data_9GCX
#
_model_server_result.job_id            i_C5nTUfkQlV0E8oBVt5Ww 
_model_server_result.datetime_utc      '2025-01-22 19:47:44' 
_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          9gcx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":502}' 
#
_entry.id    9GCX 
#
_exptl.entry_id    9GCX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          13 
_entity.src_method                  nat 
_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                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            9GCX 
_cell.length_a            210.082 
_cell.length_b            210.082 
_cell.length_c            344.844 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9GCX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
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 1 1 
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 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' 10_445 -y-1,-x-1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -105.041 -181.936349 57.474 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 13 N N N 
? 13 O 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf2 H SG CYS 55 H CYS 24 1_555 H SG CYS 99 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf3 H SG CYS 71 H CYS 40 1_555 H SG CYS 85 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
covale ? covale1 D SG CYS 121 D CYS 37 1_555 V CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.759 ? 
covale ? covale2 D SG CYS 124 D CYS 40 1_555 V CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? 
metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 N FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 O FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 N FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 O FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc5 D NE2 HIS 125 D HIS 41 1_555 V FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? 
metalc ? metalc6 D SD MET 244 D MET 160 1_555 V FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc7 E SG CYS 217 E CYS 139 1_555 X FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc8 E ND1 HIS 219 E HIS 141 1_555 X FE2 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc9 E SG CYS 236 E CYS 158 1_555 X FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc10 E ND1 HIS 239 E HIS 161 1_555 X FE2 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_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 523 n n 
CHA C4D HEM doub 524 n n 
CHA HHA HEM sing 525 n n 
CHB C4A HEM sing 526 n n 
CHB C1B HEM doub 527 n n 
CHB HHB HEM sing 528 n n 
CHC C4B HEM sing 529 n n 
CHC C1C HEM doub 530 n n 
CHC HHC HEM sing 531 n n 
CHD C4C HEM doub 532 n n 
CHD C1D HEM sing 533 n n 
CHD HHD HEM sing 534 n n 
C1A C2A HEM doub 535 n y 
C1A NA HEM sing 536 n y 
C2A C3A HEM sing 537 n y 
C2A CAA HEM sing 538 n n 
C3A C4A HEM doub 539 n y 
C3A CMA HEM sing 540 n n 
C4A NA HEM sing 541 n y 
CMA HMA HEM sing 542 n n 
CMA HMAA HEM sing 543 n n 
CMA HMAB HEM sing 544 n n 
CAA CBA HEM sing 545 n n 
CAA HAA HEM sing 546 n n 
CAA HAAA HEM sing 547 n n 
CBA CGA HEM sing 548 n n 
CBA HBA HEM sing 549 n n 
CBA HBAA HEM sing 550 n n 
CGA O1A HEM doub 551 n n 
CGA O2A HEM sing 552 n n 
C1B C2B HEM sing 553 n n 
C1B NB HEM sing 554 n n 
C2B C3B HEM doub 555 n n 
C2B CMB HEM sing 556 n n 
C3B C4B HEM sing 557 n n 
C3B CAB HEM sing 558 n n 
C4B NB HEM doub 559 n n 
CMB HMB HEM sing 560 n n 
CMB HMBA HEM sing 561 n n 
CMB HMBB HEM sing 562 n n 
CAB CBB HEM doub 563 n n 
CAB HAB HEM sing 564 n n 
CBB HBB HEM sing 565 n n 
CBB HBBA HEM sing 566 n n 
C1C C2C HEM sing 567 n y 
C1C NC HEM sing 568 n y 
C2C C3C HEM doub 569 n y 
C2C CMC HEM sing 570 n n 
C3C C4C HEM sing 571 n y 
C3C CAC HEM sing 572 n n 
C4C NC HEM sing 573 n y 
CMC HMC HEM sing 574 n n 
CMC HMCA HEM sing 575 n n 
CMC HMCB HEM sing 576 n n 
CAC CBC HEM doub 577 n n 
CAC HAC HEM sing 578 n n 
CBC HBC HEM sing 579 n n 
CBC HBCA HEM sing 580 n n 
C1D C2D HEM sing 581 n n 
C1D ND HEM doub 582 n n 
C2D C3D HEM doub 583 n n 
C2D CMD HEM sing 584 n n 
C3D C4D HEM sing 585 n n 
C3D CAD HEM sing 586 n n 
C4D ND HEM sing 587 n n 
CMD HMD HEM sing 588 n n 
CMD HMDA HEM sing 589 n n 
CMD HMDB HEM sing 590 n n 
CAD CBD HEM sing 591 n n 
CAD HAD HEM sing 592 n n 
CAD HADA HEM sing 593 n n 
CBD CGD HEM sing 594 n n 
CBD HBD HEM sing 595 n n 
CBD HBDA HEM sing 596 n n 
CGD O1D HEM doub 597 n n 
CGD O2D HEM sing 598 n n 
O2A H2A HEM sing 599 n n 
O2D H2D HEM sing 600 n n 
FE NA HEM sing 601 n n 
FE NB HEM sing 602 n n 
FE NC HEM sing 603 n n 
FE ND HEM sing 604 n n 
#
_atom_sites.entry_id                     9GCX 
_atom_sites.fract_transf_matrix[1][1]    0.00476 
_atom_sites.fract_transf_matrix[1][2]    0.002748 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005496 
_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]    0.0029 
_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 11 LOP A 1 501 501 LOP LOP . 
