data_4JEB
#
_model_server_result.job_id            A5xr92gpU2ifuZDimUbmLQ 
_model_server_result.datetime_utc      '2024-11-26 18:04:47' 
_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          4jeb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":201}' 
#
_entry.id    4JEB 
#
_exptl.entry_id    4JEB 
_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    2 
_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         120 
_cell.entry_id            4JEB 
_cell.length_a            54.942 
_cell.length_b            54.942 
_cell.length_c            145.658 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4JEB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        151 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 1 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_554 -y,-x,-z-1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -48.552667 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 F 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 81 A CYS 81 1_555 B SG CYS 81 B CYS 81 4_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 A SG CYS 96 A CYS 96 1_555 A SG CYS 96 A CYS 96 4_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf3 B SG CYS 96 B CYS 96 1_555 B SG CYS 96 B CYS 96 4_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc1 A SD MET 7 A MET 7 1_555 C FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc2 A OD1 ASP 39 A ASP 39 1_555 E ZN ZN . A ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc3 A NE2 HIS 63 A HIS 63 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc4 A NE2 HIS 73 A HIS 73 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc5 A NE2 HIS 77 A HIS 77 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc6 A NE2 HIS 102 A HIS 102 1_555 C FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc7 D ZN ZN . A ZN 202 1_555 H O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc8 D ZN ZN . A ZN 202 1_555 B NE2 HIS 63 B HIS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc9 E ZN ZN . A ZN 203 1_555 H O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc10 B SD MET 7 B MET 7 1_555 F FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc11 B NE2 HIS 73 B HIS 73 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc12 B NE2 HIS 77 B HIS 77 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc13 B NE2 HIS 102 B HIS 102 1_555 F FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
metalc ? metalc14 G ZN ZN . B ZN 202 1_555 I O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
#
_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                     4JEB 
_atom_sites.fract_transf_matrix[1][1]    0.018201 
_atom_sites.fract_transf_matrix[1][2]    0.010508 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021017 
_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]    0.006865 
_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
C 2 HEM A 1 201 150 HEM HEM . 
D 3 ZN A 1 202 3 ZN ZN . 
E 3 ZN A 1 203 4 ZN ZN . 
F 2 HEM B 1 201 150 HEM HEM . 
G 3 ZN B 1 202 2 ZN ZN . 
H 4 HOH A 1 301 2 HOH HOH . 
H 4 HOH A 2 302 3 HOH HOH . 
H 4 HOH A 3 303 5 HOH HOH . 
H 4 HOH A 4 304 7 HOH HOH . 
H 4 HOH A 5 305 8 HOH HOH . 
H 4 HOH A 6 306 9 HOH HOH . 
H 4 HOH A 7 307 10 HOH HOH . 
H 4 HOH A 8 308 15 HOH HOH . 
H 4 HOH A 9 309 16 HOH HOH . 
H 4 HOH A 10 310 17 HOH HOH . 
H 4 HOH A 11 311 20 HOH HOH . 
H 4 HOH A 12 312 21 HOH HOH . 
H 4 HOH A 13 313 24 HOH HOH . 
H 4 HOH A 14 314 25 HOH HOH . 
H 4 HOH A 15 315 27 HOH HOH . 
H 4 HOH A 16 316 28 HOH HOH . 
H 4 HOH A 17 317 33 HOH HOH . 
H 4 HOH A 18 318 34 HOH HOH . 
H 4 HOH A 19 319 35 HOH HOH . 
I 4 HOH B 1 301 1 HOH HOH . 
I 4 HOH B 2 302 4 HOH HOH . 
I 4 HOH B 3 303 6 HOH HOH . 
I 4 HOH B 4 304 11 HOH HOH . 
I 4 HOH B 5 305 12 HOH HOH . 
I 4 HOH B 6 306 13 HOH HOH . 
I 4 HOH B 7 307 14 HOH HOH . 
I 4 HOH B 8 308 18 HOH HOH . 
I 4 HOH B 9 309 19 HOH HOH . 
I 4 HOH B 10 310 22 HOH HOH . 
I 4 HOH B 11 311 23 HOH HOH . 
I 4 HOH B 12 312 26 HOH HOH . 
I 4 HOH B 13 313 29 HOH HOH . 
I 4 HOH B 14 314 30 HOH HOH . 
I 4 HOH B 15 315 31 HOH HOH . 
I 4 HOH B 16 316 32 HOH HOH . 
I 4 HOH B 17 317 36 HOH HOH . 
I 4 HOH B 18 318 37 HOH HOH . 
I 4 HOH B 19 319 38 HOH HOH . 
