data_6UDM
#
_model_server_result.job_id            86-hUjDGWXUaR_wy4CH0WA 
_model_server_result.datetime_utc      '2024-11-28 14:19:53' 
_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          6udm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":601}' 
#
_entry.id    6UDM 
#
_exptl.entry_id    6UDM 
_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         120 
_cell.entry_id            6UDM 
_cell.length_a            241.281 
_cell.length_b            241.281 
_cell.length_c            125.298 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6UDM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G 1 1 
B,H,I 2 1 
C,J,K 3 1 
D,L,M 4 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 H N N 
? 2 J N N 
? 2 L N N 
#
_struct_conn.conn_type_id                   metalc 
_struct_conn.details                        ? 
_struct_conn.id                             metalc1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            SG 
_struct_conn.ptnr1_label_comp_id            CYS 
_struct_conn.ptnr1_label_seq_id             430 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             CYS 
_struct_conn.ptnr1_auth_seq_id              457 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            E 
_struct_conn.ptnr2_label_atom_id            FE 
_struct_conn.ptnr2_label_comp_id            HEM 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             HEM 
_struct_conn.ptnr2_auth_seq_id              601 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.67 
_struct_conn.pdbx_value_order               ? 
#
_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 232 n n 
CHA C4D HEM doub 233 n n 
CHA HHA HEM sing 234 n n 
CHB C4A HEM sing 235 n n 
CHB C1B HEM doub 236 n n 
CHB HHB HEM sing 237 n n 
CHC C4B HEM sing 238 n n 
CHC C1C HEM doub 239 n n 
CHC HHC HEM sing 240 n n 
CHD C4C HEM doub 241 n n 
CHD C1D HEM sing 242 n n 
CHD HHD HEM sing 243 n n 
C1A C2A HEM doub 244 n y 
C1A NA HEM sing 245 n y 
C2A C3A HEM sing 246 n y 
C2A CAA HEM sing 247 n n 
C3A C4A HEM doub 248 n y 
C3A CMA HEM sing 249 n n 
C4A NA HEM sing 250 n y 
CMA HMA HEM sing 251 n n 
CMA HMAA HEM sing 252 n n 
CMA HMAB HEM sing 253 n n 
CAA CBA HEM sing 254 n n 
CAA HAA HEM sing 255 n n 
CAA HAAA HEM sing 256 n n 
CBA CGA HEM sing 257 n n 
CBA HBA HEM sing 258 n n 
CBA HBAA HEM sing 259 n n 
CGA O1A HEM doub 260 n n 
CGA O2A HEM sing 261 n n 
C1B C2B HEM sing 262 n n 
C1B NB HEM sing 263 n n 
C2B C3B HEM doub 264 n n 
C2B CMB HEM sing 265 n n 
C3B C4B HEM sing 266 n n 
C3B CAB HEM sing 267 n n 
C4B NB HEM doub 268 n n 
CMB HMB HEM sing 269 n n 
CMB HMBA HEM sing 270 n n 
CMB HMBB HEM sing 271 n n 
CAB CBB HEM doub 272 n n 
CAB HAB HEM sing 273 n n 
CBB HBB HEM sing 274 n n 
CBB HBBA HEM sing 275 n n 
C1C C2C HEM sing 276 n y 
C1C NC HEM sing 277 n y 
C2C C3C HEM doub 278 n y 
C2C CMC HEM sing 279 n n 
C3C C4C HEM sing 280 n y 
C3C CAC HEM sing 281 n n 
C4C NC HEM sing 282 n y 
CMC HMC HEM sing 283 n n 
CMC HMCA HEM sing 284 n n 
CMC HMCB HEM sing 285 n n 
CAC CBC HEM doub 286 n n 
CAC HAC HEM sing 287 n n 
CBC HBC HEM sing 288 n n 
CBC HBCA HEM sing 289 n n 
C1D C2D HEM sing 290 n n 
C1D ND HEM doub 291 n n 
C2D C3D HEM doub 292 n n 
C2D CMD HEM sing 293 n n 
C3D C4D HEM sing 294 n n 
C3D CAD HEM sing 295 n n 
C4D ND HEM sing 296 n n 
CMD HMD HEM sing 297 n n 
CMD HMDA HEM sing 298 n n 
CMD HMDB HEM sing 299 n n 
CAD CBD HEM sing 300 n n 
CAD HAD HEM sing 301 n n 
CAD HADA HEM sing 302 n n 
CBD CGD HEM sing 303 n n 
CBD HBD HEM sing 304 n n 
CBD HBDA HEM sing 305 n n 
CGD O1D HEM doub 306 n n 
CGD O2D HEM sing 307 n n 
O2A H2A HEM sing 308 n n 
O2D H2D HEM sing 309 n n 
FE NA HEM sing 310 n n 
FE NB HEM sing 311 n n 
FE NC HEM sing 312 n n 
FE ND HEM sing 313 n n 
#
_atom_sites.entry_id                     6UDM 
_atom_sites.fract_transf_matrix[1][1]    0.004145 
_atom_sites.fract_transf_matrix[1][2]    0.002393 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004786 
_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]    0.007981 
_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 1 601 601 HEM HEM . 