M 12 CDL A 1 502 502 CDL CDL . 
N 13 HEM C 1 501 501 HEM HEM . 
O 13 HEM C 1 502 502 HEM HEM . 
P 11 LOP C 1 503 503 LOP LOP . 
Q 12 CDL C 1 504 504 CDL CDL . 
R 14 A1IKG C 1 505 509 A1IKG SG1 . 
S 11 LOP C 1 506 512 LOP LOP . 
T 11 LOP C 1 507 513 LOP LOP . 
U 15 LMT C 1 508 515 LMT LMT . 
V 16 HEC D 1 501 501 HEC HEC . 
W 12 CDL D 1 502 502 CDL CDL . 
X 17 FES E 1 201 201 FES FES . 
Y 11 LOP E 1 202 201 LOP LOP . 
Z 18 PSC E 1 203 202 PSC PSC . 
AA 19 SO4 F 1 201 3 SO4 SO4 . 
BA 11 LOP G 1 101 514 LOP LOP . 
CA 19 SO4 G 1 102 1 SO4 SO4 . 
DA 19 SO4 G 1 103 2 SO4 SO4 . 
EA 20 HOH A 1 601 301 HOH HOH . 
EA 20 HOH A 2 602 521 HOH HOH . 
EA 20 HOH A 3 603 518 HOH HOH . 
FA 20 HOH B 1 501 522 HOH HOH . 
GA 20 HOH C 1 601 16 HOH HOH . 
GA 20 HOH C 2 602 254 HOH HOH . 
GA 20 HOH C 3 603 523 HOH HOH . 
GA 20 HOH C 4 604 516 HOH HOH . 
HA 20 HOH E 1 301 514 HOH HOH . 
IA 20 HOH F 1 301 519 HOH HOH . 
