . . C 2 10.034 -9.336 3.983 1 38.33 ? O2D HEM 500 A 1 
HETATM 39 N NA HEM . . . C 2 4.438 -4.531 6.186 1 24.19 ? NA HEM 500 A 1 
HETATM 40 N NB HEM . . . C 2 1.823 -4.139 7.045 1 23 ? NB HEM 500 A 1 
HETATM 41 N NC HEM . . . C 2 1.398 -7.015 7.295 1 23.06 ? NC HEM 500 A 1 
HETATM 42 N ND HEM . . . C 2 4.032 -7.441 6.396 1 24.7 ? ND HEM 500 A 1 
HETATM 43 FE FE HEM . . . C 2 2.933 -5.772 6.725 1 26.05 ? FE HEM 500 A 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#