data_6Y9B
#
_model_server_result.job_id            4tL9izjL4HcUbsWvU5cQyw 
_model_server_result.datetime_utc      '2024-11-05 05:30:49' 
_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          6y9b 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":401}' 
#
_entry.id    6Y9B 
#
_exptl.entry_id    6Y9B 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    3 
_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            6Y9B 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6Y9B 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    nonameric 
_pdbx_struct_assembly.oligomeric_count      9 
_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,G,H,I,J,K,L,M,N,O 
_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    ? 
_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
? 4 J N N 
? 4 L N N 
? 4 N 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 B SG CYS 23 L CYS 23 1_555 B SG CYS 94 L CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf2 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 D SG CYS 22 I CYS 22 1_555 D SG CYS 96 I CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 E SG CYS 22 J CYS 22 1_555 E SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf5 F SG CYS 23 M CYS 23 1_555 F SG CYS 94 M CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf6 G SG CYS 23 N CYS 23 1_555 G SG CYS 94 N CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc1 A NE2 HIS 177 C HIS 175 1_555 J FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc2 A NE2 HIS 270 C HIS 268 1_555 J FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc3 H NE2 HIS 177 A HIS 175 1_555 L FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? 
metalc ? metalc4 H NE2 HIS 270 A HIS 268 1_555 L FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
metalc ? metalc5 I NE2 HIS 177 B HIS 175 1_555 N FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc6 I NE2 HIS 270 B HIS 268 1_555 N FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
#
_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 129 n n 
CHA C4D HEM doub 130 n n 
CHA HHA HEM sing 131 n n 
CHB C4A HEM sing 132 n n 
CHB C1B HEM doub 133 n n 
CHB HHB HEM sing 134 n n 
CHC C4B HEM sing 135 n n 
CHC C1C HEM doub 136 n n 
CHC HHC HEM sing 137 n n 
CHD C4C HEM doub 138 n n 
CHD C1D HEM sing 139 n n 
CHD HHD HEM sing 140 n n 
C1A C2A HEM doub 141 n y 
C1A NA HEM sing 142 n y 
C2A C3A HEM sing 143 n y 
C2A CAA HEM sing 144 n n 
C3A C4A HEM doub 145 n y 
C3A CMA HEM sing 146 n n 
C4A NA HEM sing 147 n y 
CMA HMA HEM sing 148 n n 
CMA HMAA HEM sing 149 n n 
CMA HMAB HEM sing 150 n n 
CAA CBA HEM sing 151 n n 
CAA HAA HEM sing 152 n n 
CAA HAAA HEM sing 153 n n 
CBA CGA HEM sing 154 n n 
CBA HBA HEM sing 155 n n 
CBA HBAA HEM sing 156 n n 
CGA O1A HEM doub 157 n n 
CGA O2A HEM sing 158 n n 
C1B C2B HEM sing 159 n n 
C1B NB HEM sing 160 n n 
C2B C3B HEM doub 161 n n 
C2B CMB HEM sing 162 n n 
C3B C4B HEM sing 163 n n 
C3B CAB HEM sing 164 n n 
C4B NB HEM doub 165 n n 
CMB HMB HEM sing 166 n n 
CMB HMBA HEM sing 167 n n 
CMB HMBB HEM sing 168 n n 
CAB CBB HEM doub 169 n n 
CAB HAB HEM sing 170 n n 
CBB HBB HEM sing 171 n n 
CBB HBBA HEM sing 172 n n 
C1C C2C HEM sing 173 n y 
C1C NC HEM sing 174 n y 
C2C C3C HEM doub 175 n y 
C2C CMC HEM sing 176 n n 
C3C C4C HEM sing 177 n y 
C3C CAC HEM sing 178 n n 
C4C NC HEM sing 179 n y 
CMC HMC HEM sing 180 n n 
CMC HMCA HEM sing 181 n n 
CMC HMCB HEM sing 182 n n 
CAC CBC HEM doub 183 n n 
CAC HAC HEM sing 184 n n 
CBC HBC HEM sing 185 n n 
CBC HBCA HEM sing 186 n n 
C1D C2D HEM sing 187 n n 
C1D ND HEM doub 188 n n 
C2D C3D HEM doub 189 n n 
C2D CMD HEM sing 190 n n 
C3D C4D HEM sing 191 n n 
C3D CAD HEM sing 192 n n 
C4D ND HEM sing 193 n n 
CMD HMD HEM sing 194 n n 
CMD HMDA HEM sing 195 n n 
CMD HMDB HEM sing 196 n n 
CAD CBD HEM sing 197 n n 
CAD HAD HEM sing 198 n n 
CAD HADA HEM sing 199 n n 
CBD CGD HEM sing 200 n n 
CBD HBD HEM sing 201 n n 
CBD HBDA HEM sing 202 n n 
CGD O1D HEM doub 203 n n 
CGD O2D HEM sing 204 n n 
O2A H2A HEM sing 205 n n 
O2D H2D HEM sing 206 n n 
FE NA HEM sing 207 n n 
FE NB HEM sing 208 n n 
FE NC HEM sing 209 n n 
FE ND HEM sing 210 n n 
#
_atom_sites.entry_id                     6Y9B 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
J 4 HEM C 1 401 1073 HEM HEM . 
K 5 XP4 C 1 402 1101 XP4 UI9 . 
L 4 HEM A 1 401 1073 HEM HEM . 
M 5 XP4 A 1 402 1101 XP4 UI9 . 
N 4 HEM B 1 401 1073 HEM HEM . 
O 5 XP4 B 1 402 1101 XP4 UI9 . 
