data_5IRV
#
_model_server_result.job_id            SD4O8kAxDpE-R2I18w9VJQ 
_model_server_result.datetime_utc      '2024-10-16 00:23:45' 
_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          5irv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":600}' 
#
_entry.id    5IRV 
#
_exptl.entry_id    5IRV 
_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    4 
_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            5IRV 
_cell.length_a            90.954 
_cell.length_b            153.499 
_cell.length_c            169.035 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5IRV 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F 1 1 
B,G,H 2 1 
C,I,J 3 1 
D,K,L 4 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 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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 E FE HEM . A HEM 600 1_555 F N27 6D8 . A 6D8 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc2 G FE HEM . B HEM 600 1_555 H N26 6D8 . B 6D8 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc3 G FE HEM . B HEM 600 1_555 H N27 6D8 . B 6D8 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc4 I FE HEM . C HEM 600 1_555 J N27 6D8 . C 6D8 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc5 K FE HEM . D HEM 600 1_555 L N26 6D8 . D 6D8 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? 
metalc ? metalc6 K FE HEM . D HEM 600 1_555 L N27 6D8 . D 6D8 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
#
_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 176 n n 
CHA C4D HEM doub 177 n n 
CHA HHA HEM sing 178 n n 
CHB C4A HEM sing 179 n n 
CHB C1B HEM doub 180 n n 
CHB HHB HEM sing 181 n n 
CHC C4B HEM sing 182 n n 
CHC C1C HEM doub 183 n n 
CHC HHC HEM sing 184 n n 
CHD C4C HEM doub 185 n n 
CHD C1D HEM sing 186 n n 
CHD HHD HEM sing 187 n n 
C1A C2A HEM doub 188 n y 
C1A NA HEM sing 189 n y 
C2A C3A HEM sing 190 n y 
C2A CAA HEM sing 191 n n 
C3A C4A HEM doub 192 n y 
C3A CMA HEM sing 193 n n 
C4A NA HEM sing 194 n y 
CMA HMA HEM sing 195 n n 
CMA HMAA HEM sing 196 n n 
CMA HMAB HEM sing 197 n n 
CAA CBA HEM sing 198 n n 
CAA HAA HEM sing 199 n n 
CAA HAAA HEM sing 200 n n 
CBA CGA HEM sing 201 n n 
CBA HBA HEM sing 202 n n 
CBA HBAA HEM sing 203 n n 
CGA O1A HEM doub 204 n n 
CGA O2A HEM sing 205 n n 
C1B C2B HEM sing 206 n n 
C1B NB HEM sing 207 n n 
C2B C3B HEM doub 208 n n 
C2B CMB HEM sing 209 n n 
C3B C4B HEM sing 210 n n 
C3B CAB HEM sing 211 n n 
C4B NB HEM doub 212 n n 
CMB HMB HEM sing 213 n n 
CMB HMBA HEM sing 214 n n 
CMB HMBB HEM sing 215 n n 
CAB CBB HEM doub 216 n n 
CAB HAB HEM sing 217 n n 
CBB HBB HEM sing 218 n n 
CBB HBBA HEM sing 219 n n 
C1C C2C HEM sing 220 n y 
C1C NC HEM sing 221 n y 
C2C C3C HEM doub 222 n y 
C2C CMC HEM sing 223 n n 
C3C C4C HEM sing 224 n y 
C3C CAC HEM sing 225 n n 
C4C NC HEM sing 226 n y 
CMC HMC HEM sing 227 n n 
CMC HMCA HEM sing 228 n n 
CMC HMCB HEM sing 229 n n 
CAC CBC HEM doub 230 n n 
CAC HAC HEM sing 231 n n 
CBC HBC HEM sing 232 n n 
CBC HBCA HEM sing 233 n n 
C1D C2D HEM sing 234 n n 
C1D ND HEM doub 235 n n 
C2D C3D HEM doub 236 n n 
C2D CMD HEM sing 237 n n 
C3D C4D HEM sing 238 n n 
C3D CAD HEM sing 239 n n 
C4D ND HEM sing 240 n n 
CMD HMD HEM sing 241 n n 
CMD HMDA HEM sing 242 n n 
CMD HMDB HEM sing 243 n n 
CAD CBD HEM sing 244 n n 
CAD HAD HEM sing 245 n n 
CAD HADA HEM sing 246 n n 
CBD CGD HEM sing 247 n n 
CBD HBD HEM sing 248 n n 
CBD HBDA HEM sing 249 n n 
CGD O1D HEM doub 250 n n 
CGD O2D HEM sing 251 n n 
O2A H2A HEM sing 252 n n 
O2D H2D HEM sing 253 n n 
FE NA HEM sing 254 n n 
FE NB HEM sing 255 n n 
FE NC HEM sing 256 n n 
FE ND HEM sing 257 n n 
#
_atom_sites.entry_id                     5IRV 
_atom_sites.fract_transf_matrix[1][1]    0.010995 
_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]    0.006515 
_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]    0.005916 
_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 2 HEM A 1 600 600 HEM HEM . 
