data_5GPN
#
_model_server_result.job_id            XYjUSfk_2qGWcWyOCJKWnw 
_model_server_result.datetime_utc      '2025-02-05 13:01:29' 
_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":"IC","auth_seq_id":301}' 
#
_entry.id    5GPN 
#
_exptl.entry_id    5GPN 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              618.503 
_entity.id                          65 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            'HEME C' 
_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    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
? 65 IC N N 
? 65 MC 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 H34 Fe N4 O4' 
_chem_comp.formula_weight    618.503 
_chem_comp.id                HEC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'HEME C' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
FE NA HEC sing 310 n n 
FE NB HEC sing 311 n n 
FE NC HEC sing 312 n n 
FE ND HEC sing 313 n n 
CHA C1A HEC doub 314 n n 
CHA C4D HEC sing 315 n n 
CHA HHA HEC sing 316 n n 
CHB C4A HEC doub 317 n n 
CHB C1B HEC sing 318 n n 
CHB HHB HEC sing 319 n n 
CHC C4B HEC doub 320 n n 
CHC C1C HEC sing 321 n n 
CHC HHC HEC sing 322 n n 
CHD C4C HEC doub 323 n n 
CHD C1D HEC sing 324 n n 
CHD HHD HEC sing 325 n n 
NA C1A HEC sing 326 n y 
NA C4A HEC sing 327 n y 
C1A C2A HEC sing 328 n y 
C2A C3A HEC doub 329 n y 
C2A CAA HEC sing 330 n n 
C3A C4A HEC sing 331 n y 
C3A CMA HEC sing 332 n n 
CMA HMA1 HEC sing 333 n n 
CMA HMA2 HEC sing 334 n n 
CMA HMA3 HEC sing 335 n n 
CAA CBA HEC sing 336 n n 
CAA HAA1 HEC sing 337 n n 
CAA HAA2 HEC sing 338 n n 
CBA CGA HEC sing 339 n n 
CBA HBA1 HEC sing 340 n n 
CBA HBA2 HEC sing 341 n n 
CGA O1A HEC doub 342 n n 
CGA O2A HEC sing 343 n n 
O2A H2A HEC sing 344 n n 
NB C1B HEC sing 345 n y 
NB C4B HEC sing 346 n y 
C1B C2B HEC doub 347 n y 
C2B C3B HEC sing 348 n y 
C2B CMB HEC sing 349 n n 
C3B C4B HEC sing 350 n y 
C3B CAB HEC doub 351 e n 
CMB HMB1 HEC sing 352 n n 
CMB HMB2 HEC sing 353 n n 
CMB HMB3 HEC sing 354 n n 
CAB CBB HEC sing 355 n n 
CAB HAB HEC sing 356 n n 
CBB HBB1 HEC sing 357 n n 
CBB HBB2 HEC sing 358 n n 
CBB HBB3 HEC sing 359 n n 
NC C1C HEC sing 360 n y 
NC C4C HEC sing 361 n y 
C1C C2C HEC doub 362 n y 
C2C C3C HEC sing 363 n y 
C2C CMC HEC sing 364 n n 
C3C C4C HEC sing 365 n y 
C3C CAC HEC doub 366 e n 
CMC HMC1 HEC sing 367 n n 
CMC HMC2 HEC sing 368 n n 
CMC HMC3 HEC sing 369 n n 
CAC CBC HEC sing 370 n n 
CAC HAC HEC sing 371 n n 
CBC HBC1 HEC sing 372 n n 
CBC HBC2 HEC sing 373 n n 
CBC HBC3 HEC sing 374 n n 
ND C1D HEC sing 375 n y 
ND C4D HEC sing 376 n y 
C1D C2D HEC doub 377 n y 
C2D C3D HEC sing 378 n y 
C2D CMD HEC sing 379 n n 
C3D C4D HEC doub 380 n y 
C3D CAD HEC sing 381 n n 
CMD HMD1 HEC sing 382 n n 
CMD HMD2 HEC sing 383 n n 
CMD HMD3 HEC sing 384 n n 
CAD CBD HEC sing 385 n n 
CAD HAD1 HEC sing 386 n n 
CAD HAD2 HEC sing 387 n n 
CBD CGD HEC sing 388 n n 
CBD HBD1 HEC sing 389 n n 
CBD HBD2 HEC sing 390 n n 
CGD O1D HEC doub 391 n n 
CGD O2D HEC sing 392 n n 
O2D H2D HEC sing 393 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 FE FE HEC . . . IC 65 211.861 306.095 199.7 1 37.14 ? FE HEC 301 D 1 
HETATM 2 C CHA HEC . . . IC 65 214.363 307.428 201.601 1 45.12 ? CHA HEC 301 D 1 
HETATM 3 C CHB HEC . . . IC 65 209.907 305.771 202.468 1 36.26 ? CHB HEC 301 D 1 
HETATM 4 C CHC HEC . . . IC 65 209.2 305.394 197.713 1 36.23 ? CHC HEC 301 D 1 
