data_5EM4
#
_model_server_result.job_id            4IfS4GDf_WPQan6igT_1Hg 
_model_server_result.datetime_utc      '2024-11-24 00:48:22' 
_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          5em4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":501}' 
#
_entry.id    5EM4 
#
_exptl.entry_id    5EM4 
_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            5EM4 
_cell.length_a            92.03 
_cell.length_b            92.03 
_cell.length_c            151.85 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EM4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31' 
#
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,E,I 1 1 
B,F,G,H,J 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 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 A SG CYS 436 A CYS 436 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc2 B SG CYS 436 B CYS 436 1_555 F FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
#
_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 207 n n 
CHA C4D HEM doub 208 n n 
CHA HHA HEM sing 209 n n 
CHB C4A HEM sing 210 n n 
CHB C1B HEM doub 211 n n 
CHB HHB HEM sing 212 n n 
CHC C4B HEM sing 213 n n 
CHC C1C HEM doub 214 n n 
CHC HHC HEM sing 215 n n 
CHD C4C HEM doub 216 n n 
CHD C1D HEM sing 217 n n 
CHD HHD HEM sing 218 n n 
C1A C2A HEM doub 219 n y 
C1A NA HEM sing 220 n y 
C2A C3A HEM sing 221 n y 
C2A CAA HEM sing 222 n n 
C3A C4A HEM doub 223 n y 
C3A CMA HEM sing 224 n n 
C4A NA HEM sing 225 n y 
CMA HMA HEM sing 226 n n 
CMA HMAA HEM sing 227 n n 
CMA HMAB HEM sing 228 n n 
CAA CBA HEM sing 229 n n 
CAA HAA HEM sing 230 n n 
CAA HAAA HEM sing 231 n n 
CBA CGA HEM sing 232 n n 
CBA HBA HEM sing 233 n n 
CBA HBAA HEM sing 234 n n 
CGA O1A HEM doub 235 n n 
CGA O2A HEM sing 236 n n 
C1B C2B HEM sing 237 n n 
C1B NB HEM sing 238 n n 
C2B C3B HEM doub 239 n n 
C2B CMB HEM sing 240 n n 
C3B C4B HEM sing 241 n n 
C3B CAB HEM sing 242 n n 
C4B NB HEM doub 243 n n 
CMB HMB HEM sing 244 n n 
CMB HMBA HEM sing 245 n n 
CMB HMBB HEM sing 246 n n 
CAB CBB HEM doub 247 n n 
CAB HAB HEM sing 248 n n 
CBB HBB HEM sing 249 n n 
CBB HBBA HEM sing 250 n n 
C1C C2C HEM sing 251 n y 
C1C NC HEM sing 252 n y 
C2C C3C HEM doub 253 n y 
C2C CMC HEM sing 254 n n 
C3C C4C HEM sing 255 n y 
C3C CAC HEM sing 256 n n 
C4C NC HEM sing 257 n y 
CMC HMC HEM sing 258 n n 
CMC HMCA HEM sing 259 n n 
CMC HMCB HEM sing 260 n n 
CAC CBC HEM doub 261 n n 
CAC HAC HEM sing 262 n n 
CBC HBC HEM sing 263 n n 
CBC HBCA HEM sing 264 n n 
C1D C2D HEM sing 265 n n 
C1D ND HEM doub 266 n n 
C2D C3D HEM doub 267 n n 
C2D CMD HEM sing 268 n n 
C3D C4D HEM sing 269 n n 
C3D CAD HEM sing 270 n n 
C4D ND HEM sing 271 n n 
CMD HMD HEM sing 272 n n 
CMD HMDA HEM sing 273 n n 
CMD HMDB HEM sing 274 n n 
CAD CBD HEM sing 275 n n 
CAD HAD HEM sing 276 n n 
CAD HADA HEM sing 277 n n 
CBD CGD HEM sing 278 n n 
CBD HBD HEM sing 279 n n 
CBD HBDA HEM sing 280 n n 
CGD O1D HEM doub 281 n n 
CGD O2D HEM sing 282 n n 
O2A H2A HEM sing 283 n n 
O2D H2D HEM sing 284 n n 
FE NA HEM sing 285 n n 
FE NB HEM sing 286 n n 
FE NC HEM sing 287 n n 
FE ND HEM sing 288 n n 
#
_atom_sites.entry_id                     5EM4 
_atom_sites.fract_transf_matrix[1][1]    0.010866 
_atom_sites.fract_transf_matrix[1][2]    0.006274 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012547 
_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]    0.006585 
_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 1 501 501 HEM HEM . 
