data_8DME
#
_model_server_result.job_id            mACq3xbFBo_kfeLJELt7Ng 
_model_server_result.datetime_utc      '2024-10-18 19:30:08' 
_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          8dme 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1101}' 
#
_entry.id    8DME 
#
_exptl.entry_id    8DME 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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 C N N 
? 2 L 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 398 A CYS 400 1_555 C FE HEM . A HEM 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc2 B SG CYS 398 B CYS 400 1_555 L FE HEM . B HEM 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
#
_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 318 n n 
CHA C4D HEM doub 319 n n 
CHA HHA HEM sing 320 n n 
CHB C4A HEM sing 321 n n 
CHB C1B HEM doub 322 n n 
CHB HHB HEM sing 323 n n 
CHC C4B HEM sing 324 n n 
CHC C1C HEM doub 325 n n 
CHC HHC HEM sing 326 n n 
CHD C4C HEM doub 327 n n 
CHD C1D HEM sing 328 n n 
CHD HHD HEM sing 329 n n 
C1A C2A HEM doub 330 n y 
C1A NA HEM sing 331 n y 
C2A C3A HEM sing 332 n y 
C2A CAA HEM sing 333 n n 
C3A C4A HEM doub 334 n y 
C3A CMA HEM sing 335 n n 
C4A NA HEM sing 336 n y 
CMA HMA HEM sing 337 n n 
CMA HMAA HEM sing 338 n n 
CMA HMAB HEM sing 339 n n 
CAA CBA HEM sing 340 n n 
CAA HAA HEM sing 341 n n 
CAA HAAA HEM sing 342 n n 
CBA CGA HEM sing 343 n n 
CBA HBA HEM sing 344 n n 
CBA HBAA HEM sing 345 n n 
CGA O1A HEM doub 346 n n 
CGA O2A HEM sing 347 n n 
C1B C2B HEM sing 348 n n 
C1B NB HEM sing 349 n n 
C2B C3B HEM doub 350 n n 
C2B CMB HEM sing 351 n n 
C3B C4B HEM sing 352 n n 
C3B CAB HEM sing 353 n n 
C4B NB HEM doub 354 n n 
CMB HMB HEM sing 355 n n 
CMB HMBA HEM sing 356 n n 
CMB HMBB HEM sing 357 n n 
CAB CBB HEM doub 358 n n 
CAB HAB HEM sing 359 n n 
CBB HBB HEM sing 360 n n 
CBB HBBA HEM sing 361 n n 
C1C C2C HEM sing 362 n y 
C1C NC HEM sing 363 n y 
C2C C3C HEM doub 364 n y 
C2C CMC HEM sing 365 n n 
C3C C4C HEM sing 366 n y 
C3C CAC HEM sing 367 n n 
C4C NC HEM sing 368 n y 
CMC HMC HEM sing 369 n n 
CMC HMCA HEM sing 370 n n 
CMC HMCB HEM sing 371 n n 
CAC CBC HEM doub 372 n n 
CAC HAC HEM sing 373 n n 
CBC HBC HEM sing 374 n n 
CBC HBCA HEM sing 375 n n 
C1D C2D HEM sing 376 n n 
C1D ND HEM doub 377 n n 
C2D C3D HEM doub 378 n n 
C2D CMD HEM sing 379 n n 
C3D C4D HEM sing 380 n n 
C3D CAD HEM sing 381 n n 
C4D ND HEM sing 382 n n 
CMD HMD HEM sing 383 n n 
CMD HMDA HEM sing 384 n n 
CMD HMDB HEM sing 385 n n 
CAD CBD HEM sing 386 n n 
CAD HAD HEM sing 387 n n 
CAD HADA HEM sing 388 n n 
CBD CGD HEM sing 389 n n 
CBD HBD HEM sing 390 n n 
CBD HBDA HEM sing 391 n n 
CGD O1D HEM doub 392 n n 
CGD O2D HEM sing 393 n n 
O2A H2A HEM sing 394 n n 
O2D H2D HEM sing 395 n n 
FE NA HEM sing 396 n n 
FE NB HEM sing 397 n n 
FE NC HEM sing 398 n n 
FE ND HEM sing 399 n n 
#
_atom_sites.entry_id                     8DME 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 1101 501 HEM HEM . 
D 3 1C6 A 1 1102 502 1C6 1C6 . 
E 4 FMN A 1 1103 1002 FMN FMN . 
F 5 FAD A 1 1104 1101 FAD FAD . 
G 6 SO4 A 1 1105 1102 SO4 SO4 . 
H 6 SO4 A 1 1106 1103 SO4 SO4 . 
I 6 SO4 A 1 1107 1104 SO4 SO4 . 
J 7 PG4 A 1 1108 1105 PG4 PG4 . 
K 7 PG4 A 1 1109 1106 PG4 PG4 . 
L 2 HEM B 1 1101 501 HEM HEM . 
M 3 1C6 B 1 1102 502 1C6 1C6 . 
N 4 FMN B 1 1103 1002 FMN FMN . 
O 5 FAD B 1 1104 1101 FAD FAD . 
P 6 SO4 B 1 1105 1102 SO4 SO4 . 
Q 6 SO4 B 1 1106 1103 SO4 SO4 . 
R 6 SO4 B 1 1107 1104 SO4 SO4 . 
S 7 PG4 B 1 1108 1105 PG4 PG4 . 
T 7 PG4 B 1 1109 1106 PG4 PG4 . 
