data_3K9Y
#
_model_server_result.job_id            GN0L83d7EL6zLFNjDCEfJA 
_model_server_result.datetime_utc      '2024-12-12 11:19:20' 
_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          3k9y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":520}' 
#
_entry.id    3K9Y 
#
_exptl.entry_id    3K9Y 
_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          122.44 
_cell.angle_gamma         90 
_cell.entry_id            3K9Y 
_cell.length_a            182.297 
_cell.length_b            81.303 
_cell.length_c            108.707 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3K9Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E 1 1 
B,F 2 1 
A,C,D,E 3 1 
B,F 3 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' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -58.312187 0 91.743669 
#
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
metalc ? metalc1 A SG CYS 430 A CYS 462 1_555 C FE HEM . A HEM 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc2 B SG CYS 430 B CYS 462 1_555 F FE HEM . B HEM 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
#
_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 207 n n 
CHA C4D HEM doub 208 n n 
CHA HHA HEM sing 209 n n 
CHB C4A HEM sing 210 n n 
CHB C1B HEM doub 211 n n 
CHB HHB HEM sing 212 n n 
CHC C4B HEM sing 213 n n 
CHC C1C HEM doub 214 n n 
CHC HHC HEM sing 215 n n 
CHD C4C HEM doub 216 n n 
CHD C1D HEM sing 217 n n 
CHD HHD HEM sing 218 n n 
C1A C2A HEM doub 219 n y 
C1A NA HEM sing 220 n y 
C2A C3A HEM sing 221 n y 
C2A CAA HEM sing 222 n n 
C3A C4A HEM doub 223 n y 
C3A CMA HEM sing 224 n n 
C4A NA HEM sing 225 n y 
CMA HMA HEM sing 226 n n 
CMA HMAA HEM sing 227 n n 
CMA HMAB HEM sing 228 n n 
CAA CBA HEM sing 229 n n 
CAA HAA HEM sing 230 n n 
CAA HAAA HEM sing 231 n n 
CBA CGA HEM sing 232 n n 
CBA HBA HEM sing 233 n n 
CBA HBAA HEM sing 234 n n 
CGA O1A HEM doub 235 n n 
CGA O2A HEM sing 236 n n 
C1B C2B HEM sing 237 n n 
C1B NB HEM sing 238 n n 
C2B C3B HEM doub 239 n n 
C2B CMB HEM sing 240 n n 
C3B C4B HEM sing 241 n n 
C3B CAB HEM sing 242 n n 
C4B NB HEM doub 243 n n 
CMB HMB HEM sing 244 n n 
CMB HMBA HEM sing 245 n n 
CMB HMBB HEM sing 246 n n 
CAB CBB HEM doub 247 n n 
CAB HAB HEM sing 248 n n 
CBB HBB HEM sing 249 n n 
CBB HBBA HEM sing 250 n n 
C1C C2C HEM sing 251 n y 
C1C NC HEM sing 252 n y 
C2C C3C HEM doub 253 n y 
C2C CMC HEM sing 254 n n 
C3C C4C HEM sing 255 n y 
C3C CAC HEM sing 256 n n 
C4C NC HEM sing 257 n y 
CMC HMC HEM sing 258 n n 
CMC HMCA HEM sing 259 n n 
CMC HMCB HEM sing 260 n n 
CAC CBC HEM doub 261 n n 
CAC HAC HEM sing 262 n n 
CBC HBC HEM sing 263 n n 
CBC HBCA HEM sing 264 n n 
C1D C2D HEM sing 265 n n 
C1D ND HEM doub 266 n n 
C2D C3D HEM doub 267 n n 
C2D CMD HEM sing 268 n n 
C3D C4D HEM sing 269 n n 
C3D CAD HEM sing 270 n n 
C4D ND HEM sing 271 n n 
CMD HMD HEM sing 272 n n 
CMD HMDA HEM sing 273 n n 
CMD HMDB HEM sing 274 n n 
CAD CBD HEM sing 275 n n 
CAD HAD HEM sing 276 n n 
CAD HADA HEM sing 277 n n 
CBD CGD HEM sing 278 n n 
CBD HBD HEM sing 279 n n 
CBD HBDA HEM sing 280 n n 
CGD O1D HEM doub 281 n n 
CGD O2D HEM sing 282 n n 
O2A H2A HEM sing 283 n n 
O2D H2D HEM sing 284 n n 
FE NA HEM sing 285 n n 
FE NB HEM sing 286 n n 
FE NC HEM sing 287 n n 
FE ND HEM sing 288 n n 
#
_atom_sites.entry_id                     3K9Y 
_atom_sites.fract_transf_matrix[1][1]    0.005486 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003487 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.0123 
_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]    0.0109 
_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 1 520 520 HEM HEM . 
D 3 CM5 A 1 516 504 CM5 CM5 . 
E 3 CM5 A 1 517 505 CM5 CM5 . 
F 2 HEM B 1 520 520 HEM HEM . 
