data_4WD4
#
_model_server_result.job_id            IizcqdRcDn1fuxdAj9In4Q 
_model_server_result.datetime_utc      '2024-12-26 23:01:08' 
_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          4wd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":301}' 
#
_entry.id    4WD4 
#
_exptl.entry_id    4WD4 
_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          99.09 
_cell.angle_gamma         90 
_cell.entry_id            4WD4 
_cell.length_a            74.08 
_cell.length_b            54.41 
_cell.length_c            122.28 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WD4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,K,L 1 1 
C,D,H,I,J,M,N 2 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    x,y,z 
_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
? 2 E N N 
? 2 F N N 
? 2 H N N 
? 2 I N N 
#
_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 149 n n 
CHA C4D HEM doub 150 n n 
CHA HHA HEM sing 151 n n 
CHB C4A HEM sing 152 n n 
CHB C1B HEM doub 153 n n 
CHB HHB HEM sing 154 n n 
CHC C4B HEM sing 155 n n 
CHC C1C HEM doub 156 n n 
CHC HHC HEM sing 157 n n 
CHD C4C HEM doub 158 n n 
CHD C1D HEM sing 159 n n 
CHD HHD HEM sing 160 n n 
C1A C2A HEM doub 161 n y 
C1A NA HEM sing 162 n y 
C2A C3A HEM sing 163 n y 
C2A CAA HEM sing 164 n n 
C3A C4A HEM doub 165 n y 
C3A CMA HEM sing 166 n n 
C4A NA HEM sing 167 n y 
CMA HMA HEM sing 168 n n 
CMA HMAA HEM sing 169 n n 
CMA HMAB HEM sing 170 n n 
CAA CBA HEM sing 171 n n 
CAA HAA HEM sing 172 n n 
CAA HAAA HEM sing 173 n n 
CBA CGA HEM sing 174 n n 
CBA HBA HEM sing 175 n n 
CBA HBAA HEM sing 176 n n 
CGA O1A HEM doub 177 n n 
CGA O2A HEM sing 178 n n 
C1B C2B HEM sing 179 n n 
C1B NB HEM sing 180 n n 
C2B C3B HEM doub 181 n n 
C2B CMB HEM sing 182 n n 
C3B C4B HEM sing 183 n n 
C3B CAB HEM sing 184 n n 
C4B NB HEM doub 185 n n 
CMB HMB HEM sing 186 n n 
CMB HMBA HEM sing 187 n n 
CMB HMBB HEM sing 188 n n 
CAB CBB HEM doub 189 n n 
CAB HAB HEM sing 190 n n 
CBB HBB HEM sing 191 n n 
CBB HBBA HEM sing 192 n n 
C1C C2C HEM sing 193 n y 
C1C NC HEM sing 194 n y 
C2C C3C HEM doub 195 n y 
C2C CMC HEM sing 196 n n 
C3C C4C HEM sing 197 n y 
C3C CAC HEM sing 198 n n 
C4C NC HEM sing 199 n y 
CMC HMC HEM sing 200 n n 
CMC HMCA HEM sing 201 n n 
CMC HMCB HEM sing 202 n n 
CAC CBC HEM doub 203 n n 
CAC HAC HEM sing 204 n n 
CBC HBC HEM sing 205 n n 
CBC HBCA HEM sing 206 n n 
C1D C2D HEM sing 207 n n 
C1D ND HEM doub 208 n n 
C2D C3D HEM doub 209 n n 
C2D CMD HEM sing 210 n n 
C3D C4D HEM sing 211 n n 
C3D CAD HEM sing 212 n n 
C4D ND HEM sing 213 n n 
CMD HMD HEM sing 214 n n 
CMD HMDA HEM sing 215 n n 
CMD HMDB HEM sing 216 n n 
CAD CBD HEM sing 217 n n 
CAD HAD HEM sing 218 n n 
CAD HADA HEM sing 219 n n 
CBD CGD HEM sing 220 n n 
CBD HBD HEM sing 221 n n 
CBD HBDA HEM sing 222 n n 
CGD O1D HEM doub 223 n n 
CGD O2D HEM sing 224 n n 
O2A H2A HEM sing 225 n n 
O2D H2D HEM sing 226 n n 
FE NA HEM sing 227 n n 
FE NB HEM sing 228 n n 
FE NC HEM sing 229 n n 
FE ND HEM sing 230 n n 
#
_atom_sites.entry_id                     4WD4 
_atom_sites.fract_transf_matrix[1][1]    0.013499 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00216 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018379 
_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]    0.008282 
_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 1 300 300 HEM HEM . 
