data_5NMI
#
_model_server_result.job_id            Zem40M7fGPV9o2WxWeheYg 
_model_server_result.datetime_utc      '2025-07-16 14:23:26' 
_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          5nmi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":501}' 
#
_entry.id    5NMI 
#
_exptl.entry_id    5NMI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          11 
_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            5NMI 
_cell.length_a            129.477 
_cell.length_b            129.477 
_cell.length_c            720.294 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NMI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    22-meric 
_pdbx_struct_assembly.oligomeric_count      22 
_pdbx_struct_assembly.details               software_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 
_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    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
? 11 W N N 
? 11 X N N 
? 11 IA N N 
? 11 JA 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
disulf ? disulf1 E SG CYS 222 E CYS 144 1_555 E SG CYS 238 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf2 H SG CYS 37 H CYS 24 1_555 H SG CYS 81 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 H SG CYS 53 H CYS 40 1_555 H SG CYS 67 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf4 S SG CYS 37 U CYS 24 1_555 S SG CYS 81 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf5 S SG CYS 53 U CYS 40 1_555 S SG CYS 67 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
covale ? covale1 D SG CYS 36 D CYS 37 1_555 CA CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? 
covale ? covale2 D SG CYS 39 D CYS 40 1_555 CA CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.665 ? 
covale ? covale3 O SG CYS 36 Q CYS 37 1_555 OA CAB HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.626 ? 
covale ? covale4 O SG CYS 39 Q CYS 40 1_555 OA CAC HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.678 ? 
metalc ? metalc1 C NE2 HIS 76 C HIS 83 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? 
metalc ? metalc2 C NE2 HIS 90 C HIS 97 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? 
metalc ? metalc3 C NE2 HIS 175 C HIS 182 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? 
metalc ? metalc4 C NE2 HIS 189 C HIS 196 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc5 D NE2 HIS 40 D HIS 41 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? 
metalc ? metalc6 D SD MET 159 D MET 160 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
metalc ? metalc7 E SG CYS 217 E CYS 139 1_555 FA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc8 E ND1 HIS 219 E HIS 141 1_555 FA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? 
metalc ? metalc9 E SG CYS 236 E CYS 158 1_555 FA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc10 E ND1 HIS 239 E HIS 161 1_555 FA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? 
metalc ? metalc11 N NE2 HIS 76 P HIS 83 1_555 IA FE HEM . P HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? 
metalc ? metalc12 N NE2 HIS 90 P HIS 97 1_555 JA FE HEM . P HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? 
metalc ? metalc13 N NE2 HIS 175 P HIS 182 1_555 IA FE HEM . P HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? 
metalc ? metalc14 N NE2 HIS 189 P HIS 196 1_555 JA FE HEM . P HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? 
