data_3G93
#
_model_server_result.job_id            P11uAA2Ye5xmMdkJ-lQW_A 
_model_server_result.datetime_utc      '2024-10-18 05:24:35' 
_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          3g93 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":500}' 
#
_entry.id    3G93 
#
_exptl.entry_id    3G93 
_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    4 
_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            3G93 
_cell.length_a            86.91 
_cell.length_b            151.815 
_cell.length_c            181.583 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3G93 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 software_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
C,I,J,O 1 1 
D,K,L,P 1 2 
A,B,E,F,G,H,M,N 1 3 
A,E,F,G,M 2 3 
B,H,N 3 3 
C,I,J,O 4 3 
D,K,L,P 5 3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'crystal symmetry operation' 2_655 -x+3/2,-y,z+1/2 -1 0 0 0 -1 0 0 0 1 130.365 0 90.7915 
2 'crystal symmetry operation' 3_645 -x+1,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 86.91 -75.9075 90.7915 
3 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 H N N 
? 2 I N N 
? 2 K 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 SG CYS 417 A CYS 436 1_555 E FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc2 G NAD PB2 . A PB2 496 1_555 H FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc3 E FE HEM . A HEM 500 1_555 F NAD PB2 . A PB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc4 B SG CYS 417 B CYS 436 1_555 H FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc5 C SG CYS 417 C CYS 436 1_555 I FE HEM . C HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc6 I FE HEM . C HEM 500 1_555 J NAD PB2 . C PB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? 
metalc ? metalc7 D SG CYS 417 D CYS 436 1_555 K FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc8 K FE HEM . D HEM 500 1_555 L NAD PB2 . D PB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
#
_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                     3G93 
_atom_sites.fract_transf_matrix[1][1]    0.011506 
_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]    0.006587 
_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]    0.005507 
_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
E 2 HEM A 1 500 500 HEM HEM . 
F 3 PB2 A 1 501 501 PB2 PB2 . 
G 3 PB2 A 1 496 496 PB2 PB2 . 
H 2 HEM B 1 500 500 HEM HEM . 
I 2 HEM C 1 500 500 HEM HEM . 
J 3 PB2 C 1 501 501 PB2 PB2 . 
K 2 HEM D 1 500 500 HEM HEM . 
L 3 PB2 D 1 501 501 PB2 PB2 . 
M 4 HOH A 1 3 3 HOH HOH . 
M 4 HOH A 2 8 8 HOH HOH . 
M 4 HOH A 3 9 9 HOH HOH . 
M 4 HOH A 4 10 10 HOH HOH . 
M 4 HOH A 5 14 14 HOH HOH . 
M 4 HOH A 6 17 17 HOH HOH . 
M 4 HOH A 7 497 497 HOH HOH . 
M 4 HOH A 8 498 498 HOH HOH . 
M 4 HOH A 9 499 499 HOH HOH . 
N 4 HOH B 1 2 2 HOH HOH . 
N 4 HOH B 2 5 5 HOH HOH . 
N 4 HOH B 3 6 6 HOH HOH . 
N 4 HOH B 4 7 7 HOH HOH . 
N 4 HOH B 5 18 18 HOH HOH . 
N 4 HOH B 6 496 496 HOH HOH . 
N 4 HOH B 7 497 497 HOH HOH . 
N 4 HOH B 8 498 498 HOH HOH . 
N 4 HOH B 9 499 499 HOH HOH . 
O 4 HOH C 1 12 12 HOH HOH . 
O 4 HOH C 2 13 13 HOH HOH . 
O 4 HOH C 3 15 15 HOH HOH . 
O 4 HOH C 4 16 16 HOH HOH . 
O 4 HOH C 5 496 496 HOH HOH . 
O 4 HOH C 6 497 497 HOH HOH . 
O 4 HOH C 7 498 498 HOH HOH . 
O 4 HOH C 8 499 499 HOH HOH . 
O 4 HOH C 9 502 502 HOH HOH . 
O 4 HOH C 10 503 503 HOH HOH . 
O 4 HOH C 11 504 504 HOH HOH . 
O 4 HOH C 12 505 505 HOH HOH . 
O 4 HOH C 13 506 506 HOH HOH . 
P 4 HOH D 1 1 1 HOH HOH . 
P 4 HOH D 2 4 4 HOH HOH . 