F 3 6D8 A 1 601 601 6D8 LIG . 
G 2 HEM B 1 600 600 HEM HEM . 
H 3 6D8 B 1 601 601 6D8 LIG . 
I 2 HEM C 1 600 600 HEM HEM . 
J 3 6D8 C 1 601 601 6D8 LIG . 
K 2 HEM D 1 600 600 HEM HEM . 
L 3 6D8 D 1 601 601 6D8 LIG . 
#
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 . . . K 2 54.517 -133.632 66.009 1 55.57 ? CHA HEM 600 D 1 
HETATM 2 C CHB HEM . . . K 2 52.352 -133.028 70.308 1 59.7 ? CHB HEM 600 D 1 
HETATM 3 C CHC HEM . . . K 2 51.984 -128.287 69.412 1 59.89 ? CHC HEM 600 D 1 
HETATM 4 C CHD HEM . . . K 2 53.955 -128.886 65.032 1 57.21 ? CHD HEM 600 D 1 
HETATM 5 C C1A HEM . . . K 2 53.96 -133.893 67.24 1 53.1 ? C1A HEM 600 D 1 
HETATM 6 C C2A HEM . . . K 2 53.876 -135.19 67.878 1 50.22 ? C2A HEM 600 D 1 
HETATM 7 C C3A HEM . . . K 2 53.268 -135.03 69.061 1 47.33 ? C3A HEM 600 D 1 
HETATM 8 C C4A HEM . . . K 2 52.967 -133.621 69.223 1 59.22 ? C4A HEM 600 D 1 
HETATM 9 C CMA HEM . . . K 2 52.942 -136.129 70.093 1 48.85 ? CMA HEM 600 D 1 
HETATM 10 C CAA HEM . . . K 2 54.374 -136.504 67.229 1 54.96 ? CAA HEM 600 D 1 
HETATM 11 C CBA HEM . . . K 2 55.501 -137.15 68.027 1 63.69 ? CBA HEM 600 D 1 
HETATM 12 C CGA HEM . . . K 2 55.975 -138.363 67.265 1 51.95 ? CGA HEM 600 D 1 
HETATM 13 O O1A HEM . . . K 2 55.317 -138.74 66.261 1 42.67 ? O1A HEM 600 D 1 
HETATM 14 O O2A HEM . . . K 2 57.012 -138.954 67.656 1 49.13 ? O2A HEM 600 D 1 
HETATM 15 C C1B HEM . . . K 2 52.069 -131.684 70.438 1 53.41 ? C1B HEM 600 D 1 
HETATM 16 C C2B HEM . . . K 2 51.434 -131.041 71.575 1 58.28 ? C2B HEM 600 D 1 
HETATM 17 C C3B HEM . . . K 2 51.311 -129.733 71.305 1 60.89 ? C3B HEM 600 D 1 
HETATM 18 C C4B HEM . . . K 2 51.906 -129.514 70.016 1 56.61 ? C4B HEM 600 D 1 
HETATM 19 C CMB HEM . . . K 2 50.958 -131.83 72.809 1 52.35 ? CMB HEM 600 D 1 
HETATM 20 C CAB HEM . . . K 2 50.753 -128.546 72.125 1 56.75 ? CAB HEM 600 D 1 
HETATM 21 C CBB HEM . . . K 2 50.455 -128.6 73.423 1 62.58 ? CBB HEM 600 D 1 
HETATM 22 C C1C HEM . . . K 2 52.479 -128.04 68.163 1 56.11 ? C1C HEM 600 D 1 
HETATM 23 C C2C HEM . . . K 2 52.504 -126.741 67.546 1 50.53 ? C2C HEM 600 D 1 