metalc ? metalc15 O NE2 HIS 40 Q HIS 41 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? 
metalc ? metalc16 O SD MET 159 Q MET 160 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
#
_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 472 n n 
CHA C4D HEM doub 473 n n 
CHA HHA HEM sing 474 n n 
CHB C4A HEM sing 475 n n 
CHB C1B HEM doub 476 n n 
CHB HHB HEM sing 477 n n 
CHC C4B HEM sing 478 n n 
CHC C1C HEM doub 479 n n 
CHC HHC HEM sing 480 n n 
CHD C4C HEM doub 481 n n 
CHD C1D HEM sing 482 n n 
CHD HHD HEM sing 483 n n 
C1A C2A HEM doub 484 n y 
C1A NA HEM sing 485 n y 
C2A C3A HEM sing 486 n y 
C2A CAA HEM sing 487 n n 
C3A C4A HEM doub 488 n y 
C3A CMA HEM sing 489 n n 
C4A NA HEM sing 490 n y 
CMA HMA HEM sing 491 n n 
CMA HMAA HEM sing 492 n n 
CMA HMAB HEM sing 493 n n 
CAA CBA HEM sing 494 n n 
CAA HAA HEM sing 495 n n 
CAA HAAA HEM sing 496 n n 
CBA CGA HEM sing 497 n n 
CBA HBA HEM sing 498 n n 
CBA HBAA HEM sing 499 n n 
CGA O1A HEM doub 500 n n 
CGA O2A HEM sing 501 n n 
C1B C2B HEM sing 502 n n 
C1B NB HEM sing 503 n n 
C2B C3B HEM doub 504 n n 
C2B CMB HEM sing 505 n n 
C3B C4B HEM sing 506 n n 
C3B CAB HEM sing 507 n n 
C4B NB HEM doub 508 n n 
CMB HMB HEM sing 509 n n 
CMB HMBA HEM sing 510 n n 
CMB HMBB HEM sing 511 n n 
CAB CBB HEM doub 512 n n 
CAB HAB HEM sing 513 n n 
CBB HBB HEM sing 514 n n 
CBB HBBA HEM sing 515 n n 
C1C C2C HEM sing 516 n y 
C1C NC HEM sing 517 n y 
C2C C3C HEM doub 518 n y 
C2C CMC HEM sing 519 n n 
C3C C4C HEM sing 520 n y 
C3C CAC HEM sing 521 n n 
C4C NC HEM sing 522 n y 
CMC HMC HEM sing 523 n n 
CMC HMCA HEM sing 524 n n 
CMC HMCB HEM sing 525 n n 
CAC CBC HEM doub 526 n n 
CAC HAC HEM sing 527 n n 
CBC HBC HEM sing 528 n n 
CBC HBCA HEM sing 529 n n 
C1D C2D HEM sing 530 n n 
C1D ND HEM doub 531 n n 
C2D C3D HEM doub 532 n n 
C2D CMD HEM sing 533 n n 
C3D C4D HEM sing 534 n n 
C3D CAD HEM sing 535 n n 
C4D ND HEM sing 536 n n 
CMD HMD HEM sing 537 n n 
CMD HMDA HEM sing 538 n n 
CMD HMDB HEM sing 539 n n 
CAD CBD HEM sing 540 n n 
CAD HAD HEM sing 541 n n 
CAD HADA HEM sing 542 n n 
CBD CGD HEM sing 543 n n 
CBD HBD HEM sing 544 n n 
CBD HBDA HEM sing 545 n n 
CGD O1D HEM doub 546 n n 
CGD O2D HEM sing 547 n n 
O2A H2A HEM sing 548 n n 
O2D H2D HEM sing 549 n n 
FE NA HEM sing 550 n n 
FE NB HEM sing 551 n n 
FE NC HEM sing 552 n n 
FE ND HEM sing 553 n n 
#
_atom_sites.entry_id                     5NMI 
_atom_sites.fract_transf_matrix[1][1]    0.007723 
_atom_sites.fract_transf_matrix[1][2]    0.004459 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008918 
_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]    0.001388 
_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
W 11 HEM C 1 501 501 HEM HEM . 
X 11 HEM C 1 502 502 HEM HEM . 
Y 12 MJM C 1 503 503 MJM MJM . 
Z 13 PEE C 1 504 504 PEE PEE . 
AA 14 CDL C 1 505 505 CDL CDL . 
BA 14 CDL C 1 506 501 CDL CDL . 
CA 15 HEC D 1 501 501 HEC HEC . 
DA 13 PEE D 1 502 502 PEE PEE . 
EA 14 CDL D 1 503 503 CDL CDL . 
FA 16 FES E 1 501 501 FES FES . 
GA 13 PEE E 1 502 502 PEE PEE . 
HA 14 CDL P 1 401 503 CDL CDL . 
IA 11 HEM P 1 402 501 HEM HEM . 
JA 11 HEM P 1 403 502 HEM HEM . 
KA 12 MJM P 1 404 503 MJM MJM . 
LA 13 PEE P 1 405 504 PEE PEE . 
MA 14 CDL P 1 406 505 CDL CDL . 
NA 14 CDL P 1 407 501 CDL CDL . 
OA 15 HEC Q 1 501 501 HEC HEC . 
PA 13 PEE R 1 201 502 PEE PEE . 
QA 13 PEE R 1 202 502 PEE PEE . 
