data_7LYX
#
_model_server_result.job_id            -YkjZ3d67iQeBbEjevU_aw 
_model_server_result.datetime_utc      '2025-02-05 17:01:39' 
_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          7lyx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
#
_entry.id    7LYX 
#
_exptl.entry_id    7LYX 
_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    1 
_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            7LYX 
_cell.length_a            58.344 
_cell.length_b            89.234 
_cell.length_c            107.984 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7LYX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_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 
#
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 422 A CYS 440 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N19 YHM . A YHM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? 
#
_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 142 n n 
CHA C4D HEM doub 143 n n 
CHA HHA HEM sing 144 n n 
CHB C4A HEM sing 145 n n 
CHB C1B HEM doub 146 n n 
CHB HHB HEM sing 147 n n 
CHC C4B HEM sing 148 n n 
CHC C1C HEM doub 149 n n 
CHC HHC HEM sing 150 n n 
CHD C4C HEM doub 151 n n 
CHD C1D HEM sing 152 n n 
CHD HHD HEM sing 153 n n 
C1A C2A HEM doub 154 n y 
C1A NA HEM sing 155 n y 
C2A C3A HEM sing 156 n y 
C2A CAA HEM sing 157 n n 
C3A C4A HEM doub 158 n y 
C3A CMA HEM sing 159 n n 
C4A NA HEM sing 160 n y 
CMA HMA HEM sing 161 n n 
CMA HMAA HEM sing 162 n n 
CMA HMAB HEM sing 163 n n 
CAA CBA HEM sing 164 n n 
CAA HAA HEM sing 165 n n 
CAA HAAA HEM sing 166 n n 
CBA CGA HEM sing 167 n n 
CBA HBA HEM sing 168 n n 
CBA HBAA HEM sing 169 n n 
CGA O1A HEM doub 170 n n 
CGA O2A HEM sing 171 n n 
C1B C2B HEM sing 172 n n 
C1B NB HEM sing 173 n n 
C2B C3B HEM doub 174 n n 
C2B CMB HEM sing 175 n n 
C3B C4B HEM sing 176 n n 
C3B CAB HEM sing 177 n n 
C4B NB HEM doub 178 n n 
CMB HMB HEM sing 179 n n 
CMB HMBA HEM sing 180 n n 
CMB HMBB HEM sing 181 n n 
CAB CBB HEM doub 182 n n 
CAB HAB HEM sing 183 n n 
CBB HBB HEM sing 184 n n 
CBB HBBA HEM sing 185 n n 
C1C C2C HEM sing 186 n y 
C1C NC HEM sing 187 n y 
C2C C3C HEM doub 188 n y 
C2C CMC HEM sing 189 n n 
C3C C4C HEM sing 190 n y 
C3C CAC HEM sing 191 n n 
C4C NC HEM sing 192 n y 
CMC HMC HEM sing 193 n n 
CMC HMCA HEM sing 194 n n 
CMC HMCB HEM sing 195 n n 
CAC CBC HEM doub 196 n n 
CAC HAC HEM sing 197 n n 
CBC HBC HEM sing 198 n n 
CBC HBCA HEM sing 199 n n 
C1D C2D HEM sing 200 n n 
C1D ND HEM doub 201 n n 
C2D C3D HEM doub 202 n n 
C2D CMD HEM sing 203 n n 
C3D C4D HEM sing 204 n n 
C3D CAD HEM sing 205 n n 
C4D ND HEM sing 206 n n 
CMD HMD HEM sing 207 n n 
CMD HMDA HEM sing 208 n n 
CMD HMDB HEM sing 209 n n 
CAD CBD HEM sing 210 n n 
CAD HAD HEM sing 211 n n 
CAD HADA HEM sing 212 n n 
CBD CGD HEM sing 213 n n 
CBD HBD HEM sing 214 n n 
CBD HBDA HEM sing 215 n n 
CGD O1D HEM doub 216 n n 
CGD O2D HEM sing 217 n n 
O2A H2A HEM sing 218 n n 
O2D H2D HEM sing 219 n n 
FE NA HEM sing 220 n n 
FE NB HEM sing 221 n n 
FE NC HEM sing 222 n n 
FE ND HEM sing 223 n n 
#
_atom_sites.entry_id                     7LYX 
_atom_sites.fract_transf_matrix[1][1]    0.01714 
_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]    0.011206 
_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]    0.009261 
_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
B 2 HEM A 1 601 600 HEM HEM . 
