data_5IKI
#
_model_server_result.job_id            fbzyK0aC1HO-28KoiNE6Jw 
_model_server_result.datetime_utc      '2024-12-27 06:30:07' 
_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          5iki 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    5IKI 
#
_exptl.entry_id    5IKI 
_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         72.37 
_cell.angle_beta          75.19 
_cell.angle_gamma         75.7 
_cell.entry_id            5IKI 
_cell.length_a            48.91 
_cell.length_b            57.39 
_cell.length_c            84.24 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5IKI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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,F 1 1 
B,D,E,G 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 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
metalc ? metalc1 A SG CYS 355 A CYS 355 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc2 B SG CYS 355 B CYS 355 1_555 D FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
#
_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 183 n n 
CHA C4D HEM doub 184 n n 
CHA HHA HEM sing 185 n n 
CHB C4A HEM sing 186 n n 
CHB C1B HEM doub 187 n n 
CHB HHB HEM sing 188 n n 
CHC C4B HEM sing 189 n n 
CHC C1C HEM doub 190 n n 
CHC HHC HEM sing 191 n n 
CHD C4C HEM doub 192 n n 
CHD C1D HEM sing 193 n n 
CHD HHD HEM sing 194 n n 
C1A C2A HEM doub 195 n y 
C1A NA HEM sing 196 n y 
C2A C3A HEM sing 197 n y 
C2A CAA HEM sing 198 n n 
C3A C4A HEM doub 199 n y 
C3A CMA HEM sing 200 n n 
C4A NA HEM sing 201 n y 
CMA HMA HEM sing 202 n n 
CMA HMAA HEM sing 203 n n 
CMA HMAB HEM sing 204 n n 
CAA CBA HEM sing 205 n n 
CAA HAA HEM sing 206 n n 
CAA HAAA HEM sing 207 n n 
CBA CGA HEM sing 208 n n 
CBA HBA HEM sing 209 n n 
CBA HBAA HEM sing 210 n n 
CGA O1A HEM doub 211 n n 
CGA O2A HEM sing 212 n n 
C1B C2B HEM sing 213 n n 
C1B NB HEM sing 214 n n 
C2B C3B HEM doub 215 n n 
C2B CMB HEM sing 216 n n 
C3B C4B HEM sing 217 n n 
C3B CAB HEM sing 218 n n 
C4B NB HEM doub 219 n n 
CMB HMB HEM sing 220 n n 
CMB HMBA HEM sing 221 n n 
CMB HMBB HEM sing 222 n n 
CAB CBB HEM doub 223 n n 
CAB HAB HEM sing 224 n n 
CBB HBB HEM sing 225 n n 
CBB HBBA HEM sing 226 n n 
C1C C2C HEM sing 227 n y 
C1C NC HEM sing 228 n y 
C2C C3C HEM doub 229 n y 
C2C CMC HEM sing 230 n n 
C3C C4C HEM sing 231 n y 
C3C CAC HEM sing 232 n n 
C4C NC HEM sing 233 n y 
CMC HMC HEM sing 234 n n 
CMC HMCA HEM sing 235 n n 
CMC HMCB HEM sing 236 n n 
CAC CBC HEM doub 237 n n 
CAC HAC HEM sing 238 n n 
CBC HBC HEM sing 239 n n 
CBC HBCA HEM sing 240 n n 
C1D C2D HEM sing 241 n n 
C1D ND HEM doub 242 n n 
C2D C3D HEM doub 243 n n 
C2D CMD HEM sing 244 n n 
C3D C4D HEM sing 245 n n 
C3D CAD HEM sing 246 n n 
C4D ND HEM sing 247 n n 
CMD HMD HEM sing 248 n n 
CMD HMDA HEM sing 249 n n 
CMD HMDB HEM sing 250 n n 
CAD CBD HEM sing 251 n n 
CAD HAD HEM sing 252 n n 
CAD HADA HEM sing 253 n n 
CBD CGD HEM sing 254 n n 
CBD HBD HEM sing 255 n n 
CBD HBDA HEM sing 256 n n 
CGD O1D HEM doub 257 n n 
CGD O2D HEM sing 258 n n 
O2A H2A HEM sing 259 n n 
O2D H2D HEM sing 260 n n 
FE NA HEM sing 261 n n 
FE NB HEM sing 262 n n 
FE NC HEM sing 263 n n 
FE ND HEM sing 264 n n 
#
_atom_sites.entry_id                     5IKI 
_atom_sites.fract_transf_matrix[1][1]    0.020446 
_atom_sites.fract_transf_matrix[1][2]    -0.005212 
_atom_sites.fract_transf_matrix[1][3]    -0.004212 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017982 
_atom_sites.fract_transf_matrix[2][3]    -0.004762 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.012702 
_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 1 501 410 HEM HEM . 
