data_4PD4
#
_model_server_result.job_id            Xa40z0-UvMmsFlG9ZVmZLw 
_model_server_result.datetime_utc      '2024-11-16 21:49:26' 
_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          4pd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":4002}' 
#
_entry.id    4PD4 
#
_exptl.entry_id    4PD4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          14 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          115.18 
_cell.angle_gamma         90 
_cell.entry_id            4PD4 
_cell.length_a            212.26 
_cell.length_b            150.88 
_cell.length_c            143.09 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PD4 
_symmetry.cell_setting             . 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    22-meric 
_pdbx_struct_assembly.oligomeric_count      22 
_pdbx_struct_assembly.details               author_and_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_756 -x+2,y,-z+1 -1 0 0 0 1 0 0 0 -1 363.640439 0 129.492962 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 14 N N N 
? 14 O N N 
? 14 T 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 134 E CYS 164 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
disulf ? disulf2 F SG CYS 28 F CYS 101 1_555 F SG CYS 50 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf3 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf4 K SG CYS 23 K CYS 23 1_555 K SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
metalc ? metalc1 C NE2 HIS 82 C HIS 82 1_555 N FE HEM . C HEM 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? 
metalc ? metalc2 C NE2 HIS 96 C HIS 96 1_555 O FE HEM . C HEM 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 N FE HEM . C HEM 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 O FE HEM . C HEM 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 T FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc6 D SD MET 164 D MET 225 1_555 T FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc7 E SG CYS 129 E CYS 159 1_555 U FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc8 E ND1 HIS 131 E HIS 161 1_555 U FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc9 E SG CYS 148 E CYS 178 1_555 U FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc10 E ND1 HIS 151 E HIS 181 1_555 U FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? 
#
_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 437 n n 
CHA C4D HEM doub 438 n n 
CHA HHA HEM sing 439 n n 
CHB C4A HEM sing 440 n n 
CHB C1B HEM doub 441 n n 
CHB HHB HEM sing 442 n n 
CHC C4B HEM sing 443 n n 
CHC C1C HEM doub 444 n n 
CHC HHC HEM sing 445 n n 
CHD C4C HEM doub 446 n n 
CHD C1D HEM sing 447 n n 
CHD HHD HEM sing 448 n n 
C1A C2A HEM doub 449 n y 
C1A NA HEM sing 450 n y 
C2A C3A HEM sing 451 n y 
C2A CAA HEM sing 452 n n 
C3A C4A HEM doub 453 n y 
C3A CMA HEM sing 454 n n 
C4A NA HEM sing 455 n y 
CMA HMA HEM sing 456 n n 
CMA HMAA HEM sing 457 n n 
