data_4D78
#
_model_server_result.job_id            -GgyPeCgoPwbB6HRvSXNmQ 
_model_server_result.datetime_utc      '2024-10-11 02:19:10' 
_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          4d78 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1500}' 
#
_entry.id    4D78 
#
_exptl.entry_id    4D78 
_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            4D78 
_cell.length_a            75.92 
_cell.length_b            100.36 
_cell.length_c            124.75 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D78 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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 442 1_555 B FE HEM . A HEM 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc2 B FE HEM . A HEM 1500 1_555 C N22 J9K . A J9K 1600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
#
_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                     4D78 
_atom_sites.fract_transf_matrix[1][1]    0.013172 
_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]    0.009964 
_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]    0.008016 
_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 1500 1500 HEM HEM . 
C 3 J9K A 1 1600 1600 J9K J9K . 
D 4 GOL A 1 1601 1601 GOL GOL . 
E 4 GOL A 1 1602 1602 GOL GOL . 
F 5 HOH A 1 2001 2001 HOH HOH . 
F 5 HOH A 2 2002 2002 HOH HOH . 
F 5 HOH A 3 2003 2003 HOH HOH . 
F 5 HOH A 4 2004 2004 HOH HOH . 
F 5 HOH A 5 2005 2005 HOH HOH . 
F 5 HOH A 6 2006 2006 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 -14.963 30.321 -8.889 1 59.02 ? CHA HEM 1500 A 1 
HETATM 2 C CHB HEM . . . B 2 -15.688 27.636 -12.851 1 53.74 ? CHB HEM 1500 A 1 
HETATM 3 C CHC HEM . . . B 2 -16.072 23.686 -10.04 1 63.47 ? CHC HEM 1500 A 1 
HETATM 4 C CHD HEM . . . B 2 -15.527 26.425 -6.099 1 63.9 ? CHD HEM 1500 A 1 
HETATM 5 C C1A HEM . . . B 2 -15.128 29.899 -10.189 1 56.75 ? C1A HEM 1500 A 1 
HETATM 6 C C2A HEM . . . B 2 -15.108 30.784 -11.288 1 51.24 ? C2A HEM 1500 A 1 
HETATM 7 C C3A HEM . . . B 2 -15.29 30.023 -12.413 1 50.67 ? C3A HEM 1500 A 1 
HETATM 8 C C4A HEM . . . B 2 -15.446 28.69 -11.998 1 51.68 ? C4A HEM 1500 A 1 
HETATM 9 C CMA HEM . . . B 2 -15.306 30.478 -13.844 1 46.2 ? CMA HEM 1500 A 1 
HETATM 10 C CAA HEM . . . B 2 -14.847 32.257 -11.165 1 44.12 ? CAA HEM 1500 A 1 
HETATM 11 C CBA HEM . . . B 2 -13.317 32.459 -11.167 1 52.42 ? CBA HEM 1500 A 1 
HETATM 12 C CGA HEM . . . B 2 -12.94 33.82 -11.738 1 60.99 ? CGA HEM 1500 A 1 
HETATM 13 O O1A HEM . . . B 2 -13.84 34.597 -12.134 1 63.15 ? O1A HEM 1500 A 1 
HETATM 14 O O2A HEM . . . B 2 -11.745 34.209 -11.839 1 62.22 ? O2A HEM 1500 A 1 
HETATM 15 C C1B HEM . . . B 2 -15.863 26.321 -12.417 1 55.17 ? C1B HEM 1500 A 1 
HETATM 16 C C2B HEM . . . B 2 -16.097 25.232 -13.297 1 60.85 ? C2B HEM 1500 A 1 
HETATM 17 C C3B HEM . . . B 2 -16.207 24.088 -12.51 1 57.76 ? C3B HEM 1500 A 1 
HETATM 18 C C4B HEM . . . B 2 -16.033 24.552 -11.134 1 57.21 ? C4B HEM 1500 A 1 
HETATM 19 C CMB HEM . . . B 2 -16.19 25.387 -14.809 1 58.48 ? CMB HEM 1500 A 1 
HETATM 20 C CAB HEM . . . B 2 -16.459 22.664 -12.831 1 55.69 ? CAB HEM 1500 A 1 
HETATM 21 C CBB HEM . . . B 2 -16.388 22.149 -14.049 1 52.99 ? CBB HEM 1500 A 1 
HETATM 22 C C1C HEM . . . B 2 -15.926 24.084 -8.705 1 63.87 ? C1C HEM 1500 A 1 
HETATM 23 C C2C HEM . . . B 2 -15.973 23.217 -7.588 1 67.11 ? C2C HEM 1500 A 1 
HETATM 24 C C3C HEM . . . B 2 -15.815 23.999 -6.466 1 63.34 ? C3C HEM 1500 A 1 
HETATM 25 C C4C HEM . . . B 2 -15.672 25.343 -6.92 1 62.93 ? C4C HEM 1500 A 1 
HETATM 26 C CMC HEM . . . B 2 -16.154 21.708 -7.613 1 65.24 ? CMC HEM 1500 A 1 
HETATM 27 C CAC HEM . . . B 2 -15.819 23.508 -5.081 1 60.21 ? CAC HEM 1500 A 1 
HETATM 28 C CBC HEM . . . B 2 -14.684 23.291 -4.475 1 61.62 ? CBC HEM 1500 A 1 
HETATM 29 C C1D HEM . . . B 2 -15.336 27.703 -6.615 1 63.02 ? C1D HEM 1500 A 1 
HETATM 30 C C2D HEM . . . B 2 -15.133 28.831 -5.683 1 64.61 ? C2D HEM 1500 A 1 
HETATM 31 C C3D HEM . . . B 2 -14.974 29.916 -6.456 1 63.46 ? C3D HEM 1500 A 1 
HETATM 32 C C4D HEM . . . B 2 -15.073 29.44 -7.848 1 60.81 ? C4D HEM 1500 A 1 
HETATM 33 C CMD HEM . . . B 2 -15.107 28.782 -4.172 1 64.1 ? CMD HEM 1500 A 1 
HETATM 34 C CAD HEM . . . B 2 -14.709 31.32 -5.983 1 63.63 ? CAD HEM 1500 A 1 
HETATM 35 C CBD HEM . . . B 2 -13.184 31.525 -5.934 1 66.67 ? CBD HEM 1500 A 1 
HETATM 36 C CGD HEM . . . B 2 -12.832 32.805 -5.23 1 70.07 ? CGD HEM 1500 A 1 
HETATM 37 O O1D HEM . . . B 2 -13.456 33.862 -5.553 1 66.26 ? O1D HEM 1500 A 1 
HETATM 38 O O2D HEM . . . B 2 -11.934 32.779 -4.334 1 63.51 ? O2D HEM 1500 A 1 
HETATM 39 N NA HEM . . . B 2 -15.369 28.629 -10.638 1 51.47 ? NA HEM 1500 A 1 
HETATM 40 N NB HEM . . . B 2 -15.821 25.871 -11.175 1 56.12 ? NB HEM 1500 A 1 
HETATM 41 N NC HEM . . . B 2 -15.753 25.359 -8.28 1 57.37 ? NC HEM 1500 A 1 
HETATM 42 N ND HEM . . . B 2 -15.291 28.112 -7.914 1 62.64 ? ND HEM 1500 A 1 
HETATM 43 FE FE HEM . . . B 2 -15.54 27.051 -9.48 1 56.02 ? FE HEM 1500 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           43 
#