data_5GPN
#
_model_server_result.job_id            dSZfSqSb9ka9WhCxhP7hXA 
_model_server_result.datetime_utc      '2025-02-05 12:54:45' 
_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          5gpn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"HC","auth_seq_id":402}' 
#
_entry.id    5GPN 
#
_exptl.entry_id    5GPN 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          64 
_entity.src_method                  nat 
_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                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    84-meric 
_pdbx_struct_assembly.oligomeric_count      84 
_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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC,MC,NC,OC,PC,QC,RC,SC,TC,UC,VC,WC,XC,YC,ZC,AD,BD,CD,DD,ED 
_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
? 64 GC N N 
? 64 HC N N 
? 64 KC N N 
? 64 LC 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
covale ? covale1 K CB ARG 11 K ARG 11 1_555 DB CB ALA 26 7 ALA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 W NH2 ARG 101 W ARG 101 1_555 W O VAL 159 W VAL 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? 
covale ? covale3 W CB LYS 161 W LYS 161 1_555 Y CG ASN 285 Z ASN 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.642 ? 
covale ? covale4 W CB LYS 161 W LYS 161 1_555 Y OD1 ASN 285 Z ASN 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? 
covale ? covale5 Z SD MET 106 a MET 106 1_555 Z CE2 PHE 113 a PHE 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.651 ? 
metalc ? metalc1 X SG CYS 64 Y CYS 64 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? 
metalc ? metalc2 X O ASN 74 Y ASN 74 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? 
metalc ? metalc3 X O CYS 75 Y CYS 75 1_555 QC FE1 FES . Y FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc4 X NE2 HIS 124 Y HIS 124 1_555 OC FE2 SF4 . Y SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
metalc ? metalc5 X NE2 HIS 124 Y HIS 124 1_555 OC FE3 SF4 . Y SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? 
metalc ? metalc6 X O ILE 177 Y ILE 177 1_555 PC FE1 SF4 . Y SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc7 Z SG CYS 92 a CYS 92 1_555 RC FE1 SF4 . a SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? 
metalc ? metalc8 Z SG CYS 186 a CYS 186 1_555 RC FE2 SF4 . a SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? 
metalc ? metalc9 AA SG CYS 113 b CYS 113 1_555 SC FE1 SF4 . b SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? 
metalc ? metalc10 AA N CYS 155 b CYS 155 1_555 TC FE4 SF4 . b SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? 
metalc ? metalc11 AA N GLY 156 b GLY 156 1_555 TC FE4 SF4 . b SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? 
metalc ? metalc12 BA O SER 378 c SER 378 1_555 UC FE3 SF4 . c SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc13 BA OG1 THR 423 c THR 423 1_555 UC FE1 SF4 . c SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? 
metalc ? metalc14 IB O GLU 198 z GLU 198 1_555 ED CU CU . z CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc15 DD CU CU . z CU 301 1_555 ED CU CU . z CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