P 4 HOH D 3 11 11 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 . . . I 2 83.056 -12.923 4.723 1 40.78 ? CHA HEM 500 C 1 
HETATM 2 C CHB HEM . . . I 2 80.538 -10.872 8.024 1 31.18 ? CHB HEM 500 C 1 
HETATM 3 C CHC HEM . . . I 2 83.66 -11.952 11.314 1 34.61 ? CHC HEM 500 C 1 
HETATM 4 C CHD HEM . . . I 2 86.287 -14.129 7.969 1 31.17 ? CHD HEM 500 C 1 
HETATM 5 C C1A HEM . . . I 2 82.171 -12.25 5.431 1 31.56 ? C1A HEM 500 C 1 
HETATM 6 C C2A HEM . . . I 2 81.122 -11.555 4.787 1 32.62 ? C2A HEM 500 C 1 
HETATM 7 C C3A HEM . . . I 2 80.454 -11.002 5.705 1 37.8 ? C3A HEM 500 C 1 
HETATM 8 C C4A HEM . . . I 2 81.067 -11.342 6.922 1 30.78 ? C4A HEM 500 C 1 
HETATM 9 C CMA HEM . . . I 2 79.206 -10.146 5.498 1 39.83 ? CMA HEM 500 C 1 
HETATM 10 C CAA HEM . . . I 2 80.793 -11.427 3.303 1 39.45 ? CAA HEM 500 C 1 
HETATM 11 C CBA HEM . . . I 2 80.636 -12.742 2.582 1 48.81 ? CBA HEM 500 C 1 
HETATM 12 C CGA HEM . . . I 2 80.532 -12.388 1.155 1 38.59 ? CGA HEM 500 C 1 
HETATM 13 O O1A HEM . . . I 2 81.475 -11.796 0.638 1 26.24 ? O1A HEM 500 C 1 
HETATM 14 O O2A HEM . . . I 2 79.501 -12.687 0.562 1 38.15 ? O2A HEM 500 C 1 
HETATM 15 C C1B HEM . . . I 2 81.142 -11.087 9.159 1 29.91 ? C1B HEM 500 C 1 
HETATM 16 C C2B HEM . . . I 2 80.465 -10.869 10.362 1 32.56 ? C2B HEM 500 C 1 
HETATM 17 C C3B HEM . . . I 2 81.271 -11.164 11.315 1 45.41 ? C3B HEM 500 C 1 
HETATM 18 C C4B HEM . . . I 2 82.52 -11.566 10.704 1 43.89 ? C4B HEM 500 C 1 
HETATM 19 C CMB HEM . . . I 2 79.025 -10.409 10.509 1 23.62 ? CMB HEM 500 C 1 
HETATM 20 C CAB HEM . . . I 2 80.816 -11.033 12.77 1 32.07 ? CAB HEM 500 C 1 
HETATM 21 C CBB HEM . . . I 2 81.508 -11.594 13.741 1 38.24 ? CBB HEM 500 C 1 
HETATM 22 C C1C HEM . . . I 2 84.583 -12.679 10.629 1 41.59 ? C1C HEM 500 C 1 
HETATM 23 C C2C HEM . . . I 2 85.613 -13.416 11.275 1 33.73 ? C2C HEM 500 C 1 
HETATM 24 C C3C HEM . . . I 2 86.325 -14.029 10.387 1 32.29 ? C3C HEM 500 C 1 
HETATM 25 C C4C HEM . . . I 2 85.775 -13.692 9.121 1 39.1 ? C4C HEM 500 C 1 
HETATM 26 C CMC HEM . . . I 2 85.811 -13.497 12.775 1 56.52 ? CMC HEM 500 C 1 
HETATM 27 C CAC HEM . . . I 2 87.518 -14.918 10.696 1 26.49 ? CAC HEM 500 C 1 
HETATM 28 C CBC HEM . . . I 2 87.953 -15.768 9.785 1 26.56 ? CBC HEM 500 C 1 
HETATM 29 C C1D HEM . . . I 2 85.65 -13.887 6.804 1 47.89 ? C1D HEM 500 C 1 
HETATM 30 C C2D HEM . . . I 2 86.286 -14.113 5.52 1 44.39 ? C2D HEM 500 C 1 
HETATM 31 C C3D HEM . . . I 2 85.244 -13.744 4.516 1 28.44 ? C3D HEM 500 C 1 
HETATM 32 C C4D HEM . . . I 2 84.155 -13.336 5.321 1 43.73 ? C4D HEM 500 C 1 
HETATM 33 C CMD HEM . . . I 2 87.698 -14.632 5.232 1 30.07 ? CMD HEM 500 C 1 
HETATM 34 C CAD HEM . . . I 2 85.379 -13.766 3 1 40.06 ? CAD HEM 500 C 1 
HETATM 35 C CBD HEM . . . I 2 84.188 -14.219 2.194 1 53.58 ? CBD HEM 500 C 1 
HETATM 36 C CGD HEM . . . I 2 84.683 -15.028 1.031 1 50.74 ? CGD HEM 500 C 1 
HETATM 37 O O1D HEM . . . I 2 84.964 -16.217 1.179 1 42.84 ? O1D HEM 500 C 1 
HETATM 38 O O2D HEM . . . I 2 84.772 -14.517 -0.081 1 31.98 ? O2D HEM 500 C 1 
HETATM 39 N NA HEM . . . I 2 82.17 -12.128 6.787 1 24.02 ? NA HEM 500 C 1 
HETATM 40 N NB HEM . . . I 2 82.418 -11.534 9.327 1 43.7 ? NB HEM 500 C 1 
HETATM 41 N NC HEM . . . I 2 84.686 -12.863 9.254 1 53.06 ? NC HEM 500 C 1 
HETATM 42 N ND HEM . . . I 2 84.357 -13.418 6.69 1 42.31 ? ND HEM 500 C 1 
HETATM 43 FE FE HEM . . . I 2 83.509 -12.653 7.897 1 30.32 ? FE HEM 500 C 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#