D 2 HEM B 1 501 410 HEM HEM . 
E 3 A9H B 1 502 1 A9H SYL . 
F 4 HOH A 1 601 31 HOH HOH . 
F 4 HOH A 2 602 39 HOH HOH . 
F 4 HOH A 3 603 51 HOH HOH . 
F 4 HOH A 4 604 20 HOH HOH . 
F 4 HOH A 5 605 54 HOH HOH . 
F 4 HOH A 6 606 25 HOH HOH . 
F 4 HOH A 7 607 48 HOH HOH . 
F 4 HOH A 8 608 33 HOH HOH . 
F 4 HOH A 9 609 45 HOH HOH . 
F 4 HOH A 10 610 43 HOH HOH . 
F 4 HOH A 11 611 32 HOH HOH . 
F 4 HOH A 12 612 30 HOH HOH . 
F 4 HOH A 13 613 55 HOH HOH . 
F 4 HOH A 14 614 11 HOH HOH . 
F 4 HOH A 15 615 29 HOH HOH . 
F 4 HOH A 16 616 52 HOH HOH . 
F 4 HOH A 17 617 41 HOH HOH . 
F 4 HOH A 18 618 12 HOH HOH . 
F 4 HOH A 19 619 42 HOH HOH . 
F 4 HOH A 20 620 2 HOH HOH . 
F 4 HOH A 21 621 3 HOH HOH . 
F 4 HOH A 22 622 15 HOH HOH . 
F 4 HOH A 23 623 21 HOH HOH . 
F 4 HOH A 24 624 19 HOH HOH . 
F 4 HOH A 25 625 24 HOH HOH . 
F 4 HOH A 26 626 9 HOH HOH . 
F 4 HOH A 27 627 26 HOH HOH . 
F 4 HOH A 28 628 50 HOH HOH . 
F 4 HOH A 29 629 34 HOH HOH . 
F 4 HOH A 30 630 6 HOH HOH . 
G 4 HOH B 1 601 35 HOH HOH . 
G 4 HOH B 2 602 16 HOH HOH . 
G 4 HOH B 3 603 37 HOH HOH . 
G 4 HOH B 4 604 8 HOH HOH . 
G 4 HOH B 5 605 17 HOH HOH . 
G 4 HOH B 6 606 44 HOH HOH . 
G 4 HOH B 7 607 46 HOH HOH . 
G 4 HOH B 8 608 38 HOH HOH . 
G 4 HOH B 9 609 5 HOH HOH . 
G 4 HOH B 10 610 40 HOH HOH . 
G 4 HOH B 11 611 22 HOH HOH . 
G 4 HOH B 12 612 13 HOH HOH . 
G 4 HOH B 13 613 10 HOH HOH . 
G 4 HOH B 14 614 4 HOH HOH . 
G 4 HOH B 15 615 53 HOH HOH . 
G 4 HOH B 16 616 47 HOH HOH . 
G 4 HOH B 17 617 28 HOH HOH . 
G 4 HOH B 18 618 23 HOH HOH . 
G 4 HOH B 19 619 14 HOH HOH . 
G 4 HOH B 20 620 18 HOH HOH . 
G 4 HOH B 21 621 1 HOH HOH . 
G 4 HOH B 22 622 7 HOH HOH . 
G 4 HOH B 23 623 49 HOH HOH . 
