data_4YT0
#
_model_server_result.job_id            qFT4vqyjHZV5boetfCU1Lg 
_model_server_result.datetime_utc      '2024-10-12 10:18:51' 
_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          4yt0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":201}' 
#
_entry.id    4YT0 
#
_exptl.entry_id    4YT0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          10 
_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            4YT0 
_cell.length_a            122.803 
_cell.length_b            123.392 
_cell.length_c            219.001 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YT0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 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,C,D,I,J,K,L,M,N,O 1 1 
E,F,G,H,P,Q,R,S,T,U,V 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
? 10 N N N 
? 10 U 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
disulf ? disulf1 A SG CYS 191 A CYS 191 1_555 A SG CYS 193 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 E SG CYS 191 E CYS 191 1_555 E SG CYS 193 E CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 F SG CYS 89 F CYS 89 1_555 F SG CYS 94 F CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? 
metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc5 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc6 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc7 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc8 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc9 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? 
metalc ? metalc10 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc11 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? 
metalc ? metalc12 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? 
metalc ? metalc13 F SG CYS 94 F CYS 94 1_555 R FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc14 F SG CYS 97 F CYS 97 1_555 R FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? 
metalc ? metalc15 F SG CYS 109 F CYS 109 1_555 R FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc16 F SG CYS 182 F CYS 182 1_555 S FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc17 F SG CYS 188 F CYS 188 1_555 S FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc18 F SG CYS 192 F CYS 192 1_555 T FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc19 F SG CYS 239 F CYS 239 1_555 T FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? 
metalc ? metalc20 F SG CYS 245 F CYS 245 1_555 T FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? 
metalc ? metalc21 F SG CYS 249 F CYS 249 1_555 S FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc22 G NE2 HIS 131 G HIS 131 1_555 U FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc23 U FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
#
_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 233 n n 
CHA C4D HEM doub 234 n n 
CHA HHA HEM sing 235 n n 
CHB C4A HEM sing 236 n n 
CHB C1B HEM doub 237 n n 
CHB HHB HEM sing 238 n n 
CHC C4B HEM sing 239 n n 
CHC C1C HEM doub 240 n n 
CHC HHC HEM sing 241 n n 
CHD C4C HEM doub 242 n n 