F 2 HEM B 1 301 300 HEM HEM . 
G 3 EPE B 1 302 1 EPE EPE . 
H 2 HEM C 1 300 300 HEM HEM . 
I 2 HEM D 1 301 300 HEM HEM . 
J 3 EPE D 1 302 2 EPE EPE . 
K 4 HOH A 1 401 6 HOH HOH . 
K 4 HOH A 2 402 7 HOH HOH . 
K 4 HOH A 3 403 17 HOH HOH . 
K 4 HOH A 4 404 18 HOH HOH . 
K 4 HOH A 5 405 19 HOH HOH . 
K 4 HOH A 6 406 23 HOH HOH . 
L 4 HOH B 1 401 1 HOH HOH . 
L 4 HOH B 2 402 15 HOH HOH . 
L 4 HOH B 3 403 20 HOH HOH . 
L 4 HOH B 4 404 22 HOH HOH . 
M 4 HOH C 1 401 8 HOH HOH . 
M 4 HOH C 2 402 9 HOH HOH . 
M 4 HOH C 3 403 11 HOH HOH . 
M 4 HOH C 4 404 12 HOH HOH . 
M 4 HOH C 5 405 13 HOH HOH . 
M 4 HOH C 6 406 16 HOH HOH . 
N 4 HOH D 1 401 3 HOH HOH . 
N 4 HOH D 2 402 4 HOH HOH . 
N 4 HOH D 3 403 2 HOH HOH . 
N 4 HOH D 4 404 5 HOH HOH . 
N 4 HOH D 5 405 10 HOH HOH . 
N 4 HOH D 6 406 14 HOH HOH . 
N 4 HOH D 7 407 21 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 17.097 -5.2 170.051 1 98.05 ? CHA HEM 301 B 1 
HETATM 2 C CHB HEM . . . F 2 14.508 -2.051 167.455 1 100.82 ? CHB HEM 301 B 1 
HETATM 3 C CHC HEM . . . F 2 12.403 -0.456 171.569 1 88.06 ? CHC HEM 301 B 1 
HETATM 4 C CHD HEM . . . F 2 14.576 -4.034 174.018 1 99.5 ? CHD HEM 301 B 1 
HETATM 5 C C1A HEM . . . F 2 16.569 -4.462 169.017 1 96.86 ? C1A HEM 301 B 1 
HETATM 6 C C2A HEM . . . F 2 16.911 -4.663 167.655 1 93.51 ? C2A HEM 301 B 1 
HETATM 7 C C3A HEM . . . F 2 16.182 -3.78 166.905 1 97.69 ? C3A HEM 301 B 1 
HETATM 8 C C4A HEM . . . F 2 15.39 -3.045 167.823 1 100.14 ? C4A HEM 301 B 1 
HETATM 9 C CMA HEM . . . F 2 16.177 -3.588 165.399 1 94.84 ? CMA HEM 301 B 1 
HETATM 10 C CAA HEM . . . F 2 17.917 -5.715 167.251 1 88.18 ? CAA HEM 301 B 1 
HETATM 11 C CBA HEM . . . F 2 18.16 -5.954 165.765 1 84.4 ? CBA HEM 301 B 1 
HETATM 12 C CGA HEM . . . F 2 19.649 -6.023 165.65 1 87.59 ? CGA HEM 301 B 1 
HETATM 13 O O1A HEM . . . F 2 20.28 -4.984 165.343 1 90.7 ? O1A HEM 301 B 1 
HETATM 14 O O2A HEM . . . F 2 20.236 -7.103 165.893 1 84.09 ? O2A HEM 301 B 1 
HETATM 15 C C1B HEM . . . F 2 13.722 -1.348 168.369 1 100.51 ? C1B HEM 301 B 1 
HETATM 16 C C2B HEM . . . F 2 12.86 -0.305 167.938 1 96.06 ? C2B HEM 301 B 1 
