data_1JAF
#
_model_server_result.job_id            gJlZFh9RWB0xynJnUmIfgA 
_model_server_result.datetime_utc      '2025-03-06 09:22:42' 
_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          1jaf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":130}' 
#
_entry.id    1JAF 
#
_exptl.entry_id    1JAF 
_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         120 
_cell.entry_id            1JAF 
_cell.length_a            70.18 
_cell.length_b            70.18 
_cell.length_c            126.85 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1JAF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 5_556 x-y,-y,-z+5/3 1 0 0 0 -1 0 0 0 -1 0 0 211.416667 
#
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 D 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
covale ? covale1 A SG CYS 119 A CYS 119 1_555 C CAB HEM . A HEM 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? 
covale ? covale2 A SG CYS 122 A CYS 122 1_555 C CAC HEM . A HEM 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.762 ? 
covale ? covale3 B SG CYS 119 B CYS 119 1_555 D CAB HEM . B HEM 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.798 ? 
covale ? covale4 B SG CYS 122 B CYS 122 1_555 D CAC HEM . B HEM 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
metalc ? metalc1 A NE2 HIS 123 A HIS 123 1_555 C FE HEM . A HEM 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc2 B NE2 HIS 123 B HIS 123 1_555 D FE HEM . B HEM 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? 
#
_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                     1JAF 
_atom_sites.fract_transf_matrix[1][1]    0.014249 
_atom_sites.fract_transf_matrix[1][2]    0.008227 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016453 
_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]    0.007883 
_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 1 130 129 HEM HEM . 
D 2 HEM B 1 130 129 HEM HEM . 
E 3 HOH A 1 201 201 HOH HOH . 
E 3 HOH A 2 203 203 HOH HOH . 
E 3 HOH A 3 204 204 HOH HOH . 
E 3 HOH A 4 210 210 HOH HOH . 
E 3 HOH A 5 211 211 HOH HOH . 
E 3 HOH A 6 212 212 HOH HOH . 
E 3 HOH A 7 215 215 HOH HOH . 
E 3 HOH A 8 219 219 HOH HOH . 
E 3 HOH A 9 223 223 HOH HOH . 
E 3 HOH A 10 224 224 HOH HOH . 
E 3 HOH A 11 227 227 HOH HOH . 
E 3 HOH A 12 229 229 HOH HOH . 
E 3 HOH A 13 231 231 HOH HOH . 
E 3 HOH A 14 232 232 HOH HOH . 
E 3 HOH A 15 233 233 HOH HOH . 
E 3 HOH A 16 235 235 HOH HOH . 
E 3 HOH A 17 236 236 HOH HOH . 
E 3 HOH A 18 237 237 HOH HOH . 
E 3 HOH A 19 241 241 HOH HOH . 
E 3 HOH A 20 242 242 HOH HOH . 
E 3 HOH A 21 244 244 HOH HOH . 
E 3 HOH A 22 246 246 HOH HOH . 
E 3 HOH A 23 247 247 HOH HOH . 
E 3 HOH A 24 248 248 HOH HOH . 
E 3 HOH A 25 249 249 HOH HOH . 
E 3 HOH A 26 250 250 HOH HOH . 
E 3 HOH A 27 253 253 HOH HOH . 
E 3 HOH A 28 254 254 HOH HOH . 
F 3 HOH B 1 202 202 HOH HOH . 
F 3 HOH B 2 205 205 HOH HOH . 
F 3 HOH B 3 206 206 HOH HOH . 
F 3 HOH B 4 207 207 HOH HOH . 
F 3 HOH B 5 208 208 HOH HOH . 
F 3 HOH B 6 209 209 HOH HOH . 
F 3 HOH B 7 213 213 HOH HOH . 
F 3 HOH B 8 214 214 HOH HOH . 
F 3 HOH B 9 216 216 HOH HOH . 
F 3 HOH B 10 217 217 HOH HOH . 
F 3 HOH B 11 218 218 HOH HOH . 
F 3 HOH B 12 220 220 HOH HOH . 
F 3 HOH B 13 221 221 HOH HOH . 
F 3 HOH B 14 222 222 HOH HOH . 
F 3 HOH B 15 225 225 HOH HOH . 
F 3 HOH B 16 226 226 HOH HOH . 
F 3 HOH B 17 228 228 HOH HOH . 
F 3 HOH B 18 230 230 HOH HOH . 
F 3 HOH B 19 234 234 HOH HOH . 
F 3 HOH B 20 238 238 HOH HOH . 
F 3 HOH B 21 239 239 HOH HOH . 
F 3 HOH B 22 240 240 HOH HOH . 
F 3 HOH B 23 243 243 HOH HOH . 
F 3 HOH B 24 245 245 HOH HOH . 
F 3 HOH B 25 251 251 HOH HOH . 
F 3 HOH B 26 252 252 HOH HOH . 