C 3 YHM A 1 602 701 YHM LIG . 
D 4 GOL A 1 603 702 GOL GOL . 
E 5 K A 1 604 1 K K . 
F 6 HOH A 1 701 4 HOH HOH . 
F 6 HOH A 2 702 14 HOH HOH . 
F 6 HOH A 3 703 21 HOH HOH . 
F 6 HOH A 4 704 17 HOH HOH . 
F 6 HOH A 5 705 26 HOH HOH . 
F 6 HOH A 6 706 8 HOH HOH . 
F 6 HOH A 7 707 22 HOH HOH . 
F 6 HOH A 8 708 19 HOH HOH . 
F 6 HOH A 9 709 27 HOH HOH . 
F 6 HOH A 10 710 25 HOH HOH . 
F 6 HOH A 11 711 16 HOH HOH . 
F 6 HOH A 12 712 7 HOH HOH . 
F 6 HOH A 13 713 15 HOH HOH . 
F 6 HOH A 14 714 13 HOH HOH . 
F 6 HOH A 15 715 24 HOH HOH . 
F 6 HOH A 16 716 28 HOH HOH . 
F 6 HOH A 17 717 23 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 . . . B 2 -17.834 -4.346 9.802 1 52.06 ? CHA HEM 601 A 1 
HETATM 2 C CHB HEM . . . B 2 -15.848 -3.367 14.131 1 50.45 ? CHB HEM 601 A 1 
HETATM 3 C CHC HEM . . . B 2 -18.202 0.874 14.241 1 44.22 ? CHC HEM 601 A 1 
HETATM 4 C CHD HEM . . . B 2 -20.389 -0.221 10.038 1 45.37 ? CHD HEM 601 A 1 
HETATM 5 C C1A HEM . . . B 2 -17.09 -4.465 10.962 1 52.55 ? C1A HEM 601 A 1 
HETATM 6 C C2A HEM . . . B 2 -16.24 -5.583 11.336 1 54.26 ? C2A HEM 601 A 1 
HETATM 7 C C3A HEM . . . B 2 -15.697 -5.308 12.53 1 52.39 ? C3A HEM 601 A 1 
HETATM 8 C C4A HEM . . . B 2 -16.171 -4.009 12.956 1 46.42 ? C4A HEM 601 A 1 
HETATM 9 C CMA HEM . . . B 2 -14.723 -6.212 13.319 1 48.37 ? CMA HEM 601 A 1 
HETATM 10 C CAA HEM . . . B 2 -16.001 -6.867 10.501 1 53.05 ? CAA HEM 601 A 1 
HETATM 11 C CBA HEM . . . B 2 -14.641 -6.771 9.817 1 57.56 ? CBA HEM 601 A 1 
HETATM 12 C CGA HEM . . . B 2 -14.379 -7.946 8.908 1 64.75 ? CGA HEM 601 A 1 
HETATM 13 O O1A HEM . . . B 2 -13.332 -7.916 8.214 1 62.51 ? O1A HEM 601 A 1 
HETATM 14 O O2A HEM . . . B 2 -15.204 -8.889 8.876 1 57.23 ? O2A HEM 601 A 1 
HETATM 15 C C1B HEM . . . B 2 -16.328 -2.144 14.545 1 44.43 ? C1B HEM 601 A 1 
HETATM 16 C C2B HEM . . . B 2 -16.033 -1.517 15.813 1 44.84 ? C2B HEM 601 A 1 
HETATM 17 C C3B HEM . . . B 2 -16.689 -0.347 15.865 1 43.57 ? C3B HEM 601 A 1 
HETATM 18 C C4B HEM . . . B 2 -17.408 -0.19 14.611 1 40.53 ? C4B HEM 601 A 1 
HETATM 19 C CMB HEM . . . B 2 -15.125 -2.162 16.887 1 49.57 ? CMB HEM 601 A 1 