#
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 4 168.352 148.821 146.424 1 80.07 ? CHA HEM 401 B 1 
HETATM 2 C CHB HEM . . . N 4 164.581 151.821 146.1 1 80.07 ? CHB HEM 401 B 1 
HETATM 3 C CHC HEM . . . N 4 165.672 152.66 141.431 1 80.07 ? CHC HEM 401 B 1 
HETATM 4 C CHD HEM . . . N 4 169.267 149.442 141.708 1 80.07 ? CHD HEM 401 B 1 
HETATM 5 C C1A HEM . . . N 4 167.259 149.594 146.707 1 80.07 ? C1A HEM 401 B 1 
HETATM 6 C C2A HEM . . . N 4 166.678 149.686 147.981 1 80.07 ? C2A HEM 401 B 1 
HETATM 7 C C3A HEM . . . N 4 165.62 150.519 147.897 1 80.07 ? C3A HEM 401 B 1 
HETATM 8 C C4A HEM . . . N 4 165.537 150.957 146.57 1 80.07 ? C4A HEM 401 B 1 
HETATM 9 C CMA HEM . . . N 4 164.706 150.916 149.023 1 80.07 ? CMA HEM 401 B 1 
HETATM 10 C CAA HEM . . . N 4 167.138 148.974 149.217 1 80.07 ? CAA HEM 401 B 1 
HETATM 11 C CBA HEM . . . N 4 166.439 147.615 149.216 1 80.07 ? CBA HEM 401 B 1 
HETATM 12 C CGA HEM . . . N 4 166.515 146.983 150.577 1 80.07 ? CGA HEM 401 B 1 
HETATM 13 O O1A HEM . . . N 4 167.024 145.849 150.709 1 80.07 ? O1A HEM 401 B 1 
HETATM 14 O O2A HEM . . . N 4 166.064 147.589 151.573 1 80.07 ? O2A HEM 401 B 1 
HETATM 15 C C1B HEM . . . N 4 164.604 152.291 144.79 1 80.07 ? C1B HEM 401 B 1 
HETATM 16 C C2B HEM . . . N 4 163.659 153.241 144.346 1 80.07 ? C2B HEM 401 B 1 
HETATM 17 C C3B HEM . . . N 4 163.938 153.497 143.042 1 80.07 ? C3B HEM 401 B 1 
HETATM 18 C C4B HEM . . . N 4 165.103 152.658 142.701 1 80.07 ? C4B HEM 401 B 1 
HETATM 19 C CMB HEM . . . N 4 162.561 153.84 145.18 1 80.07 ? CMB HEM 401 B 1 
HETATM 20 C CAB HEM . . . N 4 163.241 154.423 142.137 1 80.07 ? CAB HEM 401 B 1 
HETATM 21 C CBB HEM . . . N 4 161.948 154.289 141.877 1 80.07 ? CBB HEM 401 B 1 
HETATM 22 C C1C HEM . . . N 4 166.764 151.877 141.105 1 80.07 ? C1C HEM 401 B 1 
HETATM 23 C C2C HEM . . . N 4 167.431 151.89 139.876 1 80.07 ? C2C HEM 401 B 1 
HETATM 24 C C3C HEM . . . N 4 168.455 150.97 139.959 1 80.07 ? C3C HEM 401 B 1 
HETATM 25 C C4C HEM . . . N 4 168.403 150.396 141.251 1 80.07 ? C4C HEM 401 B 1 
HETATM 26 C CMC HEM . . . N 4 167.096 152.751 138.688 1 80.07 ? CMC HEM 401 B 1 
HETATM 27 C CAC HEM . . . N 4 169.427 150.646 138.907 1 80.07 ? CAC HEM 401 B 1 
HETATM 28 C CBC HEM . . . N 4 169.04 149.96 137.839 1 80.07 ? CBC HEM 401 B 1 
HETATM 29 C C1D HEM . . . N 4 169.279 149.049 143.042 1 80.07 ? C1D HEM 401 B 1 
HETATM 30 C C2D HEM . . . N 4 170.281 148.106 143.534 1 80.07 ? C2D HEM 401 B 1 
HETATM 31 C C3D HEM . . . N 4 170.027 147.936 144.836 1 80.07 ? C3D HEM 401 B 1 
HETATM 32 C C4D HEM . . . N 4 168.875 148.776 145.145 1 80.07 ? C4D HEM 401 B 1 
HETATM 33 C CMD HEM . . . N 4 171.375 147.457 142.734 1 80.07 ? CMD HEM 401 B 1 
HETATM 34 C CAD HEM . . . N 4 170.773 147.062 145.801 1 80.07 ? CAD HEM 401 B 1 
HETATM 35 C CBD HEM . . . N 4 170.17 145.662 145.776 1 80.07 ? CBD HEM 401 B 1 
HETATM 36 C CGD HEM . . . N 4 170.689 144.887 146.954 1 80.07 ? CGD HEM 401 B 1 
HETATM 37 O O1D HEM . . . N 4 171.496 143.951 146.778 1 80.07 ? O1D HEM 401 B 1 
HETATM 38 O O2D HEM . . . N 4 170.316 145.183 148.109 1 80.07 ? O2D HEM 401 B 1 
HETATM 39 N NA HEM . . . N 4 166.527 150.359 145.841 1 80.07 ? NA HEM 401 B 1 
HETATM 40 N NB HEM . . . N 4 165.445 151.971 143.801 1 80.07 ? NB HEM 401 B 1 
HETATM 41 N NC HEM . . . N 4 167.356 150.96 141.922 1 80.07 ? NC HEM 401 B 1 
HETATM 42 N ND HEM . . . N 4 168.469 149.419 144.044 1 80.07 ? ND HEM 401 B 1 
HETATM 43 FE FE HEM . . . N 4 167.032 150.602 143.945 1 80.07 ? FE HEM 401 B 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#