CHD C1D HEM sing 243 n n 
CHD HHD HEM sing 244 n n 
C1A C2A HEM doub 245 n y 
C1A NA HEM sing 246 n y 
C2A C3A HEM sing 247 n y 
C2A CAA HEM sing 248 n n 
C3A C4A HEM doub 249 n y 
C3A CMA HEM sing 250 n n 
C4A NA HEM sing 251 n y 
CMA HMA HEM sing 252 n n 
CMA HMAA HEM sing 253 n n 
CMA HMAB HEM sing 254 n n 
CAA CBA HEM sing 255 n n 
CAA HAA HEM sing 256 n n 
CAA HAAA HEM sing 257 n n 
CBA CGA HEM sing 258 n n 
CBA HBA HEM sing 259 n n 
CBA HBAA HEM sing 260 n n 
CGA O1A HEM doub 261 n n 
CGA O2A HEM sing 262 n n 
C1B C2B HEM sing 263 n n 
C1B NB HEM sing 264 n n 
C2B C3B HEM doub 265 n n 
C2B CMB HEM sing 266 n n 
C3B C4B HEM sing 267 n n 
C3B CAB HEM sing 268 n n 
C4B NB HEM doub 269 n n 
CMB HMB HEM sing 270 n n 
CMB HMBA HEM sing 271 n n 
CMB HMBB HEM sing 272 n n 
CAB CBB HEM doub 273 n n 
CAB HAB HEM sing 274 n n 
CBB HBB HEM sing 275 n n 
CBB HBBA HEM sing 276 n n 
C1C C2C HEM sing 277 n y 
C1C NC HEM sing 278 n y 
C2C C3C HEM doub 279 n y 
C2C CMC HEM sing 280 n n 
C3C C4C HEM sing 281 n y 
C3C CAC HEM sing 282 n n 
C4C NC HEM sing 283 n y 
CMC HMC HEM sing 284 n n 
CMC HMCA HEM sing 285 n n 
CMC HMCB HEM sing 286 n n 
CAC CBC HEM doub 287 n n 
CAC HAC HEM sing 288 n n 
CBC HBC HEM sing 289 n n 
CBC HBCA HEM sing 290 n n 
C1D C2D HEM sing 291 n n 
C1D ND HEM doub 292 n n 
C2D C3D HEM doub 293 n n 
C2D CMD HEM sing 294 n n 
C3D C4D HEM sing 295 n n 
C3D CAD HEM sing 296 n n 
C4D ND HEM sing 297 n n 
CMD HMD HEM sing 298 n n 
CMD HMDA HEM sing 299 n n 
CMD HMDB HEM sing 300 n n 
CAD CBD HEM sing 301 n n 
CAD HAD HEM sing 302 n n 
CAD HADA HEM sing 303 n n 
CBD CGD HEM sing 304 n n 
CBD HBD HEM sing 305 n n 
CBD HBDA HEM sing 306 n n 
CGD O1D HEM doub 307 n n 
CGD O2D HEM sing 308 n n 
O2A H2A HEM sing 309 n n 
O2D H2D HEM sing 310 n n 
FE NA HEM sing 311 n n 
FE NB HEM sing 312 n n 
FE NC HEM sing 313 n n 
FE ND HEM sing 314 n n 
#
_atom_sites.entry_id                     4YT0 
_atom_sites.fract_transf_matrix[1][1]    0.008143 
_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]    0.008104 
_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]    0.004566 
_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
I 5 MLI A 1 701 701 MLI MLI . 
J 6 FAD A 1 702 702 FAD FAD . 
K 7 FES B 1 301 301 FES FES . 
L 8 SF4 B 1 302 302 SF4 SF4 . 
M 9 F3S B 1 303 303 F3S F3S . 
N 10 HEM C 1 201 201 HEM HEM . 
O 11 MRN C 1 202 301 MRN DRG . 
P 5 MLI E 1 701 701 MLI MLI . 
Q 6 FAD E 1 702 702 FAD FAD . 
R 7 FES F 1 301 301 FES FES . 
S 8 SF4 F 1 302 302 SF4 SF4 . 
T 9 F3S F 1 303 303 F3S F3S . 
U 10 HEM G 1 201 201 HEM HEM . 
V 11 MRN G 1 202 301 MRN DRG . 
#
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 . . . N 10 -43.313 -67.862 -2.633 1 72.97 ? CHA HEM 201 C 1 
HETATM 2 C CHB HEM . . . N 10 -38.73 -69.158 -3.275 1 73.81 ? CHB HEM 201 C 1 
HETATM 3 C CHC HEM . . . N 10 -40.084 -73.808 -3.384 1 72.02 ? CHC HEM 201 C 1 
HETATM 4 C CHD HEM . . . N 10 -44.675 -72.489 -2.656 1 69.97 ? CHD HEM 201 C 1 
HETATM 5 C C1A HEM . . . N 10 -41.965 -67.829 -2.774 1 72.61 ? C1A HEM 201 C 1 