D 3 CM5 A 1 502 502 CM5 CM5 . 
E 3 CM5 A 1 503 503 CM5 CM5 . 
F 2 HEM B 1 501 501 HEM HEM . 
G 3 CM5 B 1 502 502 CM5 CM5 . 
H 3 CM5 B 1 503 503 CM5 CM5 . 
I 4 HOH A 1 601 601 HOH HOH . 
I 4 HOH A 2 602 602 HOH HOH . 
I 4 HOH A 3 603 603 HOH HOH . 
J 4 HOH B 1 601 601 HOH HOH . 
J 4 HOH B 2 602 602 HOH HOH . 
J 4 HOH B 3 603 603 HOH HOH . 
J 4 HOH B 4 604 604 HOH HOH . 
J 4 HOH B 5 605 605 HOH HOH . 
J 4 HOH B 6 606 606 HOH HOH . 
J 4 HOH B 7 607 607 HOH HOH . 
J 4 HOH B 8 608 608 HOH HOH . 
J 4 HOH B 9 609 609 HOH HOH . 
J 4 HOH B 10 610 610 HOH HOH . 
J 4 HOH B 11 611 611 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 2 -6.435 28.176 14.693 1 71.75 ? CHA HEM 501 B 1 
HETATM 2 C CHB HEM . . . F 2 -4.121 29.516 18.63 1 65.85 ? CHB HEM 501 B 1 
HETATM 3 C CHC HEM . . . F 2 -2.296 33.316 16.349 1 57.81 ? CHC HEM 501 B 1 
HETATM 4 C CHD HEM . . . F 2 -4.422 31.823 12.353 1 70.15 ? CHD HEM 501 B 1 
HETATM 5 C C1A HEM . . . F 2 -5.912 28.238 15.933 1 69.11 ? C1A HEM 501 B 1 
HETATM 6 C C2A HEM . . . F 2 -6.11 27.248 16.89 1 74.17 ? C2A HEM 501 B 1 
HETATM 7 C C3A HEM . . . F 2 -5.464 27.608 17.992 1 72.6 ? C3A HEM 501 B 1 
HETATM 8 C C4A HEM . . . F 2 -4.867 28.834 17.727 1 67.54 ? C4A HEM 501 B 1 
HETATM 9 C CMA HEM . . . F 2 -5.413 26.828 19.264 1 68.52 ? CMA HEM 501 B 1 
HETATM 10 C CAA HEM . . . F 2 -6.892 25.991 16.76 1 75.54 ? CAA HEM 501 B 1 
HETATM 11 C CBA HEM . . . F 2 -6.556 25.34 15.441 1 74.67 ? CBA HEM 501 B 1 
HETATM 12 C CGA HEM . . . F 2 -7.156 23.984 15.474 1 78.5 ? CGA HEM 501 B 1 
HETATM 13 O O1A HEM . . . F 2 -8.279 23.788 14.992 1 75.29 ? O1A HEM 501 B 1 
HETATM 14 O O2A HEM . . . F 2 -6.527 23.066 15.994 1 90.51 ? O2A HEM 501 B 1 
HETATM 15 C C1B HEM . . . F 2 -3.464 30.675 18.301 1 58.09 ? C1B HEM 501 B 1 
HETATM 16 C C2B HEM . . . F 2 -2.734 31.362 19.265 1 56.97 ? C2B HEM 501 B 1 
HETATM 17 C C3B HEM . . . F 2 -2.211 32.425 18.655 1 57.95 ? C3B HEM 501 B 1 
HETATM 18 C C4B HEM . . . F 2 -2.657 32.364 17.267 1 59.13 ? C4B HEM 501 B 1 