F 3 Q4P A 1 602 1 Q4P LIG . 
G 4 CPS A 1 603 1 CPS CPS . 
H 2 HEM B 1 601 601 HEM HEM . 
I 3 Q4P B 1 602 2 Q4P LIG . 
J 2 HEM C 1 601 601 HEM HEM . 
K 3 Q4P C 1 602 3 Q4P LIG . 
L 2 HEM D 1 601 601 HEM HEM . 
M 3 Q4P D 1 602 4 Q4P LIG . 
#
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 . . . J 2 -101.417 -113.31 43.193 1 64.31 ? CHA HEM 601 C 1 
HETATM 2 C CHB HEM . . . J 2 -101.3 -109.679 39.978 1 63 ? CHB HEM 601 C 1 
HETATM 3 C CHC HEM . . . J 2 -102.461 -106.537 43.493 1 62.27 ? CHC HEM 601 C 1 
HETATM 4 C CHD HEM . . . J 2 -102.312 -110.129 46.738 1 64.67 ? CHD HEM 601 C 1 
HETATM 5 C C1A HEM . . . J 2 -101.278 -112.603 42.021 1 64.02 ? C1A HEM 601 C 1 
HETATM 6 C C2A HEM . . . J 2 -100.921 -113.159 40.733 1 65 ? C2A HEM 601 C 1 
HETATM 7 C C3A HEM . . . J 2 -100.885 -112.159 39.846 1 64.21 ? C3A HEM 601 C 1 
HETATM 8 C C4A HEM . . . J 2 -101.226 -110.934 40.538 1 63.21 ? C4A HEM 601 C 1 
HETATM 9 C CMA HEM . . . J 2 -100.548 -112.272 38.343 1 64.77 ? CMA HEM 601 C 1 
HETATM 10 C CAA HEM . . . J 2 -100.625 -114.653 40.47 1 67.2 ? CAA HEM 601 C 1 
HETATM 11 C CBA HEM . . . J 2 -101.687 -115.25 39.557 1 69.4 ? CBA HEM 601 C 1 
HETATM 12 C CGA HEM . . . J 2 -101.452 -116.729 39.41 1 70.6 ? CGA HEM 601 C 1 
HETATM 13 O O1A HEM . . . J 2 -102.194 -117.376 38.626 1 73.1 ? O1A HEM 601 C 1 
HETATM 14 O O2A HEM . . . J 2 -100.523 -117.258 40.071 1 69.52 ? O2A HEM 601 C 1 
HETATM 15 C C1B HEM . . . J 2 -101.575 -108.509 40.654 1 63.04 ? C1B HEM 601 C 1 
HETATM 16 C C2B HEM . . . J 2 -101.566 -107.177 40.085 1 61.92 ? C2B HEM 601 C 1 
HETATM 17 C C3B HEM . . . J 2 -101.879 -106.306 41.056 1 61.8 ? C3B HEM 601 C 1 
HETATM 18 C C4B HEM . . . J 2 -102.108 -107.064 42.27 1 62.25 ? C4B HEM 601 C 1 
HETATM 19 C CMB HEM . . . J 2 -101.23 -106.877 38.61 1 62.35 ? CMB HEM 601 C 1 
HETATM 20 C CAB HEM . . . J 2 -102.015 -104.766 40.977 1 62.48 ? CAB HEM 601 C 1 
HETATM 21 C CBB HEM . . . J 2 -102.097 -104.113 39.813 1 62.69 ? CBB HEM 601 C 1 
HETATM 22 C C1C HEM . . . J 2 -102.559 -107.239 44.673 1 62.15 ? C1C HEM 601 C 1 
HETATM 23 C C2C HEM . . . J 2 -102.98 -106.704 45.951 1 62.62 ? C2C HEM 601 C 1 