HETATM 24 C C3C HEM . . . K 2 53.072 -126.869 66.353 1 53.57 ? C3C HEM 600 D 1 
HETATM 25 C C4C HEM . . . K 2 53.381 -128.28 66.135 1 60.18 ? C4C HEM 600 D 1 
HETATM 26 C CMC HEM . . . K 2 52.016 -125.434 68.21 1 61.08 ? CMC HEM 600 D 1 
HETATM 27 C CAC HEM . . . K 2 53.256 -125.68 65.389 1 51.41 ? CAC HEM 600 D 1 
HETATM 28 C CBC HEM . . . K 2 54.442 -125.5 64.809 1 60.16 ? CBC HEM 600 D 1 
HETATM 29 C C1D HEM . . . K 2 54.251 -130.234 64.904 1 44.98 ? C1D HEM 600 D 1 
HETATM 30 C C2D HEM . . . K 2 54.796 -130.89 63.729 1 40.65 ? C2D HEM 600 D 1 
HETATM 31 C C3D HEM . . . K 2 54.933 -132.196 63.99 1 49.71 ? C3D HEM 600 D 1 
HETATM 32 C C4D HEM . . . K 2 54.509 -132.42 65.355 1 54.75 ? C4D HEM 600 D 1 
HETATM 33 C CMD HEM . . . K 2 55.11 -130.189 62.39 1 50.39 ? CMD HEM 600 D 1 
HETATM 34 C CAD HEM . . . K 2 55.488 -133.274 63.023 1 51.74 ? CAD HEM 600 D 1 
HETATM 35 C CBD HEM . . . K 2 56.959 -133.579 63.298 1 46.47 ? CBD HEM 600 D 1 
HETATM 36 C CGD HEM . . . K 2 57.468 -134.609 62.317 1 50.55 ? CGD HEM 600 D 1 
HETATM 37 O O1D HEM . . . K 2 58.708 -134.695 62.131 1 50.31 ? O1D HEM 600 D 1 
HETATM 38 O O2D HEM . . . K 2 56.651 -135.363 61.73 1 57.17 ? O2D HEM 600 D 1 
HETATM 39 N NA HEM . . . K 2 53.408 -132.959 68.093 1 59.2 ? NA HEM 600 D 1 
HETATM 40 N NB HEM . . . K 2 52.345 -130.714 69.501 1 42.92 ? NB HEM 600 D 1 
HETATM 41 N NC HEM . . . K 2 53.006 -128.959 67.278 1 60.72 ? NC HEM 600 D 1 
HETATM 42 N ND HEM . . . K 2 54.102 -131.205 65.877 1 44.96 ? ND HEM 600 D 1 
HETATM 43 FE FE HEM . . . K 2 53.098 -130.999 67.628 1 42.51 ? FE HEM 600 D 1 
HETATM 44 H HHB HEM . . . K 2 52.005 -133.626 71.003 1 71.63 ? HHB HEM 600 D 1 
HETATM 45 H HHC HEM . . . K 2 51.713 -127.511 69.945 1 71.87 ? HHC HEM 600 D 1 
HETATM 46 H HHD HEM . . . K 2 54.172 -128.309 64.27 1 68.65 ? HHD HEM 600 D 1 
HETATM 47 H HMA HEM . . . K 2 52.352 -136.796 69.685 1 58.62 ? HMA HEM 600 D 1 
HETATM 48 H HMAA HEM . . . K 2 52.495 -135.728 70.867 1 58.62 ? HMAA HEM 600 D 1 