HETATM 19 C CMB HEM . . . F 2 -2.572 30.97 20.692 1 58.91 ? CMB HEM 501 B 1 
HETATM 20 C CAB HEM . . . F 2 -1.362 33.449 19.25 1 58.44 ? CAB HEM 501 B 1 
HETATM 21 C CBB HEM . . . F 2 -0.958 33.314 20.498 1 59 ? CBB HEM 501 B 1 
HETATM 22 C C1C HEM . . . F 2 -2.706 33.218 15.059 1 59.48 ? C1C HEM 501 B 1 
HETATM 23 C C2C HEM . . . F 2 -2.347 34.091 14.051 1 64.56 ? C2C HEM 501 B 1 
HETATM 24 C C3C HEM . . . F 2 -2.96 33.663 12.914 1 62.27 ? C3C HEM 501 B 1 
HETATM 25 C C4C HEM . . . F 2 -3.69 32.516 13.248 1 64.22 ? C4C HEM 501 B 1 
HETATM 26 C CMC HEM . . . F 2 -1.446 35.273 14.177 1 64.85 ? CMC HEM 501 B 1 
HETATM 27 C CAC HEM . . . F 2 -2.86 34.261 11.592 1 61.63 ? CAC HEM 501 B 1 
HETATM 28 C CBC HEM . . . F 2 -1.84 35.044 11.333 1 62.78 ? CBC HEM 501 B 1 
HETATM 29 C C1D HEM . . . F 2 -5.135 30.719 12.723 1 71.59 ? C1D HEM 501 B 1 
HETATM 30 C C2D HEM . . . F 2 -5.966 30.05 11.744 1 68.49 ? C2D HEM 501 B 1 
HETATM 31 C C3D HEM . . . F 2 -6.536 29.035 12.372 1 66.31 ? C3D HEM 501 B 1 
HETATM 32 C C4D HEM . . . F 2 -6.035 29.092 13.752 1 73.56 ? C4D HEM 501 B 1 
HETATM 33 C CMD HEM . . . F 2 -6.142 30.443 10.314 1 70.09 ? CMD HEM 501 B 1 
HETATM 34 C CAD HEM . . . F 2 -7.494 28.054 11.757 1 58.94 ? CAD HEM 501 B 1 
HETATM 35 C CBD HEM . . . F 2 -6.699 26.941 11.099 1 59.29 ? CBD HEM 501 B 1 
HETATM 36 C CGD HEM . . . F 2 -7.564 26.057 10.276 1 59.09 ? CGD HEM 501 B 1 
HETATM 37 O O1D HEM . . . F 2 -7.145 25.645 9.203 1 62.46 ? O1D HEM 501 B 1 
HETATM 38 O O2D HEM . . . F 2 -8.683 25.723 10.651 1 55.2 ? O2D HEM 501 B 1 
HETATM 39 N NA HEM . . . F 2 -5.142 29.212 16.465 1 66.24 ? NA HEM 501 B 1 
HETATM 40 N NB HEM . . . F 2 -3.406 31.285 17.14 1 58.6 ? NB HEM 501 B 1 
HETATM 41 N NC HEM . . . F 2 -3.536 32.289 14.562 1 58.68 ? NC HEM 501 B 1 
HETATM 42 N ND HEM . . . F 2 -5.196 30.121 13.898 1 70.76 ? ND HEM 501 B 1 
HETATM 43 FE FE HEM . . . F 2 -4.326 30.627 15.424 1 67.54 ? FE HEM 501 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           350 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           43 
#