HETATM 24 C C3C HEM . . . J 2 -102.946 -107.7 46.848 1 63.03 ? C3C HEM 601 C 1 
HETATM 25 C C4C HEM . . . J 2 -102.491 -108.891 46.163 1 63.04 ? C4C HEM 601 C 1 
HETATM 26 C CMC HEM . . . J 2 -103.397 -105.234 46.178 1 64.12 ? CMC HEM 601 C 1 
HETATM 27 C CAC HEM . . . J 2 -103.289 -107.67 48.358 1 65.87 ? CAC HEM 601 C 1 
HETATM 28 C CBC HEM . . . J 2 -103.438 -106.53 49.04 1 67.37 ? CBC HEM 601 C 1 
HETATM 29 C C1D HEM . . . J 2 -102.03 -111.297 46.069 1 64.7 ? C1D HEM 601 C 1 
HETATM 30 C C2D HEM . . . J 2 -101.825 -112.595 46.674 1 65.87 ? C2D HEM 601 C 1 
HETATM 31 C C3D HEM . . . J 2 -101.58 -113.473 45.699 1 66.4 ? C3D HEM 601 C 1 
HETATM 32 C C4D HEM . . . J 2 -101.619 -112.763 44.437 1 64.23 ? C4D HEM 601 C 1 
HETATM 33 C CMD HEM . . . J 2 -101.883 -112.898 48.186 1 68.8 ? CMD HEM 601 C 1 
HETATM 34 C CAD HEM . . . J 2 -101.304 -114.982 45.872 1 69.39 ? CAD HEM 601 C 1 
HETATM 35 C CBD HEM . . . J 2 -102.557 -115.746 45.457 1 70.49 ? CBD HEM 601 C 1 
HETATM 36 C CGD HEM . . . J 2 -102.305 -117.225 45.53 1 72.55 ? CGD HEM 601 C 1 
HETATM 37 O O1D HEM . . . J 2 -103.286 -118.004 45.43 1 73.89 ? O1D HEM 601 C 1 
HETATM 38 O O2D HEM . . . J 2 -101.124 -117.626 45.689 1 74.11 ? O2D HEM 601 C 1 
HETATM 39 N NA HEM . . . J 2 -101.461 -111.243 41.865 1 63.56 ? NA HEM 601 C 1 
HETATM 40 N NB HEM . . . J 2 -101.913 -108.401 41.99 1 62.47 ? NB HEM 601 C 1 
HETATM 41 N NC HEM . . . J 2 -102.269 -108.576 44.84 1 61.36 ? NC HEM 601 C 1 
HETATM 42 N ND HEM . . . J 2 -101.898 -111.437 44.701 1 63.99 ? ND HEM 601 C 1 
HETATM 43 FE FE HEM . . . J 2 -102.022 -109.918 43.337 1 58.09 ? FE HEM 601 C 1 
HETATM 44 H HHB HEM . . . J 2 -101.241 -109.624 39.001 1 63 ? HHB HEM 601 C 1 
HETATM 45 H HHC HEM . . . J 2 -102.571 -105.564 43.543 1 62.27 ? HHC HEM 601 C 1 
HETATM 46 H HHD HEM . . . J 2 -102.425 -110.189 47.71 1 64.67 ? HHD HEM 601 C 1 
HETATM 47 H HMA HEM . . . J 2 -99.688 -112.729 38.235 1 64.77 ? HMA HEM 601 C 1 
HETATM 48 H HMAA HEM . . . J 2 -100.492 -111.376 37.951 1 64.77 ? HMAA HEM 601 C 1 
HETATM 49 H HMAB HEM . . . J 2 -101.248 -112.784 37.887 1 64.77 ? HMAB HEM 601 C 1 
HETATM 50 H HAA HEM . . . J 2 -100.619 -115.133 41.313 1 67.2 ? HAA HEM 601 C 1 