#
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 . . . C 2 176.112 162.172 147.668 1 10.53 ? CHA HEM 1101 A 1 
HETATM 2 C CHB HEM . . . C 2 180.624 162.123 149.238 1 10.93 ? CHB HEM 1101 A 1 
HETATM 3 C CHC HEM . . . C 2 179.237 163.577 153.654 1 9.88 ? CHC HEM 1101 A 1 
HETATM 4 C CHD HEM . . . C 2 174.699 162.795 152.29 1 10.04 ? CHD HEM 1101 A 1 
HETATM 5 C C1A HEM . . . C 2 177.456 162.059 147.663 1 10.74 ? C1A HEM 1101 A 1 
HETATM 6 C C2A HEM . . . C 2 178.302 161.765 146.533 1 11.89 ? C2A HEM 1101 A 1 
HETATM 7 C C3A HEM . . . C 2 179.548 161.748 146.985 1 12.42 ? C3A HEM 1101 A 1 
HETATM 8 C C4A HEM . . . C 2 179.511 162.049 148.421 1 12.49 ? C4A HEM 1101 A 1 
HETATM 9 C CMA HEM . . . C 2 180.851 161.455 146.233 1 8.09 ? CMA HEM 1101 A 1 
HETATM 10 C CAA HEM . . . C 2 177.789 161.587 145.103 1 10.13 ? CAA HEM 1101 A 1 
HETATM 11 C CBA HEM . . . C 2 177.54 160.091 144.928 1 11.59 ? CBA HEM 1101 A 1 
HETATM 12 C CGA HEM . . . C 2 177.248 159.689 143.484 1 12.59 ? CGA HEM 1101 A 1 
HETATM 13 O O1A HEM . . . C 2 176.899 158.445 143.332 1 8.91 ? O1A HEM 1101 A 1 
HETATM 14 O O2A HEM . . . C 2 177.45 160.526 142.56 1 11.71 ? O2A HEM 1101 A 1 
HETATM 15 C C1B HEM . . . C 2 180.689 162.495 150.567 1 14.05 ? C1B HEM 1101 A 1 
HETATM 16 C C2B HEM . . . C 2 181.885 162.707 151.357 1 8.07 ? C2B HEM 1101 A 1 
HETATM 17 C C3B HEM . . . C 2 181.467 163.189 152.546 1 7.28 ? C3B HEM 1101 A 1 
HETATM 18 C C4B HEM . . . C 2 180.04 163.187 152.586 1 12.62 ? C4B HEM 1101 A 1 
HETATM 19 C CMB HEM . . . C 2 183.334 162.548 150.915 1 8.38 ? CMB HEM 1101 A 1 
HETATM 20 C CAB HEM . . . C 2 182.245 163.506 153.816 1 9.87 ? CAB HEM 1101 A 1 
HETATM 21 C CBB HEM . . . C 2 183.502 163.942 153.662 1 10.95 ? CBB HEM 1101 A 1 
HETATM 22 C C1C HEM . . . C 2 177.839 163.507 153.695 1 10.67 ? C1C HEM 1101 A 1 
HETATM 23 C C2C HEM . . . C 2 176.965 163.934 154.787 1 13.52 ? C2C HEM 1101 A 1 
HETATM 24 C C3C HEM . . . C 2 175.716 163.704 154.408 1 12.49 ? C3C HEM 1101 A 1 
HETATM 25 C C4C HEM . . . C 2 175.766 163.131 153.061 1 10.93 ? C4C HEM 1101 A 1 
HETATM 26 C CMC HEM . . . C 2 177.453 164.429 156.145 1 8.98 ? CMC HEM 1101 A 1 
HETATM 27 C CAC HEM . . . C 2 174.468 163.936 155.195 1 10.92 ? CAC HEM 1101 A 1 
HETATM 28 C CBC HEM . . . C 2 174.341 164.904 156.129 1 11.6 ? CBC HEM 1101 A 1 
HETATM 29 C C1D HEM . . . C 2 174.663 162.516 150.935 1 6.71 ? C1D HEM 1101 A 1 
HETATM 30 C C2D HEM . . . C 2 173.462 162.355 150.196 1 7.52 ? C2D HEM 1101 A 1 
HETATM 31 C C3D HEM . . . C 2 173.914 162.133 148.777 1 11.3 ? C3D HEM 1101 A 1 
HETATM 32 C C4D HEM . . . C 2 175.338 162.275 148.809 1 11.8 ? C4D HEM 1101 A 1 
HETATM 33 C CMD HEM . . . C 2 172.037 162.167 150.769 1 7.74 ? CMD HEM 1101 A 1 
HETATM 34 C CAD HEM . . . C 2 173.035 161.866 147.536 1 11.51 ? CAD HEM 1101 A 1 
HETATM 35 C CBD HEM . . . C 2 172.572 163.311 147.096 1 10.69 ? CBD HEM 1101 A 1 
HETATM 36 C CGD HEM . . . C 2 171.616 163.242 145.891 1 13.57 ? CGD HEM 1101 A 1 
HETATM 37 O O1D HEM . . . C 2 171.923 162.511 144.882 1 13.4 ? O1D HEM 1101 A 1 
HETATM 38 O O2D HEM . . . C 2 170.526 163.857 145.946 1 12.07 ? O2D HEM 1101 A 1 
HETATM 39 N NA HEM . . . C 2 178.206 162.22 148.771 1 12.82 ? NA HEM 1101 A 1 
HETATM 40 N NB HEM . . . C 2 179.586 162.852 151.324 1 8.87 ? NB HEM 1101 A 1 
HETATM 41 N NC HEM . . . C 2 177.078 163.191 152.638 1 11.5 ? NC HEM 1101 A 1 
HETATM 42 N ND HEM . . . C 2 175.711 162.584 150.08 1 9.19 ? ND HEM 1101 A 1 
HETATM 43 FE FE HEM . . . C 2 177.643 162.878 150.689 1 11.93 ? FE HEM 1101 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#