data_8YHQ
#
_model_server_result.job_id            Kdc1_WyxkdcEC3YK4RMQuA 
_model_server_result.datetime_utc      '2024-12-26 13:41:17' 
_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          8yhq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":404}' 
#
_entry.id    8YHQ 
#
_exptl.entry_id    8YHQ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          13 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    6 
_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            8YHQ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YHQ 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    eicosameric 
_pdbx_struct_assembly.oligomeric_count      20 
_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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA 
_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
? 13 W N N 
? 13 X N N 
? 13 CA N N 
? 13 GA N N 
? 13 IA N N 
? 13 KA 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 E SG CYS 129 E CYS 159 1_555 E SG CYS 134 E CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? 
disulf ? disulf2 E SG CYS 148 E CYS 178 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? 
disulf ? disulf3 F SG CYS 29 F CYS 101 1_555 F SG CYS 51 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? 
disulf ? disulf4 N SG CYS 134 N CYS 164 1_555 N SG CYS 150 N CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? 
disulf ? disulf5 P SG CYS 29 O CYS 101 1_555 P SG CYS 51 O CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? 
metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc6 G NE2 HIS 82 L HIS 82 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc7 G NE2 HIS 96 L HIS 96 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? 
metalc ? metalc8 G NE2 HIS 183 L HIS 183 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc9 G NE2 HIS 197 L HIS 197 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? 
metalc ? metalc10 M NE2 HIS 44 M HIS 105 1_555 KA FE HEM . M HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
#
_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 803 n n 
CHA C4D HEM doub 804 n n 
CHA HHA HEM sing 805 n n 
CHB C4A HEM sing 806 n n 
CHB C1B HEM doub 807 n n 
CHB HHB HEM sing 808 n n 
CHC C4B HEM sing 809 n n 
CHC C1C HEM doub 810 n n 
CHC HHC HEM sing 811 n n 
CHD C4C HEM doub 812 n n 
CHD C1D HEM sing 813 n n 
CHD HHD HEM sing 814 n n 
C1A C2A HEM doub 815 n y 
C1A NA HEM sing 816 n y 
C2A C3A HEM sing 817 n y 
C2A CAA HEM sing 818 n n 
C3A C4A HEM doub 819 n y 
C3A CMA HEM sing 820 n n 
C4A NA HEM sing 821 n y 
CMA HMA HEM sing 822 n n 
CMA HMAA HEM sing 823 n n 
CMA HMAB HEM sing 824 n n 
CAA CBA HEM sing 825 n n 
CAA HAA HEM sing 826 n n 
CAA HAAA HEM sing 827 n n 
CBA CGA HEM sing 828 n n 
CBA HBA HEM sing 829 n n 
CBA HBAA HEM sing 830 n n 
CGA O1A HEM doub 831 n n 
CGA O2A HEM sing 832 n n 
C1B C2B HEM sing 833 n n 
C1B NB HEM sing 834 n n 
C2B C3B HEM doub 835 n n 
C2B CMB HEM sing 836 n n 
C3B C4B HEM sing 837 n n 
C3B CAB HEM sing 838 n n 
C4B NB HEM doub 839 n n 
CMB HMB HEM sing 840 n n 
CMB HMBA HEM sing 841 n n 
CMB HMBB HEM sing 842 n n 
CAB CBB HEM doub 843 n n 
CAB HAB HEM sing 844 n n 
CBB HBB HEM sing 845 n n 
CBB HBBA HEM sing 846 n n 
C1C C2C HEM sing 847 n y 
C1C NC HEM sing 848 n y 
C2C C3C HEM doub 849 n y 
C2C CMC HEM sing 850 n n 
C3C C4C HEM sing 851 n y 
C3C CAC HEM sing 852 n n 
C4C NC HEM sing 853 n y 
CMC HMC HEM sing 854 n n 
CMC HMCA HEM sing 855 n n 
CMC HMCB HEM sing 856 n n 
CAC CBC HEM doub 857 n n 
CAC HAC HEM sing 858 n n 
CBC HBC HEM sing 859 n n 
CBC HBCA HEM sing 860 n n 
C1D C2D HEM sing 861 n n 
C1D ND HEM doub 862 n n 
C2D C3D HEM doub 863 n n 
C2D CMD HEM sing 864 n n 
C3D C4D HEM sing 865 n n 
C3D CAD HEM sing 866 n n 
C4D ND HEM sing 867 n n 
CMD HMD HEM sing 868 n n 
CMD HMDA HEM sing 869 n n 
CMD HMDB HEM sing 870 n n 
CAD CBD HEM sing 871 n n 
CAD HAD HEM sing 872 n n 
CAD HADA HEM sing 873 n n 
CBD CGD HEM sing 874 n n 
CBD HBD HEM sing 875 n n 
CBD HBDA HEM sing 876 n n 
CGD O1D HEM doub 877 n n 
CGD O2D HEM sing 878 n n 
O2A H2A HEM sing 879 n n 
O2D H2D HEM sing 880 n n 
FE NA HEM sing 881 n n 
FE NB HEM sing 882 n n 
FE NC HEM sing 883 n n 
FE ND HEM sing 884 n n 
#
_atom_sites.entry_id                     8YHQ 
_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
U 11 6PH C 1 401 402 6PH 6PH . 