HETATM 17 C C3B HEM . . . F 2 12.275 0.185 169.05 1 93.61 ? C3B HEM 301 B 1 
HETATM 18 C C4B HEM . . . F 2 12.784 -0.609 170.222 1 91.88 ? C4B HEM 301 B 1 
HETATM 19 C CMB HEM . . . F 2 12.607 0.228 166.536 1 90.95 ? CMB HEM 301 B 1 
HETATM 20 C CAB HEM . . . F 2 11.275 1.239 168.876 1 96.47 ? CAB HEM 301 B 1 
HETATM 21 C CBB HEM . . . F 2 10.387 1.529 169.793 1 99.92 ? CBB HEM 301 B 1 
HETATM 22 C C1C HEM . . . F 2 12.779 -1.31 172.619 1 91.87 ? C1C HEM 301 B 1 
HETATM 23 C C2C HEM . . . F 2 12.344 -1.271 173.969 1 95.21 ? C2C HEM 301 B 1 
HETATM 24 C C3C HEM . . . F 2 12.946 -2.294 174.697 1 95.63 ? C3C HEM 301 B 1 
HETATM 25 C C4C HEM . . . F 2 13.764 -2.978 173.744 1 97.84 ? C4C HEM 301 B 1 
HETATM 26 C CMC HEM . . . F 2 11.372 -0.29 174.56 1 93.06 ? CMC HEM 301 B 1 
HETATM 27 C CAC HEM . . . F 2 12.699 -2.524 176.159 1 92.91 ? CAC HEM 301 B 1 
HETATM 28 C CBC HEM . . . F 2 13.252 -3.449 176.949 1 88.53 ? CBC HEM 301 B 1 
HETATM 29 C C1D HEM . . . F 2 15.438 -4.602 173.085 1 100.66 ? C1D HEM 301 B 1 
HETATM 30 C C2D HEM . . . F 2 16.31 -5.701 173.512 1 101.23 ? C2D HEM 301 B 1 
HETATM 31 C C3D HEM . . . F 2 17.01 -6.041 172.421 1 100.49 ? C3D HEM 301 B 1 
HETATM 32 C C4D HEM . . . F 2 16.585 -5.129 171.334 1 98.38 ? C4D HEM 301 B 1 
HETATM 33 C CMD HEM . . . F 2 16.421 -6.354 174.881 1 96.64 ? CMD HEM 301 B 1 
HETATM 34 C CAD HEM . . . F 2 18.045 -7.135 172.453 1 96.59 ? CAD HEM 301 B 1 
HETATM 35 C CBD HEM . . . F 2 17.966 -8.142 171.313 1 91.59 ? CBD HEM 301 B 1 
HETATM 36 C CGD HEM . . . F 2 19.39 -8.427 170.981 1 88.49 ? CGD HEM 301 B 1 
HETATM 37 O O1D HEM . . . F 2 19.821 -9.591 171.087 1 86.83 ? O1D HEM 301 B 1 
HETATM 38 O O2D HEM . . . F 2 20.125 -7.478 170.635 1 88.15 ? O2D HEM 301 B 1 
HETATM 39 N NA HEM . . . F 2 15.63 -3.466 169.114 1 99.57 ? NA HEM 301 B 1 
HETATM 40 N NB HEM . . . F 2 13.65 -1.511 169.705 1 98.81 ? NB HEM 301 B 1 
HETATM 41 N NC HEM . . . F 2 13.668 -2.339 172.524 1 97.04 ? NC HEM 301 B 1 
HETATM 42 N ND HEM . . . F 2 15.626 -4.302 171.78 1 97.91 ? ND HEM 301 B 1 
HETATM 43 FE FE HEM . . . F 2 14.744 -2.934 170.832 1 98.59 ? FE HEM 301 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#