HETATM 49 H HMAB HEM . . . K 2 53.773 -136.561 70.384 1 58.62 ? HMAB HEM 600 D 1 
HETATM 50 H HAA HEM . . . K 2 54.693 -136.311 66.333 1 65.96 ? HAA HEM 600 D 1 
HETATM 51 H HAAA HEM . . . K 2 53.632 -137.127 67.172 1 65.96 ? HAAA HEM 600 D 1 
HETATM 52 H HBA HEM . . . K 2 55.174 -137.418 68.899 1 76.43 ? HBA HEM 600 D 1 
HETATM 53 H HBAA HEM . . . K 2 56.233 -136.522 68.129 1 76.43 ? HBAA HEM 600 D 1 
HETATM 54 H HMB HEM . . . K 2 50.297 -132.486 72.538 1 62.82 ? HMB HEM 600 D 1 
HETATM 55 H HMBA HEM . . . K 2 50.564 -131.219 73.451 1 62.82 ? HMBA HEM 600 D 1 
HETATM 56 H HMBB HEM . . . K 2 51.714 -132.283 73.215 1 62.82 ? HMBB HEM 600 D 1 
HETATM 57 H HAB HEM . . . K 2 50.612 -127.713 71.668 1 68.1 ? HAB HEM 600 D 1 
HETATM 58 H HBB HEM . . . K 2 50.104 -127.816 73.873 1 75.09 ? HBB HEM 600 D 1 
HETATM 59 H HBBA HEM . . . K 2 50.585 -129.425 73.916 1 75.09 ? HBBA HEM 600 D 1 
HETATM 60 H HMC HEM . . . K 2 52.136 -124.695 67.594 1 73.3 ? HMC HEM 600 D 1 
HETATM 61 H HMCA HEM . . . K 2 52.53 -125.27 69.016 1 73.3 ? HMCA HEM 600 D 1 
HETATM 62 H HMCB HEM . . . K 2 51.077 -125.518 68.437 1 73.3 ? HMCB HEM 600 D 1 
HETATM 63 H HAC HEM . . . K 2 52.59 -124.99 65.346 1 61.7 ? HAC HEM 600 D 1 
HETATM 64 H HBC HEM . . . K 2 54.576 -124.754 64.203 1 72.2 ? HBC HEM 600 D 1 
HETATM 65 H HBCA HEM . . . K 2 55.171 -126.111 64.995 1 72.2 ? HBCA HEM 600 D 1 
HETATM 66 H HMD HEM . . . K 2 55.469 -130.843 61.755 1 60.46 ? HMD HEM 600 D 1 
HETATM 67 H HMDA HEM . . . K 2 55.772 -129.482 62.539 1 60.46 ? HMDA HEM 600 D 1 
HETATM 68 H HMDB HEM . . . K 2 54.289 -129.796 62.026 1 60.46 ? HMDB HEM 600 D 1 
HETATM 69 H HAD HEM . . . K 2 55.396 -132.957 62.111 1 62.09 ? HAD HEM 600 D 1 
HETATM 70 H HADA HEM . . . K 2 54.972 -134.088 63.128 1 62.09 ? HADA HEM 600 D 1 
HETATM 71 H HBD HEM . . . K 2 57.053 -133.921 64.201 1 55.76 ? HBD HEM 600 D 1 
HETATM 72 H HBDA HEM . . . K 2 57.479 -132.765 63.207 1 55.76 ? HBDA HEM 600 D 1 
HETATM 73 H HHA HEM . . . K 2 54.961 -134.378 65.555 1 66.68 ? HHA HEM 600 D 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           73 
#