data_1VYD
#
_model_server_result.job_id            YBL45gB56wWVeU9I9WhBGQ 
_model_server_result.datetime_utc      '2025-09-05 00:55:12' 
_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          1vyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1117}' 
#
_entry.id    1VYD 
#
_exptl.entry_id    1VYD 
_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            1VYD 
_cell.length_a            100.23 
_cell.length_b            100.23 
_cell.length_c            162.15 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1VYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PQS monomeric 1 author_and_software_defined_assembly 1 
PQS 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,E 1 1 
B,D,F 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 NE2 HIS 17 A HIS 17 1_555 C FE HEM . A HEM 1117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc2 A SD MET 96 A MET 96 1_555 C FE HEM . A HEM 1117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc3 B NE2 HIS 17 B HIS 17 1_555 D FE HEM . B HEM 1117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc4 B SD MET 96 B MET 96 1_555 D FE HEM . B HEM 1117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? 
#
_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 110 n n 
CHA C4D HEM doub 111 n n 
CHA HHA HEM sing 112 n n 
CHB C4A HEM sing 113 n n 
CHB C1B HEM doub 114 n n 
CHB HHB HEM sing 115 n n 
CHC C4B HEM sing 116 n n 
CHC C1C HEM doub 117 n n 
CHC HHC HEM sing 118 n n 
CHD C4C HEM doub 119 n n 
CHD C1D HEM sing 120 n n 
CHD HHD HEM sing 121 n n 
C1A C2A HEM doub 122 n y 
C1A NA HEM sing 123 n y 
C2A C3A HEM sing 124 n y 
C2A CAA HEM sing 125 n n 
C3A C4A HEM doub 126 n y 
C3A CMA HEM sing 127 n n 
C4A NA HEM sing 128 n y 
CMA HMA HEM sing 129 n n 
CMA HMAA HEM sing 130 n n 
CMA HMAB HEM sing 131 n n 
CAA CBA HEM sing 132 n n 
CAA HAA HEM sing 133 n n 
CAA HAAA HEM sing 134 n n 
CBA CGA HEM sing 135 n n 
CBA HBA HEM sing 136 n n 
CBA HBAA HEM sing 137 n n 
CGA O1A HEM doub 138 n n 
CGA O2A HEM sing 139 n n 
C1B C2B HEM sing 140 n n 
C1B NB HEM sing 141 n n 
C2B C3B HEM doub 142 n n 
C2B CMB HEM sing 143 n n 
C3B C4B HEM sing 144 n n 
C3B CAB HEM sing 145 n n 
C4B NB HEM doub 146 n n 
CMB HMB HEM sing 147 n n 
CMB HMBA HEM sing 148 n n 
CMB HMBB HEM sing 149 n n 
CAB CBB HEM doub 150 n n 
CAB HAB HEM sing 151 n n 
CBB HBB HEM sing 152 n n 
CBB HBBA HEM sing 153 n n 
C1C C2C HEM sing 154 n y 
C1C NC HEM sing 155 n y 
C2C C3C HEM doub 156 n y 
C2C CMC HEM sing 157 n n 
C3C C4C HEM sing 158 n y 
C3C CAC HEM sing 159 n n 
C4C NC HEM sing 160 n y 
CMC HMC HEM sing 161 n n 
CMC HMCA HEM sing 162 n n 
CMC HMCB HEM sing 163 n n 
CAC CBC HEM doub 164 n n 
CAC HAC HEM sing 165 n n 
CBC HBC HEM sing 166 n n 
CBC HBCA HEM sing 167 n n 
C1D C2D HEM sing 168 n n 
C1D ND HEM doub 169 n n 
C2D C3D HEM doub 170 n n 
C2D CMD HEM sing 171 n n 
C3D C4D HEM sing 172 n n 
C3D CAD HEM sing 173 n n 
C4D ND HEM sing 174 n n 
CMD HMD HEM sing 175 n n 
CMD HMDA HEM sing 176 n n 
CMD HMDB HEM sing 177 n n 
CAD CBD HEM sing 178 n n 
CAD HAD HEM sing 179 n n 
CAD HADA HEM sing 180 n n 
CBD CGD HEM sing 181 n n 
CBD HBD HEM sing 182 n n 
CBD HBDA HEM sing 183 n n 
CGD O1D HEM doub 184 n n 
CGD O2D HEM sing 185 n n 
O2A H2A HEM sing 186 n n 
O2D H2D HEM sing 187 n n 
FE NA HEM sing 188 n n 
FE NB HEM sing 189 n n 
FE NC HEM sing 190 n n 
FE ND HEM sing 191 n n 
#
_atom_sites.entry_id                     1VYD 
_atom_sites.fract_transf_matrix[1][1]    0.009977 
_atom_sites.fract_transf_matrix[1][2]    0.00576 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01152 
_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]    0.006167 
_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 1117 1117 HEM HEM . 