HETATM 20 C CAB HEM . . . B 2 -16.687 0.71 17 1 42.1 ? CAB HEM 601 A 1 
HETATM 21 C CBB HEM . . . B 2 -15.775 0.68 17.98 1 41.97 ? CBB HEM 601 A 1 
HETATM 22 C C1C HEM . . . B 2 -18.97 0.961 13.092 1 43.88 ? C1C HEM 601 A 1 
HETATM 23 C C2C HEM . . . B 2 -19.744 2.113 12.674 1 44.63 ? C2C HEM 601 A 1 
HETATM 24 C C3C HEM . . . B 2 -20.354 1.804 11.521 1 42.63 ? C3C HEM 601 A 1 
HETATM 25 C C4C HEM . . . B 2 -19.975 0.459 11.163 1 42.58 ? C4C HEM 601 A 1 
HETATM 26 C CMC HEM . . . B 2 -19.831 3.433 13.476 1 42.98 ? CMC HEM 601 A 1 
HETATM 27 C CAC HEM . . . B 2 -21.289 2.671 10.633 1 40.35 ? CAC HEM 601 A 1 
HETATM 28 C CBC HEM . . . B 2 -21.394 3.988 10.787 1 42.9 ? CBC HEM 601 A 1 
HETATM 29 C C1D HEM . . . B 2 -19.941 -1.461 9.632 1 51.04 ? C1D HEM 601 A 1 
HETATM 30 C C2D HEM . . . B 2 -20.462 -2.24 8.531 1 52.46 ? C2D HEM 601 A 1 
HETATM 31 C C3D HEM . . . B 2 -19.751 -3.37 8.454 1 50.74 ? C3D HEM 601 A 1 
HETATM 32 C C4D HEM . . . B 2 -18.765 -3.364 9.518 1 53.18 ? C4D HEM 601 A 1 
HETATM 33 C CMD HEM . . . B 2 -21.621 -1.825 7.598 1 50.33 ? CMD HEM 601 A 1 
HETATM 34 C CAD HEM . . . B 2 -20.007 -4.486 7.412 1 52.76 ? CAD HEM 601 A 1 
HETATM 35 C CBD HEM . . . B 2 -18.745 -5.086 6.805 1 53.31 ? CBD HEM 601 A 1 
HETATM 36 C CGD HEM . . . B 2 -18.875 -5.002 5.304 1 57.36 ? CGD HEM 601 A 1 
HETATM 37 O O1D HEM . . . B 2 -18.977 -6.063 4.636 1 58.55 ? O1D HEM 601 A 1 
HETATM 38 O O2D HEM . . . B 2 -18.895 -3.86 4.779 1 61.7 ? O2D HEM 601 A 1 
HETATM 39 N NA HEM . . . B 2 -17.017 -3.529 11.976 1 48.1 ? NA HEM 601 A 1 
HETATM 40 N NB HEM . . . B 2 -17.169 -1.311 13.834 1 49.79 ? NB HEM 601 A 1 
HETATM 41 N NC HEM . . . B 2 -19.135 -0.032 12.143 1 46.83 ? NC HEM 601 A 1 
HETATM 42 N ND HEM . . . B 2 -18.909 -2.178 10.208 1 51.65 ? ND HEM 601 A 1 
HETATM 43 FE FE HEM . . . B 2 -18.028 -1.781 11.991 1 46.62 ? FE HEM 601 A 1 
HETATM 44 H HHB HEM . . . B 2 -15.217 -3.822 14.727 1 64.38 ? HHB HEM 601 A 1 
HETATM 45 H HHC HEM . . . B 2 -18.225 1.643 14.849 1 51.52 ? HHC HEM 601 A 1 
HETATM 46 H HHD HEM . . . B 2 -21.062 0.216 9.476 1 53.74 ? HHD HEM 601 A 1 
HETATM 47 H HMA HEM . . . B 2 -15.126 -7.096 13.446 1 59.61 ? HMA HEM 601 A 1 