V 12 9PE C 1 402 403 9PE 9PE . 
W 13 HEM C 1 403 404 HEM HEM . 
X 13 HEM C 1 404 405 HEM HEM . 
Y 14 8PE C 1 405 406 8PE 8PE . 
Z 15 CN5 C 1 406 407 CN5 CN5 . 
AA 16 UQ6 C 1 407 408 UQ6 UQ6 . 
BA 17 A1D6K C 1 408 401 A1D6K A1D . 
CA 13 HEM D 1 401 402 HEM HEM . 
DA 18 7PH D 1 402 401 7PH 7PH . 
EA 16 UQ6 L 1 401 402 UQ6 UQ6 . 
FA 12 9PE L 1 402 403 9PE 9PE . 
GA 13 HEM L 1 403 404 HEM HEM . 
HA 19 CN3 L 1 404 405 CN3 CN3 . 
IA 13 HEM L 1 405 406 HEM HEM . 
JA 17 A1D6K L 1 406 401 A1D6K A1D . 
KA 13 HEM M 1 401 401 HEM HEM . 
LA 11 6PH N 1 401 401 6PH 6PH . 
MA 18 7PH N 1 402 402 7PH 7PH . 
NA 14 8PE Q 1 101 101 8PE 8PE . 
#
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 . . . X 13 117.994 128.147 129.447 1 24.27 ? CHA HEM 404 C 1 
HETATM 2 C CHB HEM . . . X 13 121.077 127.641 125.754 1 24.27 ? CHB HEM 404 C 1 
HETATM 3 C CHC HEM . . . X 13 118.258 130.539 123.105 1 24.27 ? CHC HEM 404 C 1 
HETATM 4 C CHD HEM . . . X 13 115.744 131.686 127.063 1 24.27 ? CHD HEM 404 C 1 
HETATM 5 C C1A HEM . . . X 13 119.012 127.664 128.658 1 24.27 ? C1A HEM 404 C 1 
HETATM 6 C C2A HEM . . . X 13 119.902 126.561 128.966 1 24.27 ? C2A HEM 404 C 1 
HETATM 7 C C3A HEM . . . X 13 120.752 126.433 127.945 1 24.27 ? C3A HEM 404 C 1 
HETATM 8 C C4A HEM . . . X 13 120.44 127.438 126.957 1 24.27 ? C4A HEM 404 C 1 
HETATM 9 C CMA HEM . . . X 13 121.887 125.397 127.834 1 24.27 ? CMA HEM 404 C 1 
HETATM 10 C CAA HEM . . . X 13 119.911 125.666 130.232 1 24.27 ? CAA HEM 404 C 1 
HETATM 11 C CBA HEM . . . X 13 118.553 125.266 130.787 1 24.27 ? CBA HEM 404 C 1 
HETATM 12 C CGA HEM . . . X 13 117.627 124.744 129.728 1 24.27 ? CGA HEM 404 C 1 
HETATM 13 O O1A HEM . . . X 13 116.418 125.072 129.783 1 24.27 ? O1A HEM 404 C 1 
HETATM 14 O O2A HEM . . . X 13 118.098 124 128.84 1 24.27 ? O2A HEM 404 C 1 
HETATM 15 C C1B HEM . . . X 13 120.574 128.355 124.689 1 24.27 ? C1B HEM 404 C 1 
HETATM 16 C C2B HEM . . . X 13 121.125 128.414 123.355 1 24.27 ? C2B HEM 404 C 1 
HETATM 17 C C3B HEM . . . X 13 120.336 129.214 122.619 1 24.27 ? C3B HEM 404 C 1 
HETATM 18 C C4B HEM . . . X 13 119.275 129.689 123.474 1 24.27 ? C4B HEM 404 C 1 