D 2 HEM B 1 1117 1117 HEM HEM . 
E 3 HOH A 1 2001 2001 HOH HOH . 
E 3 HOH A 2 2002 2002 HOH HOH . 
E 3 HOH A 3 2003 2003 HOH HOH . 
E 3 HOH A 4 2004 2004 HOH HOH . 
E 3 HOH A 5 2005 2005 HOH HOH . 
E 3 HOH A 6 2006 2006 HOH HOH . 
E 3 HOH A 7 2007 2007 HOH HOH . 
E 3 HOH A 8 2008 2008 HOH HOH . 
E 3 HOH A 9 2009 2009 HOH HOH . 
E 3 HOH A 10 2010 2010 HOH HOH . 
E 3 HOH A 11 2011 2011 HOH HOH . 
E 3 HOH A 12 2012 2012 HOH HOH . 
E 3 HOH A 13 2013 2013 HOH HOH . 
E 3 HOH A 14 2014 2014 HOH HOH . 
E 3 HOH A 15 2015 2015 HOH HOH . 
E 3 HOH A 16 2016 2016 HOH HOH . 
E 3 HOH A 17 2017 2017 HOH HOH . 
E 3 HOH A 18 2018 2018 HOH HOH . 
E 3 HOH A 19 2019 2019 HOH HOH . 
E 3 HOH A 20 2020 2020 HOH HOH . 
E 3 HOH A 21 2021 2021 HOH HOH . 
E 3 HOH A 22 2022 2022 HOH HOH . 
E 3 HOH A 23 2023 2023 HOH HOH . 
E 3 HOH A 24 2024 2024 HOH HOH . 
E 3 HOH A 25 2025 2025 HOH HOH . 
E 3 HOH A 26 2026 2026 HOH HOH . 
E 3 HOH A 27 2027 2027 HOH HOH . 
E 3 HOH A 28 2028 2028 HOH HOH . 
E 3 HOH A 29 2029 2029 HOH HOH . 
E 3 HOH A 30 2030 2030 HOH HOH . 
E 3 HOH A 31 2031 2031 HOH HOH . 
E 3 HOH A 32 2032 2032 HOH HOH . 
E 3 HOH A 33 2033 2033 HOH HOH . 
E 3 HOH A 34 2034 2034 HOH HOH . 
E 3 HOH A 35 2035 2035 HOH HOH . 
E 3 HOH A 36 2036 2036 HOH HOH . 
E 3 HOH A 37 2037 2037 HOH HOH . 
E 3 HOH A 38 2038 2038 HOH HOH . 
E 3 HOH A 39 2039 2039 HOH HOH . 
F 3 HOH B 1 2001 2001 HOH HOH . 
F 3 HOH B 2 2002 2002 HOH HOH . 
F 3 HOH B 3 2003 2003 HOH HOH . 
F 3 HOH B 4 2004 2004 HOH HOH . 
F 3 HOH B 5 2005 2005 HOH HOH . 
F 3 HOH B 6 2006 2006 HOH HOH . 
F 3 HOH B 7 2007 2007 HOH HOH . 
F 3 HOH B 8 2008 2008 HOH HOH . 
F 3 HOH B 9 2009 2009 HOH HOH . 
F 3 HOH B 10 2010 2010 HOH HOH . 