#
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 -21.815 -9.818 81.113 1 30.49 ? CHA HEM 520 B 1 
HETATM 2 C CHB HEM . . . F 2 -23.364 -7.741 85.128 1 35.59 ? CHB HEM 520 B 1 
HETATM 3 C CHC HEM . . . F 2 -19.59 -4.845 85.013 1 33.56 ? CHC HEM 520 B 1 
HETATM 4 C CHD HEM . . . F 2 -18.063 -7.071 81.18 1 31.05 ? CHD HEM 520 B 1 
HETATM 5 C C1A HEM . . . F 2 -22.541 -9.633 82.304 1 33.5 ? C1A HEM 520 B 1 
HETATM 6 C C2A HEM . . . F 2 -23.724 -10.296 82.675 1 33.87 ? C2A HEM 520 B 1 
HETATM 7 C C3A HEM . . . F 2 -24.164 -9.685 83.823 1 31.34 ? C3A HEM 520 B 1 
HETATM 8 C C4A HEM . . . F 2 -23.24 -8.68 84.114 1 33.09 ? C4A HEM 520 B 1 
HETATM 9 C CMA HEM . . . F 2 -25.43 -10.034 84.648 1 31.32 ? CMA HEM 520 B 1 
HETATM 10 C CAA HEM . . . F 2 -24.359 -11.464 81.931 1 32.89 ? CAA HEM 520 B 1 
HETATM 11 C CBA HEM . . . F 2 -23.868 -12.804 82.381 1 32.53 ? CBA HEM 520 B 1 
HETATM 12 C CGA HEM . . . F 2 -24.54 -13.963 81.695 1 35.77 ? CGA HEM 520 B 1 
HETATM 13 O O1A HEM . . . F 2 -25.443 -14.562 82.295 1 30.79 ? O1A HEM 520 B 1 
HETATM 14 O O2A HEM . . . F 2 -24.225 -14.311 80.572 1 35.15 ? O2A HEM 520 B 1 
HETATM 15 C C1B HEM . . . F 2 -22.451 -6.771 85.584 1 36.63 ? C1B HEM 520 B 1 
HETATM 16 C C2B HEM . . . F 2 -22.666 -5.828 86.623 1 37.46 ? C2B HEM 520 B 1 
HETATM 17 C C3B HEM . . . F 2 -21.541 -4.98 86.574 1 39.83 ? C3B HEM 520 B 1 
HETATM 18 C C4B HEM . . . F 2 -20.731 -5.474 85.508 1 37.34 ? C4B HEM 520 B 1 
HETATM 19 C CMB HEM . . . F 2 -23.861 -5.788 87.552 1 33.64 ? CMB HEM 520 B 1 
HETATM 20 C CAB HEM . . . F 2 -21.23 -3.852 87.395 1 40.73 ? CAB HEM 520 B 1 
HETATM 21 C CBB HEM . . . F 2 -21.266 -3.691 88.874 1 43.44 ? CBB HEM 520 B 1 
HETATM 22 C C1C HEM . . . F 2 -18.756 -5.194 84 1 33.32 ? C1C HEM 520 B 1 
HETATM 23 C C2C HEM . . . F 2 -17.489 -4.664 83.771 1 33.02 ? C2C HEM 520 B 1 
HETATM 24 C C3C HEM . . . F 2 -17.012 -5.289 82.595 1 29.54 ? C3C HEM 520 B 1 
HETATM 25 C C4C HEM . . . F 2 -18.057 -6.157 82.212 1 31.44 ? C4C HEM 520 B 1 
HETATM 26 C CMC HEM . . . F 2 -16.761 -3.596 84.639 1 28.98 ? CMC HEM 520 B 1 
HETATM 27 C CAC HEM . . . F 2 -15.87 -5.189 81.875 1 28.76 ? CAC HEM 520 B 1 
HETATM 28 C CBC HEM . . . F 2 -14.51 -5.216 82.265 1 27.41 ? CBC HEM 520 B 1 
HETATM 29 C C1D HEM . . . F 2 -19.087 -7.776 80.668 1 28.81 ? C1D HEM 520 B 1 
HETATM 30 C C2D HEM . . . F 2 -18.949 -8.573 79.533 1 28.52 ? C2D HEM 520 B 1 
HETATM 31 C C3D HEM . . . F 2 -19.915 -9.525 79.57 1 28.72 ? C3D HEM 520 B 1 
HETATM 32 C C4D HEM . . . F 2 -20.622 -9.262 80.76 1 26.6 ? C4D HEM 520 B 1 
HETATM 33 C CMD HEM . . . F 2 -17.895 -8.423 78.41 1 29.57 ? CMD HEM 520 B 1 
HETATM 34 C CAD HEM . . . F 2 -20.13 -10.627 78.49 1 28.98 ? CAD HEM 520 B 1 
HETATM 35 C CBD HEM . . . F 2 -19.308 -11.904 78.779 1 34.5 ? CBD HEM 520 B 1 
HETATM 36 C CGD HEM . . . F 2 -19.44 -13.04 77.764 1 35.04 ? CGD HEM 520 B 1 
HETATM 37 O O1D HEM . . . F 2 -18.479 -13.413 77.115 1 33.46 ? O1D HEM 520 B 1 
HETATM 38 O O2D HEM . . . F 2 -20.557 -13.564 77.603 1 35.82 ? O2D HEM 520 B 1 
HETATM 39 N NA HEM . . . F 2 -22.263 -8.639 83.215 1 31.89 ? NA HEM 520 B 1 
HETATM 40 N NB HEM . . . F 2 -21.291 -6.532 84.94 1 33.02 ? NB HEM 520 B 1 
HETATM 41 N NC HEM . . . F 2 -19.091 -6.079 83.074 1 30.21 ? NC HEM 520 B 1 
HETATM 42 N ND HEM . . . F 2 -20.087 -8.194 81.384 1 27.48 ? ND HEM 520 B 1 
HETATM 43 FE FE HEM . . . F 2 -20.713 -7.328 83.136 1 72.8 ? FE HEM 520 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           327 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           43 
#