HETATM 48 H HMAA HEM . . . B 2 -14.539 -5.809 14.194 1 59.61 ? HMAA HEM 601 A 1 
HETATM 49 H HMAB HEM . . . B 2 -13.885 -6.304 12.82 1 59.61 ? HMAB HEM 601 A 1 
HETATM 50 H HAA HEM . . . B 2 -16.697 -6.952 9.83 1 69.92 ? HAA HEM 601 A 1 
HETATM 51 H HAAA HEM . . . B 2 -16.017 -7.642 11.085 1 69.92 ? HAAA HEM 601 A 1 
HETATM 52 H HBA HEM . . . B 2 -13.951 -6.742 10.498 1 78.23 ? HBA HEM 601 A 1 
HETATM 53 H HBAA HEM . . . B 2 -14.613 -5.956 9.292 1 78.23 ? HBAA HEM 601 A 1 
HETATM 54 H HMB HEM . . . B 2 -15.077 -3.12 16.737 1 63 ? HMB HEM 601 A 1 
HETATM 55 H HMBA HEM . . . B 2 -15.494 -1.991 17.768 1 63 ? HMBA HEM 601 A 1 
HETATM 56 H HMBB HEM . . . B 2 -14.235 -1.781 16.829 1 63 ? HMBB HEM 601 A 1 
HETATM 57 H HAB HEM . . . B 2 -17.355 1.4 17 1 47.46 ? HAB HEM 601 A 1 
HETATM 58 H HBB HEM . . . B 2 -15.793 1.352 18.68 1 47.01 ? HBB HEM 601 A 1 
HETATM 59 H HBBA HEM . . . B 2 -15.096 -0.012 17.99 1 47.01 ? HBBA HEM 601 A 1 
HETATM 60 H HMC HEM . . . B 2 -19.676 3.252 14.416 1 47.99 ? HMC HEM 601 A 1 
HETATM 61 H HMCA HEM . . . B 2 -20.713 3.822 13.363 1 47.99 ? HMCA HEM 601 A 1 
HETATM 62 H HMCB HEM . . . B 2 -19.16 4.054 13.152 1 47.99 ? HMCB HEM 601 A 1 
HETATM 63 H HAC HEM . . . B 2 -21.809 2.241 9.95 1 42.08 ? HAC HEM 601 A 1 
HETATM 64 H HBC HEM . . . B 2 -21.988 4.497 10.214 1 46.73 ? HBC HEM 601 A 1 
HETATM 65 H HBCA HEM . . . B 2 -20.876 4.439 11.472 1 46.73 ? HBCA HEM 601 A 1 
HETATM 66 H HMD HEM . . . B 2 -22.316 -1.373 8.121 1 64.07 ? HMD HEM 601 A 1 
HETATM 67 H HMDA HEM . . . B 2 -22.001 -2.623 7.173 1 64.07 ? HMDA HEM 601 A 1 
HETATM 68 H HMDB HEM . . . B 2 -21.284 -1.217 6.908 1 64.07 ? HMDB HEM 601 A 1 
HETATM 69 H HAD HEM . . . B 2 -20.541 -4.113 6.694 1 69.49 ? HAD HEM 601 A 1 
HETATM 70 H HADA HEM . . . B 2 -20.502 -5.199 7.847 1 69.49 ? HADA HEM 601 A 1 
HETATM 71 H HBD HEM . . . B 2 -18.656 -6.013 7.078 1 69.74 ? HBD HEM 601 A 1 
HETATM 72 H HBDA HEM . . . B 2 -17.968 -4.586 7.098 1 69.74 ? HBDA HEM 601 A 1 
HETATM 73 H HHA HEM . . . B 2 -17.686 -5.026 9.112 1 68.17 ? HHA HEM 601 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           73 
#