CMA HMAB HEM sing 458 n n 
CAA CBA HEM sing 459 n n 
CAA HAA HEM sing 460 n n 
CAA HAAA HEM sing 461 n n 
CBA CGA HEM sing 462 n n 
CBA HBA HEM sing 463 n n 
CBA HBAA HEM sing 464 n n 
CGA O1A HEM doub 465 n n 
CGA O2A HEM sing 466 n n 
C1B C2B HEM sing 467 n n 
C1B NB HEM sing 468 n n 
C2B C3B HEM doub 469 n n 
C2B CMB HEM sing 470 n n 
C3B C4B HEM sing 471 n n 
C3B CAB HEM sing 472 n n 
C4B NB HEM doub 473 n n 
CMB HMB HEM sing 474 n n 
CMB HMBA HEM sing 475 n n 
CMB HMBB HEM sing 476 n n 
CAB CBB HEM doub 477 n n 
CAB HAB HEM sing 478 n n 
CBB HBB HEM sing 479 n n 
CBB HBBA HEM sing 480 n n 
C1C C2C HEM sing 481 n y 
C1C NC HEM sing 482 n y 
C2C C3C HEM doub 483 n y 
C2C CMC HEM sing 484 n n 
C3C C4C HEM sing 485 n y 
C3C CAC HEM sing 486 n n 
C4C NC HEM sing 487 n y 
CMC HMC HEM sing 488 n n 
CMC HMCA HEM sing 489 n n 
CMC HMCB HEM sing 490 n n 
CAC CBC HEM doub 491 n n 
CAC HAC HEM sing 492 n n 
CBC HBC HEM sing 493 n n 
CBC HBCA HEM sing 494 n n 
C1D C2D HEM sing 495 n n 
C1D ND HEM doub 496 n n 
C2D C3D HEM doub 497 n n 
C2D CMD HEM sing 498 n n 
C3D C4D HEM sing 499 n n 
C3D CAD HEM sing 500 n n 
C4D ND HEM sing 501 n n 
CMD HMD HEM sing 502 n n 
CMD HMDA HEM sing 503 n n 
CMD HMDB HEM sing 504 n n 
CAD CBD HEM sing 505 n n 
CAD HAD HEM sing 506 n n 
CAD HADA HEM sing 507 n n 
CBD CGD HEM sing 508 n n 
CBD HBD HEM sing 509 n n 
CBD HBDA HEM sing 510 n n 
CGD O1D HEM doub 511 n n 
CGD O2D HEM sing 512 n n 
O2A H2A HEM sing 513 n n 
O2D H2D HEM sing 514 n n 
FE NA HEM sing 515 n n 
FE NB HEM sing 516 n n 
FE NC HEM sing 517 n n 
FE ND HEM sing 518 n n 
#
_atom_sites.entry_id                     4PD4 
_atom_sites.fract_transf_matrix[1][1]    0.004711 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002215 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006628 
_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]    0.007722 
_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
L 12 UMQ A 1 501 721 UMQ UMQ . 
M 13 3PH A 1 502 713 3PH 3PH . 
N 14 HEM C 1 4001 4001 HEM HEM . 
O 14 HEM C 1 4002 4002 HEM HEM . 
P 15 AOQ C 1 4003 1 AOQ AOQ . 
Q 16 3PE C 1 4004 711 3PE 3PE . 
R 17 UQ6 C 1 4005 506 UQ6 UQ6 . 
S 13 3PH C 1 4006 710 3PH 3PH . 
T 14 HEM D 1 401 4003 HEM HEM . 
U 18 FES E 1 301 4004 FES FES . 
V 13 3PH E 1 302 714 3PH 3PH . 
#
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 . . . O 14 198.949 -2.167 69.187 1 7.55 ? CHA HEM 4002 C 1 
HETATM 2 C CHB HEM . . . O 14 196.439 -5.729 67.12 1 4.79 ? CHB HEM 4002 C 1 
HETATM 3 C CHC HEM . . . O 14 197.361 -8.391 70.996 1 4.28 ? CHC HEM 4002 C 1 
HETATM 4 C CHD HEM . . . O 14 198.072 -4.316 73.516 1 4.65 ? CHD HEM 4002 C 1 
HETATM 5 C C1A HEM . . . O 14 198.287 -2.902 68.219 1 6.33 ? C1A HEM 4002 C 1 
HETATM 6 C C2A HEM . . . O 14 198.096 -2.631 66.795 1 6.23 ? C2A HEM 4002 C 1 
HETATM 7 C C3A HEM . . . O 14 197.42 -3.636 66.261 1 6.8 ? C3A HEM 4002 C 1 