HETATM 19 C CMB HEM . . . X 13 122.395 127.648 122.934 1 24.27 ? CMB HEM 404 C 1 
HETATM 20 C CAB HEM . . . X 13 120.442 129.641 121.135 1 24.27 ? CAB HEM 404 C 1 
HETATM 21 C CBB HEM . . . X 13 121.518 129.458 120.379 1 24.27 ? CBB HEM 404 C 1 
HETATM 22 C C1C HEM . . . X 13 117.303 131.071 123.934 1 24.27 ? C1C HEM 404 C 1 
HETATM 23 C C2C HEM . . . X 13 116.178 131.88 123.529 1 24.27 ? C2C HEM 404 C 1 
HETATM 24 C C3C HEM . . . X 13 115.471 132.189 124.624 1 24.27 ? C3C HEM 404 C 1 
HETATM 25 C C4C HEM . . . X 13 116.145 131.596 125.752 1 24.27 ? C4C HEM 404 C 1 
HETATM 26 C CMC HEM . . . X 13 115.897 132.253 122.062 1 24.27 ? CMC HEM 404 C 1 
HETATM 27 C CAC HEM . . . X 13 114.193 133.041 124.788 1 24.27 ? CAC HEM 404 C 1 
HETATM 28 C CBC HEM . . . X 13 113.769 133.93 123.901 1 24.27 ? CBC HEM 404 C 1 
HETATM 29 C C1D HEM . . . X 13 116.124 130.823 128.06 1 24.27 ? C1D HEM 404 C 1 
HETATM 30 C C2D HEM . . . X 13 115.584 130.777 129.396 1 24.27 ? C2D HEM 404 C 1 
HETATM 31 C C3D HEM . . . X 13 116.205 129.794 130.053 1 24.27 ? C3D HEM 404 C 1 
HETATM 32 C C4D HEM . . . X 13 117.156 129.19 129.149 1 24.27 ? C4D HEM 404 C 1 
HETATM 33 C CMD HEM . . . X 13 114.486 131.717 129.942 1 24.27 ? CMD HEM 404 C 1 
HETATM 34 C CAD HEM . . . X 13 115.977 129.361 131.521 1 24.27 ? CAD HEM 404 C 1 
HETATM 35 C CBD HEM . . . X 13 114.787 128.423 131.65 1 24.27 ? CBD HEM 404 C 1 
HETATM 36 C CGD HEM . . . X 13 114.601 127.925 133.054 1 24.27 ? CGD HEM 404 C 1 
HETATM 37 O O1D HEM . . . X 13 113.454 127.561 133.398 1 24.27 ? O1D HEM 404 C 1 
HETATM 38 O O2D HEM . . . X 13 115.584 127.888 133.828 1 24.27 ? O2D HEM 404 C 1 
HETATM 39 N NA HEM . . . X 13 119.374 128.168 127.426 1 24.27 ? NA HEM 404 C 1 
HETATM 40 N NB HEM . . . X 13 119.45 129.144 124.722 1 24.27 ? NB HEM 404 C 1 
HETATM 41 N NC HEM . . . X 13 117.252 130.915 125.296 1 24.27 ? NC HEM 404 C 1 
HETATM 42 N ND HEM . . . X 13 117.079 129.841 127.942 1 24.27 ? ND HEM 404 C 1 
HETATM 43 FE FE HEM . . . X 13 118.299 129.486 126.308 1 24.27 ? FE HEM 404 C 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    44 
_model_server_stats.query_time_ms           380 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           43 
#