#
_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 394 n n 
CHA C4D HEM doub 395 n n 
CHA HHA HEM sing 396 n n 
CHB C4A HEM sing 397 n n 
CHB C1B HEM doub 398 n n 
CHB HHB HEM sing 399 n n 
CHC C4B HEM sing 400 n n 
CHC C1C HEM doub 401 n n 
CHC HHC HEM sing 402 n n 
CHD C4C HEM doub 403 n n 
CHD C1D HEM sing 404 n n 
CHD HHD HEM sing 405 n n 
C1A C2A HEM doub 406 n y 
C1A NA HEM sing 407 n y 
C2A C3A HEM sing 408 n y 
C2A CAA HEM sing 409 n n 
C3A C4A HEM doub 410 n y 
C3A CMA HEM sing 411 n n 
C4A NA HEM sing 412 n y 
CMA HMA HEM sing 413 n n 
CMA HMAA HEM sing 414 n n 
CMA HMAB HEM sing 415 n n 
CAA CBA HEM sing 416 n n 
CAA HAA HEM sing 417 n n 
CAA HAAA HEM sing 418 n n 
CBA CGA HEM sing 419 n n 
CBA HBA HEM sing 420 n n 
CBA HBAA HEM sing 421 n n 
CGA O1A HEM doub 422 n n 
CGA O2A HEM sing 423 n n 
C1B C2B HEM sing 424 n n 
C1B NB HEM sing 425 n n 
C2B C3B HEM doub 426 n n 
C2B CMB HEM sing 427 n n 
C3B C4B HEM sing 428 n n 
C3B CAB HEM sing 429 n n 
C4B NB HEM doub 430 n n 
CMB HMB HEM sing 431 n n 
CMB HMBA HEM sing 432 n n 
CMB HMBB HEM sing 433 n n 
CAB CBB HEM doub 434 n n 
CAB HAB HEM sing 435 n n 
CBB HBB HEM sing 436 n n 
CBB HBBA HEM sing 437 n n 
C1C C2C HEM sing 438 n y 
C1C NC HEM sing 439 n y 
C2C C3C HEM doub 440 n y 
C2C CMC HEM sing 441 n n 
C3C C4C HEM sing 442 n y 
C3C CAC HEM sing 443 n n 
C4C NC HEM sing 444 n y 
CMC HMC HEM sing 445 n n 
CMC HMCA HEM sing 446 n n 
CMC HMCB HEM sing 447 n n 
CAC CBC HEM doub 448 n n 
CAC HAC HEM sing 449 n n 
CBC HBC HEM sing 450 n n 
CBC HBCA HEM sing 451 n n 
C1D C2D HEM sing 452 n n 
C1D ND HEM doub 453 n n 
C2D C3D HEM doub 454 n n 
C2D CMD HEM sing 455 n n 
C3D C4D HEM sing 456 n n 
C3D CAD HEM sing 457 n n 
C4D ND HEM sing 458 n n 
CMD HMD HEM sing 459 n n 
CMD HMDA HEM sing 460 n n 
CMD HMDB HEM sing 461 n n 
CAD CBD HEM sing 462 n n 
CAD HAD HEM sing 463 n n 
CAD HADA HEM sing 464 n n 
CBD CGD HEM sing 465 n n 
CBD HBD HEM sing 466 n n 
CBD HBDA HEM sing 467 n n 
CGD O1D HEM doub 468 n n 
CGD O2D HEM sing 469 n n 
O2A H2A HEM sing 470 n n 
O2D H2D HEM sing 471 n n 
FE NA HEM sing 472 n n 
FE NB HEM sing 473 n n 
FE NC HEM sing 474 n n 
FE ND HEM sing 475 n n 
#
_atom_sites.entry_id                     5GPN 
_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
GC 64 HEM C 1 401 380 HEM HEM . 
HC 64 HEM C 1 402 381 HEM HEM . 
IC 65 HEC D 1 301 242 HEC HEC . 
JC 66 FES E 1 201 197 FES FES . 
KC 64 HEM O 1 401 380 HEM HEM . 
LC 64 HEM O 1 402 381 HEM HEM . 
MC 65 HEC P 1 301 242 HEC HEC . 
NC 66 FES Q 1 201 197 FES FES . 
OC 67 SF4 Y 1 801 717 SF4 SF4 . 
PC 67 SF4 Y 1 802 718 SF4 SF4 . 
QC 66 FES Y 1 803 719 FES FES . 
RC 67 SF4 a 1 301 208 SF4 SF4 . 
SC 67 SF4 b 1 301 213 SF4 SF4 . 
TC 67 SF4 b 1 302 214 SF4 SF4 . 
UC 67 SF4 c 1 501 457 SF4 SF4 . 
VC 68 FMN c 1 502 458 FMN FMN . 
WC 66 FES d 1 301 217 FES FES . 
XC 69 NDP p 1 401 378 NDP NDP . 
YC 70 ZN 3 1 101 99 ZN ZN . 
ZC 71 HEA y 1 601 515 HEA HEA . 
AD 71 HEA y 1 602 516 HEA HEA . 
BD 72 CU y 1 603 517 CU CU . 
CD 73 MG y 1 604 518 MG MG . 
DD 72 CU z 1 301 228 CU CU . 
ED 72 CU z 1 302 229 CU CU . 