F 3 HOH B 11 2011 2011 HOH HOH . 
F 3 HOH B 12 2012 2012 HOH HOH . 
F 3 HOH B 13 2013 2013 HOH HOH . 
F 3 HOH B 14 2014 2014 HOH HOH . 
F 3 HOH B 15 2015 2015 HOH HOH . 
F 3 HOH B 16 2016 2016 HOH HOH . 
F 3 HOH B 17 2017 2017 HOH HOH . 
F 3 HOH B 18 2018 2018 HOH HOH . 
F 3 HOH B 19 2019 2019 HOH HOH . 
F 3 HOH B 20 2020 2020 HOH HOH . 
F 3 HOH B 21 2021 2021 HOH HOH . 
F 3 HOH B 22 2022 2022 HOH HOH . 
F 3 HOH B 23 2023 2023 HOH HOH . 
F 3 HOH B 24 2024 2024 HOH HOH . 
F 3 HOH B 25 2025 2025 HOH HOH . 
F 3 HOH B 26 2026 2026 HOH HOH . 
F 3 HOH B 27 2027 2027 HOH HOH . 
F 3 HOH B 28 2028 2028 HOH HOH . 
F 3 HOH B 29 2029 2029 HOH HOH . 
F 3 HOH B 30 2030 2030 HOH HOH . 
F 3 HOH B 31 2031 2031 HOH HOH . 
F 3 HOH B 32 2032 2032 HOH HOH . 
F 3 HOH B 33 2033 2033 HOH HOH . 
F 3 HOH B 34 2034 2034 HOH HOH . 
F 3 HOH B 35 2035 2035 HOH HOH . 
F 3 HOH B 36 2036 2036 HOH HOH . 
F 3 HOH B 37 2037 2037 HOH HOH . 
F 3 HOH B 38 2038 2038 HOH HOH . 
F 3 HOH B 39 2039 2039 HOH HOH . 
F 3 HOH B 40 2040 2040 HOH HOH . 
F 3 HOH B 41 2041 2041 HOH HOH . 
F 3 HOH B 42 2042 2042 HOH HOH . 
F 3 HOH B 43 2043 2043 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 . . . C 2 10.036 50.127 3.148 1 25.42 ? CHA HEM 1117 A 1 
HETATM 2 C CHB HEM . . . C 2 8.538 46.457 0.314 1 23.55 ? CHB HEM 1117 A 1 
HETATM 3 C CHC HEM . . . C 2 4.289 48.754 -0.346 1 22.83 ? CHC HEM 1117 A 1 
HETATM 4 C CHD HEM . . . C 2 6.149 52.733 1.771 1 23.53 ? CHD HEM 1117 A 1 
HETATM 5 C C1A HEM . . . C 2 9.934 48.905 2.491 1 23.79 ? C1A HEM 1117 A 1 
HETATM 6 C C2A HEM . . . C 2 10.923 47.847 2.507 1 24.74 ? C2A HEM 1117 A 1 
HETATM 7 C C3A HEM . . . C 2 10.479 46.869 1.748 1 23.13 ? C3A HEM 1117 A 1 
HETATM 8 C C4A HEM . . . C 2 9.205 47.26 1.227 1 23.4 ? C4A HEM 1117 A 1 
HETATM 9 C CMA HEM . . . C 2 11.021 45.483 1.325 1 27.42 ? CMA HEM 1117 A 1 
HETATM 10 C CAA HEM . . . C 2 12.263 47.958 3.314 1 23.06 ? CAA HEM 1117 A 1 
HETATM 11 C CBA HEM . . . C 2 13.327 48.541 2.414 1 23.66 ? CBA HEM 1117 A 1 
HETATM 12 C CGA HEM . . . C 2 14.721 48.749 2.966 1 25.21 ? CGA HEM 1117 A 1 
HETATM 13 O O1A HEM . . . C 2 15.002 48.373 4.141 1 26 ? O1A HEM 1117 A 1 
HETATM 14 O O2A HEM . . . C 2 15.447 49.439 2.211 1 23.17 ? O2A HEM 1117 A 1 