HETATM 5 C CHD HEC . . . IC 65 213.935 306.007 197.012 1 35.99 ? CHD HEC 301 D 1 
HETATM 6 N NA HEC . . . IC 65 212.13 306.383 201.669 1 40.51 ? NA HEC 301 D 1 
HETATM 7 C C1A HEC . . . IC 65 213.161 307.132 202.218 1 44.71 ? C1A HEC 301 D 1 
HETATM 8 C C2A HEC . . . IC 65 212.768 307.583 203.536 1 43.95 ? C2A HEC 301 D 1 
HETATM 9 C C3A HEC . . . IC 65 211.542 307.141 203.781 1 41.38 ? C3A HEC 301 D 1 
HETATM 10 C C4A HEC . . . IC 65 211.125 306.387 202.622 1 40.65 ? C4A HEC 301 D 1 
HETATM 11 C CMA HEC . . . IC 65 210.659 307.358 205.026 1 44.54 ? CMA HEC 301 D 1 
HETATM 12 C CAA HEC . . . IC 65 213.675 308.465 204.415 1 44.22 ? CAA HEC 301 D 1 
HETATM 13 C CBA HEC . . . IC 65 214.026 307.859 205.761 1 43.01 ? CBA HEC 301 D 1 
HETATM 14 C CGA HEC . . . IC 65 215.33 308.427 206.275 1 46.99 ? CGA HEC 301 D 1 
HETATM 15 O O1A HEC . . . IC 65 216.357 308.003 205.694 1 44.75 ? O1A HEC 301 D 1 
HETATM 16 O O2A HEC . . . IC 65 215.258 309.265 207.201 1 52.37 ? O2A HEC 301 D 1 
HETATM 17 N NB HEC . . . IC 65 209.938 305.666 200.023 1 34.03 ? NB HEC 301 D 1 
HETATM 18 C C1B HEC . . . IC 65 209.312 305.572 201.244 1 33.91 ? C1B HEC 301 D 1 
HETATM 19 C C2B HEC . . . IC 65 207.926 305.225 201.035 1 34.42 ? C2B HEC 301 D 1 
HETATM 20 C C3B HEC . . . IC 65 207.723 305.122 199.725 1 35.55 ? C3B HEC 301 D 1 
HETATM 21 C C4B HEC . . . IC 65 208.977 305.394 199.07 1 34.26 ? C4B HEC 301 D 1 
HETATM 22 C CMB HEC . . . IC 65 206.921 305.042 202.185 1 35.89 ? CMB HEC 301 D 1 
HETATM 23 C CAB HEC . . . IC 65 206.403 304.756 198.987 1 35.37 ? CAB HEC 301 D 1 
HETATM 24 C CBB HEC . . . IC 65 205.277 305.403 199.365 1 37.04 ? CBB HEC 301 D 1 
HETATM 25 N NC HEC . . . IC 65 211.61 305.789 197.742 1 37.24 ? NC HEC 301 D 1 
HETATM 26 C C1C HEC . . . IC 65 210.43 305.447 197.111 1 36.11 ? C1C HEC 301 D 1 
HETATM 27 C C2C HEC . . . IC 65 210.705 305.157 195.726 1 36.11 ? C2C HEC 301 D 1 
HETATM 28 C C3C HEC . . . IC 65 212.015 305.336 195.547 1 35.54 ? C3C HEC 301 D 1 
HETATM 29 C C4C HEC . . . IC 65 212.609 305.728 196.789 1 35.45 ? C4C HEC 301 D 1 
HETATM 30 C CMC HEC . . . IC 65 209.656 304.732 194.68 1 34.36 ? CMC HEC 301 D 1 
HETATM 31 C CAC HEC . . . IC 65 212.749 305.122 194.199 1 32.93 ? CAC HEC 301 D 1 
HETATM 32 C CBC HEC . . . IC 65 212.268 305.883 193.18 1 35.78 ? CBC HEC 301 D 1 
HETATM 33 N ND HEC . . . IC 65 213.758 306.652 199.356 1 43.18 ? ND HEC 301 D 1 
HETATM 34 C C1D HEC . . . IC 65 214.476 306.452 198.19 1 41.36 ? C1D HEC 301 D 1 
HETATM 35 C C2D HEC . . . IC 65 215.864 306.797 198.435 1 44.43 ? C2D HEC 301 D 1 
HETATM 36 C C3D HEC . . . IC 65 215.979 307.199 199.706 1 45.52 ? C3D HEC 301 D 1 
HETATM 37 C C4D HEC . . . IC 65 214.66 307.115 200.297 1 44.37 ? C4D HEC 301 D 1 
HETATM 38 C CMD HEC . . . IC 65 216.948 306.697 197.34 1 45.19 ? CMD HEC 301 D 1 
HETATM 39 C CAD HEC . . . IC 65 217.188 307.694 200.529 1 45.54 ? CAD HEC 301 D 1 
HETATM 40 C CBD HEC . . . IC 65 217.14 309.106 201.098 1 48.43 ? CBD HEC 301 D 1 
HETATM 41 C CGD HEC . . . IC 65 218.459 309.691 201.531 1 50.72 ? CGD HEC 301 D 1 
HETATM 42 O O1D HEC . . . IC 65 218.56 310.935 201.437 1 53.07 ? O1D HEC 301 D 1 
HETATM 43 O O2D HEC . . . IC 65 219.3 308.846 201.938 1 53.31 ? O2D HEC 301 D 1 
#
_model_server_stats.io_time_ms              39 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    133 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#