data_8IB7
#
_model_server_result.job_id            -D9rxwCH0zBYRryN5cys8w 
_model_server_result.datetime_utc      '2024-10-19 20:18:58' 
_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          8ib7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":402}' 
#
_entry.id    8IB7 
#
_exptl.entry_id    8IB7 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    21-meric 
_pdbx_struct_assembly.oligomeric_count      21 
_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,OA,PA 
_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
? 11 V N N 
? 11 W N N 
? 11 GA N N 
? 11 HA 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 A SG CYS 338 AA CYS 338 1_555 A SG CYS 360 AA CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
disulf ? disulf2 E SG CYS 222 AE CYS 222 1_555 E SG CYS 238 AE CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf3 H SG CYS 51 AH CYS 51 1_555 H SG CYS 65 AH CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 L SG CYS 338 Aa CYS 338 1_555 L SG CYS 360 Aa CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 P SG CYS 222 Ae CYS 222 1_555 P SG CYS 238 Ae CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf6 S SG CYS 35 Ah CYS 35 1_555 S SG CYS 79 Ah CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf7 S SG CYS 51 Ah CYS 51 1_555 S SG CYS 65 Ah CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 C NE2 HIS 83 AC HIS 83 1_555 V FE HEM . AC HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? 
metalc ? metalc2 C NE2 HIS 97 AC HIS 97 1_555 W FE HEM . AC HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc3 C NE2 HIS 182 AC HIS 182 1_555 V FE HEM . AC HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc4 C NE2 HIS 196 AC HIS 196 1_555 W FE HEM . AC HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc5 D NE2 HIS 125 AD HIS 125 1_555 BA FE HEC . AD HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc6 D SD MET 244 AD MET 244 1_555 BA FE HEC . AD HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc7 N NE2 HIS 83 Ac HIS 83 1_555 GA FE HEM . Ac HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc8 N NE2 HIS 97 Ac HIS 97 1_555 HA FE HEM . Ac HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.775 ? 
metalc ? metalc9 N NE2 HIS 182 Ac HIS 182 1_555 GA FE HEM . Ac HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc10 N NE2 HIS 196 Ac HIS 196 1_555 HA FE HEM . Ac HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? 
metalc ? metalc11 O NE2 HIS 125 Ad HIS 125 1_555 MA FE HEC . Ad HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc12 O SD MET 244 Ad MET 244 1_555 MA FE HEC . Ad HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
#
_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 724 n n 
CHA C4D HEM doub 725 n n 
CHA HHA HEM sing 726 n n 
CHB C4A HEM sing 727 n n 
CHB C1B HEM doub 728 n n 
CHB HHB HEM sing 729 n n 
CHC C4B HEM sing 730 n n 
CHC C1C HEM doub 731 n n 
CHC HHC HEM sing 732 n n 
CHD C4C HEM doub 733 n n 
CHD C1D HEM sing 734 n n 
CHD HHD HEM sing 735 n n 
C1A C2A HEM doub 736 n y 
C1A NA HEM sing 737 n y 
C2A C3A HEM sing 738 n y 