I 4 HOH B 20 320 39 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 . . . F 2 -19.766 13.999 -7.846 1 50.05 ? CHA HEM 201 B 1 
HETATM 2 C CHB HEM . . . F 2 -17.197 16.305 -11.232 1 47.43 ? CHB HEM 201 B 1 
HETATM 3 C CHC HEM . . . F 2 -15.307 12.034 -12.711 1 41.73 ? CHC HEM 201 B 1 
HETATM 4 C CHD HEM . . . F 2 -18.004 9.709 -9.447 1 45.74 ? CHD HEM 201 B 1 
HETATM 5 C C1A HEM . . . F 2 -19.259 15.03 -8.619 1 48.71 ? C1A HEM 201 B 1 
HETATM 6 C C2A HEM . . . F 2 -19.518 16.476 -8.504 1 52.23 ? C2A HEM 201 B 1 
HETATM 7 C C3A HEM . . . F 2 -18.803 17.104 -9.45 1 49.98 ? C3A HEM 201 B 1 
HETATM 8 C C4A HEM . . . F 2 -18.074 16.084 -10.194 1 50.5 ? C4A HEM 201 B 1 
HETATM 9 C CMA HEM . . . F 2 -18.692 18.613 -9.741 1 49.7 ? CMA HEM 201 B 1 
HETATM 10 C CAA HEM . . . F 2 -20.447 17.142 -7.45 1 54.16 ? CAA HEM 201 B 1 
HETATM 11 C CBA HEM . . . F 2 -19.792 17.046 -6.058 1 59.09 ? CBA HEM 201 B 1 
HETATM 12 C CGA HEM . . . F 2 -20.445 17.965 -5.03 1 62.03 ? CGA HEM 201 B 1 
HETATM 13 O O1A HEM . . . F 2 -19.834 19.007 -4.629 1 62.47 ? O1A HEM 201 B 1 
HETATM 14 O O2A HEM . . . F 2 -21.58 17.633 -4.609 1 63.06 ? O2A HEM 201 B 1 
HETATM 15 C C1B HEM . . . F 2 -16.452 15.34 -11.876 1 46.56 ? C1B HEM 201 B 1 
HETATM 16 C C2B HEM . . . F 2 -15.496 15.579 -12.937 1 41.16 ? C2B HEM 201 B 1 
HETATM 17 C C3B HEM . . . F 2 -14.98 14.42 -13.321 1 42.31 ? C3B HEM 201 B 1 
HETATM 18 C C4B HEM . . . F 2 -15.599 13.385 -12.551 1 43.2 ? C4B HEM 201 B 1 
HETATM 19 C CMB HEM . . . F 2 -15.062 16.944 -13.53 1 45.49 ? CMB HEM 201 B 1 
HETATM 20 C CAB HEM . . . F 2 -13.888 14.159 -14.438 1 43.2 ? CAB HEM 201 B 1 
HETATM 21 C CBB HEM . . . F 2 -12.88 14.978 -14.833 1 37.85 ? CBB HEM 201 B 1 
HETATM 22 C C1C HEM . . . F 2 -15.896 11.013 -11.976 1 42.73 ? C1C HEM 201 B 1 
HETATM 23 C C2C HEM . . . F 2 -15.64 9.604 -12.117 1 43.12 ? C2C HEM 201 B 1 
HETATM 24 C C3C HEM . . . F 2 -16.36 8.954 -11.197 1 42.33 ? C3C HEM 201 B 1 
HETATM 25 C C4C HEM . . . F 2 -17.144 9.942 -10.485 1 46.02 ? C4C HEM 201 B 1 
HETATM 26 C CMC HEM . . . F 2 -14.658 9.008 -13.157 1 41.89 ? CMC HEM 201 B 1 
HETATM 27 C CAC HEM . . . F 2 -16.417 7.444 -10.906 1 45.09 ? CAC HEM 201 B 1 
HETATM 28 C CBC HEM . . . F 2 -15.469 6.566 -11.318 1 47.52 ? CBC HEM 201 B 1 
HETATM 29 C C1D HEM . . . F 2 -18.695 10.645 -8.724 1 48.15 ? C1D HEM 201 B 1 
HETATM 30 C C2D HEM . . . F 2 -19.606 10.308 -7.636 1 47.26 ? C2D HEM 201 B 1 
HETATM 31 C C3D HEM . . . F 2 -20.15 11.631 -7.139 1 50.43 ? C3D HEM 201 B 1 
HETATM 32 C C4D HEM . . . F 2 -19.513 12.636 -7.965 1 49.63 ? C4D HEM 201 B 1 
HETATM 33 C CMD HEM . . . F 2 -19.955 8.912 -7.081 1 47.26 ? CMD HEM 201 B 1 
HETATM 34 C CAD HEM . . . F 2 -21.142 11.781 -5.94 1 55.08 ? CAD HEM 201 B 1 
HETATM 35 C CBD HEM . . . F 2 -20.373 12.269 -4.706 1 57.66 ? CBD HEM 201 B 1 
HETATM 36 C CGD HEM . . . F 2 -21.236 12.599 -3.511 1 62.45 ? CGD HEM 201 B 1 
HETATM 37 O O1D HEM . . . F 2 -22.463 12.87 -3.705 1 63.6 ? O1D HEM 201 B 1 
HETATM 38 O O2D HEM . . . F 2 -20.675 12.582 -2.366 1 63.22 ? O2D HEM 201 B 1 
HETATM 39 N NA HEM . . . F 2 -18.38 14.853 -9.651 1 49.72 ? NA HEM 201 B 1 
HETATM 40 N NB HEM . . . F 2 -16.529 13.971 -11.672 1 44.26 ? NB HEM 201 B 1 
HETATM 41 N NC HEM . . . F 2 -16.84 11.171 -10.983 1 45.07 ? NC HEM 201 B 1 
HETATM 42 N ND HEM . . . F 2 -18.648 12.019 -8.902 1 46.42 ? ND HEM 201 B 1 
HETATM 43 FE FE HEM . . . F 2 -17.592 12.965 -10.306 1 49.6 ? FE HEM 201 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           231 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#