HETATM 15 C C1B HEM . . . C 2 7.266 46.823 -0.081 1 21.5 ? C1B HEM 1117 A 1 
HETATM 16 C C2B HEM . . . C 2 6.419 45.958 -0.865 1 23.67 ? C2B HEM 1117 A 1 
HETATM 17 C C3B HEM . . . C 2 5.248 46.597 -0.991 1 23.5 ? C3B HEM 1117 A 1 
HETATM 18 C C4B HEM . . . C 2 5.338 47.877 -0.368 1 22.22 ? C4B HEM 1117 A 1 
HETATM 19 C CMB HEM . . . C 2 6.859 44.57 -1.446 1 21.52 ? CMB HEM 1117 A 1 
HETATM 20 C CAB HEM . . . C 2 3.93 46.092 -1.63 1 23.4 ? CAB HEM 1117 A 1 
HETATM 21 C CBB HEM . . . C 2 3.426 44.863 -1.237 1 24.22 ? CBB HEM 1117 A 1 
HETATM 22 C C1C HEM . . . C 2 4.458 50.033 0.174 1 24.27 ? C1C HEM 1117 A 1 
HETATM 23 C C2C HEM . . . C 2 3.461 51.089 0.059 1 22.05 ? C2C HEM 1117 A 1 
HETATM 24 C C3C HEM . . . C 2 3.954 52.156 0.655 1 24.33 ? C3C HEM 1117 A 1 
HETATM 25 C C4C HEM . . . C 2 5.284 51.84 1.146 1 25.14 ? C4C HEM 1117 A 1 
HETATM 26 C CMC HEM . . . C 2 2.136 50.867 -0.693 1 21.81 ? CMC HEM 1117 A 1 
HETATM 27 C CAC HEM . . . C 2 3.3 53.522 0.951 1 28.1 ? CAC HEM 1117 A 1 
HETATM 28 C CBC HEM . . . C 2 1.957 53.685 1.189 1 29.21 ? CBC HEM 1117 A 1 
HETATM 29 C C1D HEM . . . C 2 7.38 52.368 2.286 1 22.26 ? C1D HEM 1117 A 1 
HETATM 30 C C2D HEM . . . C 2 8.16 53.194 3.169 1 21.39 ? C2D HEM 1117 A 1 
HETATM 31 C C3D HEM . . . C 2 9.233 52.474 3.546 1 22.27 ? C3D HEM 1117 A 1 
HETATM 32 C C4D HEM . . . C 2 9.122 51.157 2.965 1 25.18 ? C4D HEM 1117 A 1 
HETATM 33 C CMD HEM . . . C 2 7.779 54.644 3.508 1 21.32 ? CMD HEM 1117 A 1 
HETATM 34 C CAD HEM . . . C 2 10.353 52.837 4.518 1 24.71 ? CAD HEM 1117 A 1 
HETATM 35 C CBD HEM . . . C 2 9.946 52.228 5.909 1 27 ? CBD HEM 1117 A 1 
HETATM 36 C CGD HEM . . . C 2 10.414 52.971 7.128 1 30.22 ? CGD HEM 1117 A 1 
HETATM 37 O O1D HEM . . . C 2 9.84 52.586 8.177 1 32.31 ? O1D HEM 1117 A 1 
HETATM 38 O O2D HEM . . . C 2 11.167 53.992 7.05 1 30.83 ? O2D HEM 1117 A 1 
HETATM 39 N NA HEM . . . C 2 8.905 48.516 1.7 1 22.97 ? NA HEM 1117 A 1 
HETATM 40 N NB HEM . . . C 2 6.618 47.994 0.167 1 21.55 ? NB HEM 1117 A 1 
HETATM 41 N NC HEM . . . C 2 5.559 50.508 0.853 1 24.22 ? NC HEM 1117 A 1 
HETATM 42 N ND HEM . . . C 2 7.963 51.108 2.194 1 22.25 ? ND HEM 1117 A 1 
HETATM 43 FE FE HEM . . . C 2 7.256 49.535 1.245 1 25.71 ? FE HEM 1117 A 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           43 
#