G 4 HOH B 24 624 27 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 -9.682 3.224 -14.374 1 44.55 ? CHA HEM 501 B 1 
HETATM 2 C CHB HEM . . . D 2 -11.25 7.786 -14.504 1 46.89 ? CHB HEM 501 B 1 
HETATM 3 C CHC HEM . . . D 2 -7.84 8.762 -17.85 1 56.54 ? CHC HEM 501 B 1 
HETATM 4 C CHD HEM . . . D 2 -7 4.059 -18.357 1 48.22 ? CHD HEM 501 B 1 
HETATM 5 C C1A HEM . . . D 2 -10.334 4.393 -14.084 1 46.49 ? C1A HEM 501 B 1 
HETATM 6 C C2A HEM . . . D 2 -11.307 4.526 -13.067 1 45.92 ? C2A HEM 501 B 1 
HETATM 7 C C3A HEM . . . D 2 -11.759 5.803 -13.093 1 48.85 ? C3A HEM 501 B 1 
HETATM 8 C C4A HEM . . . D 2 -11.085 6.471 -14.148 1 45.91 ? C4A HEM 501 B 1 
HETATM 9 C CMA HEM . . . D 2 -12.794 6.379 -12.156 1 47.81 ? CMA HEM 501 B 1 
HETATM 10 C CAA HEM . . . D 2 -11.74 3.475 -12.099 1 42.93 ? CAA HEM 501 B 1 
HETATM 11 C CBA HEM . . . D 2 -12.831 2.592 -12.666 1 43.1 ? CBA HEM 501 B 1 
HETATM 12 C CGA HEM . . . D 2 -13.423 1.73 -11.564 1 46.76 ? CGA HEM 501 B 1 
HETATM 13 O O1A HEM . . . D 2 -12.997 1.679 -10.374 1 46.53 ? O1A HEM 501 B 1 
HETATM 14 O O2A HEM . . . D 2 -14.389 1.025 -11.87 1 52.16 ? O2A HEM 501 B 1 
HETATM 15 C C1B HEM . . . D 2 -10.406 8.44 -15.43 1 48.22 ? C1B HEM 501 B 1 
HETATM 16 C C2B HEM . . . D 2 -10.436 9.85 -15.63 1 44.24 ? C2B HEM 501 B 1 
HETATM 17 C C3B HEM . . . D 2 -9.482 10.152 -16.56 1 49.03 ? C3B HEM 501 B 1 
HETATM 18 C C4B HEM . . . D 2 -8.861 8.857 -16.921 1 50.06 ? C4B HEM 501 B 1 
HETATM 19 C CMB HEM . . . D 2 -11.37 10.81 -14.969 1 46.5 ? CMB HEM 501 B 1 
HETATM 20 C CAB HEM . . . D 2 -9.077 11.46 -17.136 1 50.16 ? CAB HEM 501 B 1 
HETATM 21 C CBB HEM . . . D 2 -9.574 12.637 -16.759 1 51.83 ? CBB HEM 501 B 1 
HETATM 22 C C1C HEM . . . D 2 -7.296 7.58 -18.309 1 57.83 ? C1C HEM 501 B 1 
HETATM 23 C C2C HEM . . . D 2 -6.289 7.466 -19.265 1 59.35 ? C2C HEM 501 B 1 
HETATM 24 C C3C HEM . . . D 2 -6.008 6.114 -19.458 1 57.32 ? C3C HEM 501 B 1 
HETATM 25 C C4C HEM . . . D 2 -6.909 5.416 -18.568 1 50.26 ? C4C HEM 501 B 1 
HETATM 26 C CMC HEM . . . D 2 -5.607 8.636 -19.94 1 66.37 ? CMC HEM 501 B 1 
HETATM 27 C CAC HEM . . . D 2 -4.961 5.644 -20.454 1 54.27 ? CAC HEM 501 B 1 
HETATM 28 C CBC HEM . . . D 2 -4.707 4.379 -20.81 1 48.73 ? CBC HEM 501 B 1 
HETATM 29 C C1D HEM . . . D 2 -7.685 3.493 -17.262 1 49 ? C1D HEM 501 B 1 
HETATM 30 C C2D HEM . . . D 2 -7.55 2.051 -16.958 1 46.87 ? C2D HEM 501 B 1 
HETATM 31 C C3D HEM . . . D 2 -8.287 1.818 -15.862 1 45.51 ? C3D HEM 501 B 1 
HETATM 32 C C4D HEM . . . D 2 -8.848 3.123 -15.473 1 45.56 ? C4D HEM 501 B 1 
HETATM 33 C CMD HEM . . . D 2 -6.757 1.008 -17.715 1 47.94 ? CMD HEM 501 B 1 
HETATM 34 C CAD HEM . . . D 2 -8.474 0.486 -15.173 1 46.96 ? CAD HEM 501 B 1 
HETATM 35 C CBD HEM . . . D 2 -7.604 0.457 -13.908 1 48.85 ? CBD HEM 501 B 1 
HETATM 36 C CGD HEM . . . D 2 -7.916 -0.745 -13.038 1 51.52 ? CGD HEM 501 B 1 
HETATM 37 O O1D HEM . . . D 2 -9.007 -1.365 -13.139 1 53.7 ? O1D HEM 501 B 1 
HETATM 38 O O2D HEM . . . D 2 -7.064 -1.139 -12.202 1 50.59 ? O2D HEM 501 B 1 
HETATM 39 N NA HEM . . . D 2 -10.206 5.607 -14.745 1 47.53 ? NA HEM 501 B 1 
HETATM 40 N NB HEM . . . D 2 -9.421 7.915 -16.178 1 44.34 ? NB HEM 501 B 1 
HETATM 41 N NC HEM . . . D 2 -7.657 6.36 -17.88 1 55.63 ? NC HEM 501 B 1 
HETATM 42 N ND HEM . . . D 2 -8.459 4.099 -16.326 1 45.11 ? ND HEM 501 B 1 
HETATM 43 FE FE HEM . . . D 2 -8.951 5.908 -16.281 1 42.97 ? FE HEM 501 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#