data_3S48
#
_model_server_result.job_id            sR1Volr-oDFYvRaii9A7sQ 
_model_server_result.datetime_utc      '2025-08-05 14:57:24' 
_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          3s48 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":500}' 
#
_entry.id    3S48 
#
_exptl.entry_id    3S48 
_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            3S48 
_cell.length_a            115.607 
_cell.length_b            115.607 
_cell.length_c            142.333 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3S48 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,B,E,G 1 1 
C,D,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
? 3 E N N 
? 3 F 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 B NE2 HIS 87 D HIS 87 1_555 E FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc2 E FE HEM . D HEM 500 1_555 G O HOH . D HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
metalc ? metalc3 D NE2 HIS 87 C HIS 87 1_555 F FE HEM . C HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc4 F FE HEM . C HEM 500 1_555 H O HOH . C HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? 
#
_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                     3S48 
_atom_sites.fract_transf_matrix[1][1]    0.00865 
_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]    0.00865 
_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]    0.007026 
_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 3 HEM D 1 500 500 HEM HEM . 
F 3 HEM C 1 500 500 HEM HEM . 
G 4 HOH D 1 501 501 HOH HOH . 
H 4 HOH C 1 501 501 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 . . . F 3 13.593 -64.171 4.43 1 99.14 ? CHA HEM 500 C 1 
HETATM 2 C CHB HEM . . . F 3 17.986 -62.963 2.734 1 96.42 ? CHB HEM 500 C 1 
HETATM 3 C CHC HEM . . . F 3 18.286 -59.336 5.957 1 84.97 ? CHC HEM 500 C 1 
HETATM 4 C CHD HEM . . . F 3 13.908 -60.518 7.701 1 87.6 ? CHD HEM 500 C 1 
HETATM 5 C C1A HEM . . . F 3 14.755 -64.157 3.687 1 99.6 ? C1A HEM 500 C 1 
HETATM 6 C C2A HEM . . . F 3 15.09 -65.073 2.613 1 104.48 ? C2A HEM 500 C 1 
HETATM 7 C C3A HEM . . . F 3 16.295 -64.739 2.147 1 103.28 ? C3A HEM 500 C 1 
HETATM 8 C C4A HEM . . . F 3 16.778 -63.606 2.91 1 98.2 ? C4A HEM 500 C 1 
HETATM 9 C CMA HEM . . . F 3 17.045 -65.443 0.995 1 107.56 ? CMA HEM 500 C 1 
HETATM 10 C CAA HEM . . . F 3 14.203 -66.223 2.084 1 110.8 ? CAA HEM 500 C 1 
HETATM 11 C CBA HEM . . . F 3 14.582 -67.549 2.733 1 112.4 ? CBA HEM 500 C 1 
HETATM 12 C CGA HEM . . . F 3 13.727 -68.643 2.144 1 118.66 ? CGA HEM 500 C 1 
HETATM 13 O O1A HEM . . . F 3 13.866 -68.924 0.925 1 123.01 ? O1A HEM 500 C 1 
HETATM 14 O O2A HEM . . . F 3 12.904 -69.233 2.891 1 119.73 ? O2A HEM 500 C 1 
HETATM 15 C C1B HEM . . . F 3 18.452 -61.882 3.453 1 92.63 ? C1B HEM 500 C 1 
HETATM 16 C C2B HEM . . . F 3 19.722 -61.21 3.26 1 91.58 ? C2B HEM 500 C 1 
HETATM 17 C C3B HEM . . . F 3 19.806 -60.213 4.145 1 88.53 ? C3B HEM 500 C 1 
HETATM 18 C C4B HEM . . . F 3 18.59 -60.209 4.934 1 87.31 ? C4B HEM 500 C 1 
HETATM 19 C CMB HEM . . . F 3 20.793 -61.584 2.213 1 93.9 ? CMB HEM 500 C 1 
HETATM 20 C CAB HEM . . . F 3 20.99 -59.233 4.299 1 86.86 ? CAB HEM 500 C 1 
HETATM 21 C CBB HEM . . . F 3 22.211 -59.694 4.592 1 86.24 ? CBB HEM 500 C 1 
HETATM 22 C C1C HEM . . . F 3 17.131 -59.336 6.71 1 84.75 ? C1C HEM 500 C 1 
HETATM 23 C C2C HEM . . . F 3 16.812 -58.423 7.791 1 82.88 ? C2C HEM 500 C 1 
HETATM 24 C C3C HEM . . . F 3 15.61 -58.75 8.268 1 83.67 ? C3C HEM 500 C 1 
HETATM 25 C C4C HEM . . . F 3 15.117 -59.884 7.512 1 85.95 ? C4C HEM 500 C 1 
HETATM 26 C CMC HEM . . . F 3 17.701 -57.269 8.303 1 81.11 ? CMC HEM 500 C 1 
HETATM 27 C CAC HEM . . . F 3 14.871 -58.04 9.423 1 83.24 ? CAC HEM 500 C 1 
HETATM 28 C CBC HEM . . . F 3 15.398 -58.039 10.652 1 81.86 ? CBC HEM 500 C 1 
HETATM 29 C C1D HEM . . . F 3 13.416 -61.599 6.996 1 90.31 ? C1D HEM 500 C 1 
HETATM 30 C C2D HEM . . . F 3 12.136 -62.225 7.239 1 92.26 ? C2D HEM 500 C 1 
HETATM 31 C C3D HEM . . . F 3 12.035 -63.364 6.22 1 96.44 ? C3D HEM 500 C 1 
HETATM 32 C C4D HEM . . . F 3 13.265 -63.312 5.459 1 95.65 ? C4D HEM 500 C 1 
HETATM 33 C CMD HEM . . . F 3 11.086 -61.833 8.3 1 91.69 ? CMD HEM 500 C 1 
HETATM 34 C CAD HEM . . . F 3 10.857 -64.351 6.056 1 101.24 ? CAD HEM 500 C 1 
HETATM 35 C CBD HEM . . . F 3 10.942 -65.437 7.129 1 101.08 ? CBD HEM 500 C 1 
HETATM 36 C CGD HEM . . . F 3 10.692 -66.791 6.52 1 106.31 ? CGD HEM 500 C 1 
HETATM 37 O O1D HEM . . . F 3 9.506 -67.202 6.435 1 109.77 ? O1D HEM 500 C 1 
HETATM 38 O O2D HEM . . . F 3 11.679 -67.46 6.119 1 108.02 ? O2D HEM 500 C 1 
HETATM 39 N NA HEM . . . F 3 15.811 -63.278 3.842 1 96.12 ? NA HEM 500 C 1 
HETATM 40 N NB HEM . . . F 3 17.788 -61.242 4.484 1 89.86 ? NB HEM 500 C 1 
HETATM 41 N NC HEM . . . F 3 16.073 -60.215 6.571 1 86.46 ? NC HEM 500 C 1 
HETATM 42 N ND HEM . . . F 3 14.047 -62.266 5.947 1 91.89 ? ND HEM 500 C 1 
HETATM 43 FE FE HEM . . . F 3 15.932 -61.746 5.21 1 90.48 ? FE HEM 500 C 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           342 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           43 
#