C2A CAA HEM sing 739 n n 
C3A C4A HEM doub 740 n y 
C3A CMA HEM sing 741 n n 
C4A NA HEM sing 742 n y 
CMA HMA HEM sing 743 n n 
CMA HMAA HEM sing 744 n n 
CMA HMAB HEM sing 745 n n 
CAA CBA HEM sing 746 n n 
CAA HAA HEM sing 747 n n 
CAA HAAA HEM sing 748 n n 
CBA CGA HEM sing 749 n n 
CBA HBA HEM sing 750 n n 
CBA HBAA HEM sing 751 n n 
CGA O1A HEM doub 752 n n 
CGA O2A HEM sing 753 n n 
C1B C2B HEM sing 754 n n 
C1B NB HEM sing 755 n n 
C2B C3B HEM doub 756 n n 
C2B CMB HEM sing 757 n n 
C3B C4B HEM sing 758 n n 
C3B CAB HEM sing 759 n n 
C4B NB HEM doub 760 n n 
CMB HMB HEM sing 761 n n 
CMB HMBA HEM sing 762 n n 
CMB HMBB HEM sing 763 n n 
CAB CBB HEM doub 764 n n 
CAB HAB HEM sing 765 n n 
CBB HBB HEM sing 766 n n 
CBB HBBA HEM sing 767 n n 
C1C C2C HEM sing 768 n y 
C1C NC HEM sing 769 n y 
C2C C3C HEM doub 770 n y 
C2C CMC HEM sing 771 n n 
C3C C4C HEM sing 772 n y 
C3C CAC HEM sing 773 n n 
C4C NC HEM sing 774 n y 
CMC HMC HEM sing 775 n n 
CMC HMCA HEM sing 776 n n 
CMC HMCB HEM sing 777 n n 
CAC CBC HEM doub 778 n n 
CAC HAC HEM sing 779 n n 
CBC HBC HEM sing 780 n n 
CBC HBCA HEM sing 781 n n 
C1D C2D HEM sing 782 n n 
C1D ND HEM doub 783 n n 
C2D C3D HEM doub 784 n n 
C2D CMD HEM sing 785 n n 
C3D C4D HEM sing 786 n n 
C3D CAD HEM sing 787 n n 
C4D ND HEM sing 788 n n 
CMD HMD HEM sing 789 n n 
CMD HMDA HEM sing 790 n n 
CMD HMDB HEM sing 791 n n 
CAD CBD HEM sing 792 n n 
CAD HAD HEM sing 793 n n 
CAD HADA HEM sing 794 n n 
CBD CGD HEM sing 795 n n 
CBD HBD HEM sing 796 n n 
CBD HBDA HEM sing 797 n n 
CGD O1D HEM doub 798 n n 
CGD O2D HEM sing 799 n n 
O2A H2A HEM sing 800 n n 
O2D H2D HEM sing 801 n n 
FE NA HEM sing 802 n n 
FE NB HEM sing 803 n n 
FE NC HEM sing 804 n n 
FE ND HEM sing 805 n n 
#
_atom_sites.entry_id                     8IB7 
_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
V 11 HEM AC 1 401 401 HEM HEM . 
W 11 HEM AC 1 402 402 HEM HEM . 
X 12 3PE AC 1 403 403 3PE 3PE . 
Y 13 U10 AC 1 404 505 U10 U10 . 
Z 14 UQ6 AC 1 405 506 UQ6 UQ6 . 
AA 15 CDL AC 1 406 103 CDL CDL . 
BA 16 HEC AD 1 401 395 HEC HEC . 
CA 17 3PH AD 1 402 400 3PH 3PH . 
DA 12 3PE AF 1 201 104 3PE 3PE . 
EA 15 CDL Aa 1 501 536 CDL CDL . 
FA 12 3PE Ac 1 401 535 3PE 3PE . 
GA 11 HEM Ac 1 402 401 HEM HEM . 
HA 11 HEM Ac 1 403 402 HEM HEM . 
IA 12 3PE Ac 1 404 403 3PE 3PE . 
JA 13 U10 Ac 1 405 505 U10 U10 . 
KA 14 UQ6 Ac 1 406 506 UQ6 UQ6 . 
LA 15 CDL Ac 1 407 102 CDL CDL . 
MA 16 HEC Ad 1 401 395 HEC HEC . 
NA 17 3PH Ad 1 402 400 3PH 3PH . 
OA 15 CDL Ag 1 101 103 CDL CDL . 
PA 12 3PE Ag 1 102 104 3PE 3PE . 
#
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 . . . W 11 137.333 158.194 219.201 1 33.01 0 CHA HEM 402 AC 1 
HETATM 2 C CHB HEM . . . W 11 137.519 158.29 214.366 1 28.21 0 CHB HEM 402 AC 1 
HETATM 3 C CHC HEM . . . W 11 133.012 159.992 214.236 1 39.81 0 CHC HEM 402 AC 1 
HETATM 4 C CHD HEM . . . W 11 132.887 160.132 219.061 1 32.42 0 CHD HEM 402 AC 1 
HETATM 5 C C1A HEM . . . W 11 137.742 158.054 217.898 1 30.08 0 C1A HEM 402 AC 1 
HETATM 6 C C2A HEM . . . W 11 138.991 157.544 217.487 1 25.66 0 C2A HEM 402 AC 1 