HETATM 6 C C2A HEM . . . N 10 -41.193 -66.648 -2.789 1 72.81 ? C2A HEM 201 C 1 
HETATM 7 C C3A HEM . . . N 10 -39.9 -67.015 -2.974 1 72.12 ? C3A HEM 201 C 1 
HETATM 8 C C4A HEM . . . N 10 -39.876 -68.418 -3.073 1 72.91 ? C4A HEM 201 C 1 
HETATM 9 C CMA HEM . . . N 10 -38.706 -66.096 -3.045 1 71.81 ? CMA HEM 201 C 1 
HETATM 10 C CAA HEM . . . N 10 -41.705 -65.237 -2.622 1 73.64 ? CAA HEM 201 C 1 
HETATM 11 C CBA HEM . . . N 10 -42.017 -64.642 -4.001 1 75.26 ? CBA HEM 201 C 1 
HETATM 12 C CGA HEM . . . N 10 -43.076 -63.572 -3.918 1 75.63 ? CGA HEM 201 C 1 
HETATM 13 O O1A HEM . . . N 10 -43.272 -62.961 -2.838 1 74.48 ? O1A HEM 201 C 1 
HETATM 14 O O2A HEM . . . N 10 -43.753 -63.292 -4.942 1 76.54 ? O2A HEM 201 C 1 
HETATM 15 C C1B HEM . . . N 10 -38.712 -70.552 -3.361 1 72.22 ? C1B HEM 201 C 1 
HETATM 16 C C2B HEM . . . N 10 -37.498 -71.263 -3.53 1 71.11 ? C2B HEM 201 C 1 
HETATM 17 C C3B HEM . . . N 10 -37.815 -72.589 -3.576 1 73 ? C3B HEM 201 C 1 
HETATM 18 C C4B HEM . . . N 10 -39.307 -72.648 -3.412 1 72.21 ? C4B HEM 201 C 1 
HETATM 19 C CMB HEM . . . N 10 -36.122 -70.643 -3.66 1 68.44 ? CMB HEM 201 C 1 
HETATM 20 C CAB HEM . . . N 10 -36.783 -73.651 -3.706 1 74.02 ? CAB HEM 201 C 1 
HETATM 21 C CBB HEM . . . N 10 -36.983 -74.953 -3.515 1 72.78 ? CBB HEM 201 C 1 
HETATM 22 C C1C HEM . . . N 10 -41.46 -73.862 -3.178 1 69.93 ? C1C HEM 201 C 1 
HETATM 23 C C2C HEM . . . N 10 -42.204 -75.045 -3.105 1 69.41 ? C2C HEM 201 C 1 
HETATM 24 C C3C HEM . . . N 10 -43.523 -74.706 -2.901 1 68.08 ? C3C HEM 201 C 1 
HETATM 25 C C4C HEM . . . N 10 -43.575 -73.275 -2.834 1 69 ? C4C HEM 201 C 1 
HETATM 26 C CMC HEM . . . N 10 -41.696 -76.463 -3.22 1 70.17 ? CMC HEM 201 C 1 
HETATM 27 C CAC HEM . . . N 10 -44.548 -75.759 -2.73 1 66.43 ? CAC HEM 201 C 1 
HETATM 28 C CBC HEM . . . N 10 -45.786 -75.562 -2.307 1 66.55 ? CBC HEM 201 C 1 
HETATM 29 C C1D HEM . . . N 10 -44.616 -71.102 -2.605 1 70.03 ? C1D HEM 201 C 1 
HETATM 30 C C2D HEM . . . N 10 -45.842 -70.316 -2.379 1 70.68 ? C2D HEM 201 C 1 
HETATM 31 C C3D HEM . . . N 10 -45.487 -69.025 -2.369 1 73.8 ? C3D HEM 201 C 1 
HETATM 32 C C4D HEM . . . N 10 -44.024 -69.041 -2.593 1 71.59 ? C4D HEM 201 C 1 
HETATM 33 C CMD HEM . . . N 10 -47.266 -70.789 -2.176 1 68.74 ? CMD HEM 201 C 1 
HETATM 34 C CAD HEM . . . N 10 -46.534 -67.92 -2.173 1 77.77 ? CAD HEM 201 C 1 
HETATM 35 C CBD HEM . . . N 10 -46.2 -66.416 -2.339 1 78.49 ? CBD HEM 201 C 1 
HETATM 36 C CGD HEM . . . N 10 -46.251 -65.878 -3.769 1 78.18 ? CGD HEM 201 C 1 
HETATM 37 O O1D HEM . . . N 10 -46.239 -64.638 -3.954 1 76.97 ? O1D HEM 201 C 1 
HETATM 38 O O2D HEM . . . N 10 -46.327 -66.609 -4.787 1 76.45 ? O2D HEM 201 C 1 
HETATM 39 N NA HEM . . . N 10 -41.157 -68.903 -2.973 1 72.48 ? NA HEM 201 C 1 
HETATM 40 N NB HEM . . . N 10 -39.744 -71.393 -3.289 1 71.14 ? NB HEM 201 C 1 
HETATM 41 N NC HEM . . . N 10 -42.311 -72.806 -3.032 1 68.8 ? NC HEM 201 C 1 
HETATM 42 N ND HEM . . . N 10 -43.543 -70.3 -2.718 1 69.6 ? ND HEM 201 C 1 
HETATM 43 FE FE HEM . . . N 10 -41.744 -70.804 -3.045 1 69.65 ? FE HEM 201 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#