HETATM 51 H HAAA HEM . . . J 2 -99.756 -114.737 40.048 1 67.2 ? HAAA HEM 601 C 1 
HETATM 52 H HBA HEM . . . J 2 -101.639 -114.83 38.685 1 69.4 ? HBA HEM 601 C 1 
HETATM 53 H HBAA HEM . . . J 2 -102.565 -115.099 39.941 1 69.4 ? HBAA HEM 601 C 1 
HETATM 54 H HMB HEM . . . J 2 -100.67 -107.587 38.26 1 62.35 ? HMB HEM 601 C 1 
HETATM 55 H HMBA HEM . . . J 2 -100.755 -106.035 38.544 1 62.35 ? HMBA HEM 601 C 1 
HETATM 56 H HMBB HEM . . . J 2 -102.05 -106.834 38.093 1 62.35 ? HMBB HEM 601 C 1 
HETATM 57 H HAB HEM . . . J 2 -102.041 -104.261 41.793 1 62.48 ? HAB HEM 601 C 1 
HETATM 58 H HBB HEM . . . J 2 -101.855 -103.175 39.769 1 62.69 ? HBB HEM 601 C 1 
HETATM 59 H HBBA HEM . . . J 2 -102.397 -104.571 39.014 1 62.69 ? HBBA HEM 601 C 1 
HETATM 60 H HMC HEM . . . J 2 -104.094 -105.188 46.85 1 64.12 ? HMC HEM 601 C 1 
HETATM 61 H HMCA HEM . . . J 2 -103.733 -104.866 45.346 1 64.12 ? HMCA HEM 601 C 1 
HETATM 62 H HMCB HEM . . . J 2 -102.627 -104.719 46.465 1 64.12 ? HMCB HEM 601 C 1 
HETATM 63 H HAC HEM . . . J 2 -103.4 -108.503 48.822 1 65.87 ? HAC HEM 601 C 1 
HETATM 64 H HBC HEM . . . J 2 -103.873 -106.542 49.906 1 67.37 ? HBC HEM 601 C 1 
HETATM 65 H HBCA HEM . . . J 2 -103.021 -105.714 48.724 1 67.37 ? HBCA HEM 601 C 1 
HETATM 66 H HMD HEM . . . J 2 -101.907 -113.866 48.333 1 68.8 ? HMD HEM 601 C 1 
HETATM 67 H HMDA HEM . . . J 2 -102.689 -112.492 48.566 1 68.8 ? HMDA HEM 601 C 1 
HETATM 68 H HMDB HEM . . . J 2 -101.094 -112.518 48.625 1 68.8 ? HMDB HEM 601 C 1 
HETATM 69 H HAD HEM . . . J 2 -101.09 -115.179 46.797 1 69.39 ? HAD HEM 601 C 1 
HETATM 70 H HADA HEM . . . J 2 -100.562 -115.242 45.304 1 69.39 ? HADA HEM 601 C 1 
HETATM 71 H HBD HEM . . . J 2 -102.795 -115.505 44.548 1 70.49 ? HBD HEM 601 C 1 
HETATM 72 H HBDA HEM . . . J 2 -103.287 -115.514 46.052 1 70.49 ? HBDA HEM 601 C 1 
HETATM 73 H HHA HEM . . . J 2 -101.499 -114.284 43.117 1 64.31 ? HHA HEM 601 C 1 
#
_model_server_stats.io_time_ms              107 
_model_server_stats.parse_time_ms           38 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           371 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           73 
#