#
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 . . . W 11 24.352 5.497 -17.724 1 60.09 ? CHA HEM 501 C 1 
HETATM 2 C CHB HEM . . . W 11 24.83 6.896 -13.121 1 63.35 ? CHB HEM 501 C 1 
HETATM 3 C CHC HEM . . . W 11 27.702 10.514 -14.552 1 57.96 ? CHC HEM 501 C 1 
HETATM 4 C CHD HEM . . . W 11 27.063 9.24 -19.173 1 54.77 ? CHD HEM 501 C 1 
HETATM 5 C C1A HEM . . . W 11 24.249 5.553 -16.358 1 62.12 ? C1A HEM 501 C 1 
HETATM 6 C C2A HEM . . . W 11 23.559 4.602 -15.56 1 61.97 ? C2A HEM 501 C 1 
HETATM 7 C C3A HEM . . . W 11 23.691 5.003 -14.259 1 54.42 ? C3A HEM 501 C 1 
HETATM 8 C C4A HEM . . . W 11 24.464 6.194 -14.263 1 58.01 ? C4A HEM 501 C 1 
HETATM 9 C CMA HEM . . . W 11 23.138 4.314 -13.021 1 54.13 ? CMA HEM 501 C 1 
HETATM 10 C CAA HEM . . . W 11 22.854 3.349 -16.064 1 70.53 ? CAA HEM 501 C 1 
HETATM 11 C CBA HEM . . . W 11 23.923 2.24 -16.176 1 86.51 ? CBA HEM 501 C 1 
HETATM 12 C CGA HEM . . . W 11 23.389 0.973 -16.78 1 90.19 ? CGA HEM 501 C 1 
HETATM 13 O O1A HEM . . . W 11 22.852 0.107 -16.057 1 78.18 ? O1A HEM 501 C 1 
HETATM 14 O O2A HEM . . . W 11 23.508 0.783 -18.004 1 77.02 ? O2A HEM 501 C 1 
HETATM 15 C C1B HEM . . . W 11 25.683 8.014 -13.092 1 63.21 ? C1B HEM 501 C 1 
HETATM 16 C C2B HEM . . . W 11 26.07 8.712 -11.898 1 62.54 ? C2B HEM 501 C 1 
HETATM 17 C C3B HEM . . . W 11 26.9 9.737 -12.291 1 59.03 ? C3B HEM 501 C 1 
HETATM 18 C C4B HEM . . . W 11 26.971 9.63 -13.772 1 55.95 ? C4B HEM 501 C 1 
HETATM 19 C CMB HEM . . . W 11 25.666 8.361 -10.484 1 64.57 ? CMB HEM 501 C 1 
HETATM 20 C CAB HEM . . . W 11 27.548 10.828 -11.515 1 63.21 ? CAB HEM 501 C 1 
HETATM 21 C CBB HEM . . . W 11 27.218 11.186 -10.281 1 69.74 ? CBB HEM 501 C 1 
HETATM 22 C C1C HEM . . . W 11 27.779 10.498 -15.934 1 59 ? C1C HEM 501 C 1 
HETATM 23 C C2C HEM . . . W 11 28.439 11.464 -16.678 1 64.24 ? C2C HEM 501 C 1 
HETATM 24 C C3C HEM . . . W 11 28.247 11.14 -18.017 1 55.09 ? C3C HEM 501 C 1 
HETATM 25 C C4C HEM . . . W 11 27.49 9.919 -18.058 1 52.88 ? C4C HEM 501 C 1 
HETATM 26 C CMC HEM . . . W 11 29.174 12.648 -16.082 1 66.74 ? CMC HEM 501 C 1 
HETATM 27 C CAC HEM . . . W 11 28.828 11.847 -19.14 1 51.46 ? CAC HEM 501 C 1 
HETATM 28 C CBC HEM . . . W 11 29.681 12.871 -19.006 1 52.53 ? CBC HEM 501 C 1 
HETATM 29 C C1D HEM . . . W 11 26.26 8.098 -19.11 1 57.55 ? C1D HEM 501 C 1 
HETATM 30 C C2D HEM . . . W 11 25.874 7.383 -20.343 1 62.11 ? C2D HEM 501 C 1 
HETATM 31 C C3D HEM . . . W 11 25.129 6.341 -19.948 1 58.85 ? C3D HEM 501 C 1 
HETATM 32 C C4D HEM . . . W 11 25.063 6.423 -18.474 1 56.62 ? C4D HEM 501 C 1 
HETATM 33 C CMD HEM . . . W 11 26.188 7.686 -21.799 1 62.56 ? CMD HEM 501 C 1 
HETATM 34 C CAD HEM . . . W 11 24.482 5.335 -20.887 1 55.73 ? CAD HEM 501 C 1 
HETATM 35 C CBD HEM . . . W 11 25.356 4.094 -21.124 1 55.73 ? CBD HEM 501 C 1 
HETATM 36 C CGD HEM . . . W 11 25.083 3.036 -20.085 1 60.54 ? CGD HEM 501 C 1 
HETATM 37 O O1D HEM . . . W 11 26.051 2.522 -19.481 1 66.92 ? O1D HEM 501 C 1 
HETATM 38 O O2D HEM . . . W 11 23.904 2.685 -19.824 1 56.97 ? O2D HEM 501 C 1 
HETATM 39 N NA HEM . . . W 11 24.794 6.521 -15.551 1 60.94 ? NA HEM 501 C 1 
HETATM 40 N NB HEM . . . W 11 26.233 8.596 -14.162 1 59.32 ? NB HEM 501 C 1 
HETATM 41 N NC HEM . . . W 11 27.189 9.601 -16.77 1 53.35 ? NC HEM 501 C 1 
HETATM 42 N ND HEM . . . W 11 25.758 7.486 -18.005 1 54.55 ? ND HEM 501 C 1 
HETATM 43 FE FE HEM . . . W 11 25.978 8.003 -16.175 1 55.63 ? FE HEM 501 C 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           28 
_model_server_stats.create_model_time_ms    73 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#