HETATM 7 C C3A HEM . . . W 11 139.016 157.587 216.133 1 32.26 0 C3A HEM 402 AC 1 
HETATM 8 C C4A HEM . . . W 11 137.813 158.115 215.693 1 36.89 0 C4A HEM 402 AC 1 
HETATM 9 C CMA HEM . . . W 11 140.101 157.166 215.197 1 24.4 0 CMA HEM 402 AC 1 
HETATM 10 C CAA HEM . . . W 11 140.096 157.03 218.366 1 44.25 0 CAA HEM 402 AC 1 
HETATM 11 C CBA HEM . . . W 11 140.058 155.502 218.339 1 51.11 0 CBA HEM 402 AC 1 
HETATM 12 C CGA HEM . . . W 11 138.862 155.025 219.113 1 55.87 0 CGA HEM 402 AC 1 
HETATM 13 O O1A HEM . . . W 11 138.448 155.683 220.088 1 55.5 0 O1A HEM 402 AC 1 
HETATM 14 O O2A HEM . . . W 11 138.292 153.961 218.793 1 53.16 0 O2A HEM 402 AC 1 
HETATM 15 C C1B HEM . . . W 11 136.305 158.761 214.006 1 42.51 0 C1B HEM 402 AC 1 
HETATM 16 C C2B HEM . . . W 11 136.063 158.878 212.648 1 34.86 0 C2B HEM 402 AC 1 
HETATM 17 C C3B HEM . . . W 11 134.819 159.334 212.605 1 38.4 0 C3B HEM 402 AC 1 
HETATM 18 C C4B HEM . . . W 11 134.291 159.516 213.958 1 47.38 0 C4B HEM 402 AC 1 
HETATM 19 C CMB HEM . . . W 11 136.988 158.554 211.507 1 26.8 0 CMB HEM 402 AC 1 
HETATM 20 C CAB HEM . . . W 11 134.084 159.646 211.374 1 50.73 0 CAB HEM 402 AC 1 
HETATM 21 C CBB HEM . . . W 11 134.419 160.724 210.677 1 43.03 0 CBB HEM 402 AC 1 
HETATM 22 C C1C HEM . . . W 11 132.566 160.152 215.536 1 38.55 0 C1C HEM 402 AC 1 
HETATM 23 C C2C HEM . . . W 11 131.279 160.549 215.911 1 33.22 0 C2C HEM 402 AC 1 
HETATM 24 C C3C HEM . . . W 11 131.247 160.585 217.291 1 35.48 0 C3C HEM 402 AC 1 
HETATM 25 C C4C HEM . . . W 11 132.533 160.212 217.748 1 39.8 0 C4C HEM 402 AC 1 
HETATM 26 C CMC HEM . . . W 11 130.146 160.866 214.974 1 39.15 0 CMC HEM 402 AC 1 
HETATM 27 C CAC HEM . . . W 11 130.11 160.95 218.148 1 36.7 0 CAC HEM 402 AC 1 
HETATM 28 C CBC HEM . . . W 11 128.988 160.245 218.121 1 38.02 0 CBC HEM 402 AC 1 
HETATM 29 C C1D HEM . . . W 11 134.111 159.603 219.449 1 37.47 0 C1D HEM 402 AC 1 
HETATM 30 C C2D HEM . . . W 11 134.442 159.451 220.86 1 25.66 0 C2D HEM 402 AC 1 
HETATM 31 C C3D HEM . . . W 11 135.671 158.923 220.901 1 32.93 0 C3D HEM 402 AC 1 
HETATM 32 C C4D HEM . . . W 11 136.092 158.73 219.516 1 41.1 0 C4D HEM 402 AC 1 
HETATM 33 C CMD HEM . . . W 11 133.576 159.829 222.031 1 13.14 0 CMD HEM 402 AC 1 
HETATM 34 C CAD HEM . . . W 11 136.442 158.565 222.134 1 31.89 0 CAD HEM 402 AC 1 
HETATM 35 C CBD HEM . . . W 11 136.013 157.139 222.473 1 42.1 0 CBD HEM 402 AC 1 
HETATM 36 C CGD HEM . . . W 11 136.552 156.734 223.814 1 48.93 0 CGD HEM 402 AC 1 
HETATM 37 O O1D HEM . . . W 11 135.764 156.501 224.752 1 49.53 0 O1D HEM 402 AC 1 
HETATM 38 O O2D HEM . . . W 11 137.785 156.633 223.987 1 43.36 0 O2D HEM 402 AC 1 
HETATM 39 N NA HEM . . . W 11 137.062 158.454 216.778 1 56.62 0 NA HEM 402 AC 1 
HETATM 40 N NB HEM . . . W 11 135.27 159.129 214.758 1 54.09 0 NB HEM 402 AC 1 
HETATM 41 N NC HEM . . . W 11 133.317 159.968 216.659 1 52.41 0 NC HEM 402 AC 1 
HETATM 42 N ND HEM . . . W 11 135.124 159.159 218.699 1 50.22 0 ND HEM 402 AC 1 
HETATM 43 FE FE HEM . . . W 11 135.205 159.116 216.843 1 144.38 0 FE HEM 402 AC 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#