#
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 . . . HC 64 215.964 294.152 250.128 1 7.22 ? CHA HEM 402 C 1 
HETATM 2 C CHB HEM . . . HC 64 215.581 291.98 245.882 1 2.16 ? CHB HEM 402 C 1 
HETATM 3 C CHC HEM . . . HC 64 219.112 294.63 244.147 1 5.68 ? CHC HEM 402 C 1 
HETATM 4 C CHD HEM . . . HC 64 220.125 296.088 248.561 1 5.79 ? CHD HEM 402 C 1 
HETATM 5 C C1A HEM . . . HC 64 215.468 293.378 249.096 1 6.65 ? C1A HEM 402 C 1 
HETATM 6 C C2A HEM . . . HC 64 214.201 292.677 249.073 1 6.33 ? C2A HEM 402 C 1 
HETATM 7 C C3A HEM . . . HC 64 214.079 292.064 247.893 1 5.74 ? C3A HEM 402 C 1 
HETATM 8 C C4A HEM . . . HC 64 215.289 292.312 247.125 1 2.16 ? C4A HEM 402 C 1 
HETATM 9 C CMA HEM . . . HC 64 212.97 291.178 247.318 1 4.26 ? CMA HEM 402 C 1 
HETATM 10 C CAA HEM . . . HC 64 213.233 292.786 250.266 1 5.21 ? CAA HEM 402 C 1 
HETATM 11 C CBA HEM . . . HC 64 212.267 293.979 250.227 1 9.28 ? CBA HEM 402 C 1 
HETATM 12 C CGA HEM . . . HC 64 212.707 295.401 250.231 1 7.04 ? CGA HEM 402 C 1 
HETATM 13 O O1A HEM . . . HC 64 212.468 296.141 249.239 1 12.08 ? O1A HEM 402 C 1 
HETATM 14 O O2A HEM . . . HC 64 213.319 295.931 251.176 1 2.22 ? O2A HEM 402 C 1 
HETATM 15 C C1B HEM . . . HC 64 216.494 292.424 244.998 1 4.75 ? C1B HEM 402 C 1 
HETATM 16 C C2B HEM . . . HC 64 216.706 292.026 243.633 1 2.16 ? C2B HEM 402 C 1 
HETATM 17 C C3B HEM . . . HC 64 217.69 292.792 243.138 1 5.88 ? C3B HEM 402 C 1 
HETATM 18 C C4B HEM . . . HC 64 218.146 293.649 244.209 1 5.51 ? C4B HEM 402 C 1 
HETATM 19 C CMB HEM . . . HC 64 215.848 290.977 242.896 1 2.16 ? CMB HEM 402 C 1 
HETATM 20 C CAB HEM . . . HC 64 218.336 292.851 241.756 1 6.07 ? CAB HEM 402 C 1 
HETATM 21 C CBB HEM . . . HC 64 218.877 291.809 241.143 1 8.66 ? CBB HEM 402 C 1 
HETATM 22 C C1C HEM . . . HC 64 219.705 295.334 245.175 1 6.15 ? C1C HEM 402 C 1 
HETATM 23 C C2C HEM . . . HC 64 220.877 296.246 245.058 1 2.16 ? C2C HEM 402 C 1 
HETATM 24 C C3C HEM . . . HC 64 221.193 296.533 246.347 1 2.16 ? C3C HEM 402 C 1 
HETATM 25 C C4C HEM . . . HC 64 220.153 295.964 247.195 1 6.01 ? C4C HEM 402 C 1 
HETATM 26 C CMC HEM . . . HC 64 221.553 296.583 243.744 1 7.42 ? CMC HEM 402 C 1 
HETATM 27 C CAC HEM . . . HC 64 222.205 297.513 246.885 1 4.81 ? CAC HEM 402 C 1 
HETATM 28 C CBC HEM . . . HC 64 223.396 297.702 246.35 1 2.8 ? CBC HEM 402 C 1 
HETATM 29 C C1D HEM . . . HC 64 219.079 295.718 249.359 1 5.93 ? C1D HEM 402 C 1 
HETATM 30 C C2D HEM . . . HC 64 218.982 296.029 250.755 1 2.16 ? C2D HEM 402 C 1 
HETATM 31 C C3D HEM . . . HC 64 217.813 295.521 251.221 1 6.28 ? C3D HEM 402 C 1 
HETATM 32 C C4D HEM . . . HC 64 217.17 294.826 250.121 1 6.05 ? C4D HEM 402 C 1 
HETATM 33 C CMD HEM . . . HC 64 219.99 296.832 251.594 1 6.78 ? CMD HEM 402 C 1 
HETATM 34 C CAD HEM . . . HC 64 217.213 295.587 252.653 1 2.16 ? CAD HEM 402 C 1 
HETATM 35 C CBD HEM . . . HC 64 216.504 296.855 253.12 1 2.16 ? CBD HEM 402 C 1 
HETATM 36 C CGD HEM . . . HC 64 215.728 296.863 254.353 1 4.71 ? CGD HEM 402 C 1 
HETATM 37 O O1D HEM . . . HC 64 214.605 296.349 254.336 1 2.16 ? O1D HEM 402 C 1 
HETATM 38 O O2D HEM . . . HC 64 216.254 297.389 255.364 1 2.52 ? O2D HEM 402 C 1 
HETATM 39 N NA HEM . . . HC 64 216.1 293.153 247.884 1 4.53 ? NA HEM 402 C 1 
HETATM 40 N NB HEM . . . HC 64 217.403 293.414 245.35 1 6.68 ? NB HEM 402 C 1 
HETATM 41 N NC HEM . . . HC 64 219.205 295.266 246.5 1 2.16 ? NC HEM 402 C 1 
HETATM 42 N ND HEM . . . HC 64 217.956 294.999 249.006 1 2.16 ? ND HEM 402 C 1 
HETATM 43 FE FE HEM . . . HC 64 217.606 294.23 247.176 1 2.58 ? FE HEM 402 C 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    105 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#