F 3 HOH B 27 255 255 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 2 4.72 25.304 84.78 1 11.95 ? CHA HEM 130 B 1 
HETATM 2 C CHB HEM . . . D 2 8.735 26.503 82.573 1 16.5 ? CHB HEM 130 B 1 
HETATM 3 C CHC HEM . . . D 2 8.547 22.46 80.095 1 13.15 ? CHC HEM 130 B 1 
HETATM 4 C CHD HEM . . . D 2 4.293 21.482 81.888 1 16.42 ? CHD HEM 130 B 1 
HETATM 5 C C1A HEM . . . D 2 5.856 25.954 84.385 1 17.08 ? C1A HEM 130 B 1 
HETATM 6 C C2A HEM . . . D 2 6.394 27.119 85.092 1 19.47 ? C2A HEM 130 B 1 
HETATM 7 C C3A HEM . . . D 2 7.507 27.446 84.445 1 15.32 ? C3A HEM 130 B 1 
HETATM 8 C C4A HEM . . . D 2 7.643 26.487 83.391 1 14.42 ? C4A HEM 130 B 1 
HETATM 9 C CMA HEM . . . D 2 8.441 28.548 84.821 1 13.45 ? CMA HEM 130 B 1 
HETATM 10 C CAA HEM . . . D 2 5.866 27.87 86.312 1 27.93 ? CAA HEM 130 B 1 
HETATM 11 C CBA HEM . . . D 2 6.258 27.341 87.693 1 35.16 ? CBA HEM 130 B 1 
HETATM 12 C CGA HEM . . . D 2 5.639 28.154 88.823 1 40.86 ? CGA HEM 130 B 1 
HETATM 13 O O1A HEM . . . D 2 4.398 28.192 88.927 1 47.17 ? O1A HEM 130 B 1 
HETATM 14 O O2A HEM . . . D 2 6.389 28.766 89.608 1 48.25 ? O2A HEM 130 B 1 
HETATM 15 C C1B HEM . . . D 2 9.011 25.549 81.618 1 19.23 ? C1B HEM 130 B 1 
HETATM 16 C C2B HEM . . . D 2 10.217 25.553 80.789 1 18.25 ? C2B HEM 130 B 1 
HETATM 17 C C3B HEM . . . D 2 10.19 24.367 80.111 1 19.45 ? C3B HEM 130 B 1 
HETATM 18 C C4B HEM . . . D 2 8.948 23.693 80.53 1 17.7 ? C4B HEM 130 B 1 
HETATM 19 C CMB HEM . . . D 2 11.235 26.675 80.608 1 15.23 ? CMB HEM 130 B 1 
HETATM 20 C CAB HEM . . . D 2 11.094 23.776 79.029 1 24.1 ? CAB HEM 130 B 1 
HETATM 21 C CBB HEM . . . D 2 12.589 23.78 79.4 1 22.68 ? CBB HEM 130 B 1 
HETATM 22 C C1C HEM . . . D 2 7.371 21.855 80.372 1 13.5 ? C1C HEM 130 B 1 
HETATM 23 C C2C HEM . . . D 2 6.997 20.598 79.766 1 15.49 ? C2C HEM 130 B 1 
HETATM 24 C C3C HEM . . . D 2 5.727 20.35 80.163 1 17.13 ? C3C HEM 130 B 1 
HETATM 25 C C4C HEM . . . D 2 5.396 21.46 81.057 1 16.87 ? C4C HEM 130 B 1 
HETATM 26 C CMC HEM . . . D 2 7.795 19.768 78.789 1 16.3 ? CMC HEM 130 B 1 
HETATM 27 C CAC HEM . . . D 2 4.727 19.242 79.829 1 23.69 ? CAC HEM 130 B 1 
HETATM 28 C CBC HEM . . . D 2 5.217 17.934 79.248 1 21.45 ? CBC HEM 130 B 1 
HETATM 29 C C1D HEM . . . D 2 4.057 22.44 82.834 1 16.1 ? C1D HEM 130 B 1 
HETATM 30 C C2D HEM . . . D 2 2.893 22.451 83.681 1 14.81 ? C2D HEM 130 B 1 
HETATM 31 C C3D HEM . . . D 2 3.04 23.481 84.565 1 15.81 ? C3D HEM 130 B 1 
HETATM 32 C C4D HEM . . . D 2 4.264 24.164 84.177 1 13.97 ? C4D HEM 130 B 1 
HETATM 33 C CMD HEM . . . D 2 1.722 21.554 83.564 1 15.07 ? CMD HEM 130 B 1 
HETATM 34 C CAD HEM . . . D 2 2.187 23.78 85.789 1 19.47 ? CAD HEM 130 B 1 
HETATM 35 C CBD HEM . . . D 2 2.487 22.96 87.024 1 19.32 ? CBD HEM 130 B 1 
HETATM 36 C CGD HEM . . . D 2 1.618 23.356 88.193 1 24.65 ? CGD HEM 130 B 1 
HETATM 37 O O1D HEM . . . D 2 1.075 22.457 88.86 1 28.5 ? O1D HEM 130 B 1 
HETATM 38 O O2D HEM . . . D 2 1.46 24.564 88.452 1 18.82 ? O2D HEM 130 B 1 
HETATM 39 N NA HEM . . . D 2 6.632 25.579 83.338 1 12.2 ? NA HEM 130 B 1 
HETATM 40 N NB HEM . . . D 2 8.2 24.444 81.404 1 16.47 ? NB HEM 130 B 1 
HETATM 41 N NC HEM . . . D 2 6.393 22.411 81.139 1 13.14 ? NC HEM 130 B 1 
HETATM 42 N ND HEM . . . D 2 4.881 23.521 83.109 1 15.39 ? ND HEM 130 B 1 
HETATM 43 FE FE HEM . . . D 2 6.448 24.107 82.133 1 22.3 ? FE HEM 130 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           244 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#