HETATM 8 C C4A HEM . . . O 14 197.135 -4.577 67.305 1 6.36 ? C4A HEM 4002 C 1 
HETATM 9 C CMA HEM . . . O 14 196.988 -3.779 64.789 1 8.16 ? CMA HEM 4002 C 1 
HETATM 10 C CAA HEM . . . O 14 198.568 -1.466 65.923 1 10.2 ? CAA HEM 4002 C 1 
HETATM 11 C CBA HEM . . . O 14 199.928 -1.875 65.377 1 10.47 ? CBA HEM 4002 C 1 
HETATM 12 C CGA HEM . . . O 14 200.801 -1.951 66.584 1 8.71 ? CGA HEM 4002 C 1 
HETATM 13 O O1A HEM . . . O 14 201.405 -3.044 66.785 1 7.56 ? O1A HEM 4002 C 1 
HETATM 14 O O2A HEM . . . O 14 200.815 -0.921 67.332 1 8.27 ? O2A HEM 4002 C 1 
HETATM 15 C C1B HEM . . . O 14 196.498 -6.772 67.988 1 5.01 ? C1B HEM 4002 C 1 
HETATM 16 C C2B HEM . . . O 14 195.904 -8.08 67.748 1 6.1 ? C2B HEM 4002 C 1 
HETATM 17 C C3B HEM . . . O 14 196.173 -8.837 68.835 1 5.4 ? C3B HEM 4002 C 1 
HETATM 18 C C4B HEM . . . O 14 196.909 -8.004 69.768 1 4.09 ? C4B HEM 4002 C 1 
HETATM 19 C CMB HEM . . . O 14 195.144 -8.475 66.452 1 3.34 ? CMB HEM 4002 C 1 
HETATM 20 C CAB HEM . . . O 14 195.743 -10.297 69.127 1 3.41 ? CAB HEM 4002 C 1 
HETATM 21 C CBB HEM . . . O 14 194.606 -10.81 68.646 1 2.26 ? CBB HEM 4002 C 1 
HETATM 22 C C1C HEM . . . O 14 197.625 -7.512 72.024 1 4.56 ? C1C HEM 4002 C 1 
HETATM 23 C C2C HEM . . . O 14 197.864 -7.928 73.37 1 3.13 ? C2C HEM 4002 C 1 
HETATM 24 C C3C HEM . . . O 14 198.092 -6.816 74.095 1 3.23 ? C3C HEM 4002 C 1 
HETATM 25 C C4C HEM . . . O 14 197.966 -5.664 73.204 1 4.31 ? C4C HEM 4002 C 1 
HETATM 26 C CMC HEM . . . O 14 197.868 -9.434 73.709 1 2.25 ? CMC HEM 4002 C 1 
HETATM 27 C CAC HEM . . . O 14 198.395 -6.677 75.606 1 2.64 ? CAC HEM 4002 C 1 
HETATM 28 C CBC HEM . . . O 14 198.329 -7.682 76.488 1 2.76 ? CBC HEM 4002 C 1 
HETATM 29 C C1D HEM . . . O 14 198.409 -3.321 72.619 1 4.73 ? C1D HEM 4002 C 1 
HETATM 30 C C2D HEM . . . O 14 198.785 -1.959 72.907 1 4.32 ? C2D HEM 4002 C 1 
HETATM 31 C C3D HEM . . . O 14 199.064 -1.306 71.564 1 4.66 ? C3D HEM 4002 C 1 
HETATM 32 C C4D HEM . . . O 14 198.833 -2.328 70.571 1 6.45 ? C4D HEM 4002 C 1 
HETATM 33 C CMD HEM . . . O 14 198.894 -1.281 74.274 1 5.1 ? CMD HEM 4002 C 1 
HETATM 34 C CAD HEM . . . O 14 199.516 0.13 71.314 1 5.09 ? CAD HEM 4002 C 1 
HETATM 35 C CBD HEM . . . O 14 200.959 0.002 70.843 1 6.88 ? CBD HEM 4002 C 1 
HETATM 36 C CGD HEM . . . O 14 201.534 1.344 70.472 1 10.6 ? CGD HEM 4002 C 1 
HETATM 37 O O1D HEM . . . O 14 202.263 1.405 69.447 1 11.87 ? O1D HEM 4002 C 1 
HETATM 38 O O2D HEM . . . O 14 201.252 2.358 71.165 1 11.75 ? O2D HEM 4002 C 1 
HETATM 39 N NA HEM . . . O 14 197.686 -4.11 68.487 1 6.06 ? NA HEM 4002 C 1 
HETATM 40 N NB HEM . . . O 14 197.095 -6.75 69.227 1 4.58 ? NB HEM 4002 C 1 
HETATM 41 N NC HEM . . . O 14 197.679 -6.125 71.946 1 4.51 ? NC HEM 4002 C 1 
HETATM 42 N ND HEM . . . O 14 198.441 -3.488 71.243 1 5.18 ? ND HEM 4002 C 1 
HETATM 43 FE FE HEM . . . O 14 197.661 -5.047 70.185 1 3.26 ? FE HEM 4002 C 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#