#
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 13 -68.392 -65.194 38.398 1 98.81 ? CHA HEM 502 C 1 
HETATM 2 C CHB HEM . . . O 13 -66.01 -68.489 35.886 1 97.87 ? CHB HEM 502 C 1 
HETATM 3 C CHC HEM . . . O 13 -64.073 -70.079 39.987 1 97.61 ? CHC HEM 502 C 1 
HETATM 4 C CHD HEM . . . O 13 -67.25 -67.477 42.443 1 107.42 ? CHD HEM 502 C 1 
HETATM 5 C C1A HEM . . . O 13 -67.806 -65.897 37.37 1 95.54 ? C1A HEM 502 C 1 
HETATM 6 C C2A HEM . . . O 13 -67.957 -65.541 36.023 1 86.55 ? C2A HEM 502 C 1 
HETATM 7 C C3A HEM . . . O 13 -67.312 -66.453 35.267 1 77.16 ? C3A HEM 502 C 1 
HETATM 8 C C4A HEM . . . O 13 -66.748 -67.379 36.184 1 87.25 ? C4A HEM 502 C 1 
HETATM 9 C CMA HEM . . . O 13 -67.232 -66.469 33.771 1 62.54 ? CMA HEM 502 C 1 
HETATM 10 C CAA HEM . . . O 13 -68.705 -64.325 35.585 1 92.16 ? CAA HEM 502 C 1 
HETATM 11 C CBA HEM . . . O 13 -67.649 -63.229 35.335 1 111.03 ? CBA HEM 502 C 1 
HETATM 12 C CGA HEM . . . O 13 -67.14 -62.559 36.602 1 112.78 ? CGA HEM 502 C 1 
HETATM 13 O O1A HEM . . . O 13 -65.879 -62.576 36.908 1 103.49 ? O1A HEM 502 C 1 
HETATM 14 O O2A HEM . . . O 13 -68.029 -61.991 37.313 1 99.95 ? O2A HEM 502 C 1 
HETATM 15 C C1B HEM . . . O 13 -65.246 -69.182 36.814 1 86.45 ? C1B HEM 502 C 1 
HETATM 16 C C2B HEM . . . O 13 -64.316 -70.171 36.439 1 82.84 ? C2B HEM 502 C 1 
HETATM 17 C C3B HEM . . . O 13 -63.758 -70.632 37.564 1 90.47 ? C3B HEM 502 C 1 
HETATM 18 C C4B HEM . . . O 13 -64.398 -69.881 38.65 1 95.2 ? C4B HEM 502 C 1 
HETATM 19 C CMB HEM . . . O 13 -63.992 -70.611 35.056 1 82.75 ? CMB HEM 502 C 1 
HETATM 20 C CAB HEM . . . O 13 -62.714 -71.648 37.745 1 99.88 ? CAB HEM 502 C 1 
HETATM 21 C CBB HEM . . . O 13 -62.441 -72.602 36.863 1 107.26 ? CBB HEM 502 C 1 
HETATM 22 C C1C HEM . . . O 13 -64.736 -69.505 41.043 1 89.71 ? C1C HEM 502 C 1 
HETATM 23 C C2C HEM . . . O 13 -64.419 -69.668 42.397 1 96.24 ? C2C HEM 502 C 1 
HETATM 24 C C3C HEM . . . O 13 -65.335 -68.914 43.111 1 104.27 ? C3C HEM 502 C 1 
HETATM 25 C C4C HEM . . . O 13 -66.191 -68.293 42.139 1 98.63 ? C4C HEM 502 C 1 
HETATM 26 C CMC HEM . . . O 13 -63.292 -70.492 42.954 1 96.69 ? CMC HEM 502 C 1 
HETATM 27 C CAC HEM . . . O 13 -65.427 -68.767 44.593 1 99.06 ? CAC HEM 502 C 1 
HETATM 28 C CBC HEM . . . O 13 -64.727 -69.495 45.458 1 87.16 ? CBC HEM 502 C 1 
HETATM 29 C C1D HEM . . . O 13 -67.802 -66.628 41.507 1 108.61 ? C1D HEM 502 C 1 
HETATM 30 C C2D HEM . . . O 13 -68.747 -65.568 41.894 1 112.11 ? C2D HEM 502 C 1 
HETATM 31 C C3D HEM . . . O 13 -69.076 -64.93 40.767 1 101.71 ? C3D HEM 502 C 1 
HETATM 32 C C4D HEM . . . O 13 -68.329 -65.623 39.708 1 98.42 ? C4D HEM 502 C 1 
HETATM 33 C CMD HEM . . . O 13 -69.264 -65.242 43.271 1 124.12 ? CMD HEM 502 C 1 
HETATM 34 C CAD HEM . . . O 13 -70.029 -63.763 40.639 1 102.58 ? CAD HEM 502 C 1 
HETATM 35 C CBD HEM . . . O 13 -69.29 -62.432 40.657 1 111.28 ? CBD HEM 502 C 1 
HETATM 36 C CGD HEM . . . O 13 -70.203 -61.238 40.502 1 104.33 ? CGD HEM 502 C 1 
HETATM 37 O O1D HEM . . . O 13 -71.122 -61.207 39.643 1 95.9 ? O1D HEM 502 C 1 
HETATM 38 O O2D HEM . . . O 13 -70.003 -60.254 41.246 1 91.56 ? O2D HEM 502 C 1 
HETATM 39 N NA HEM . . . O 13 -67.059 -67.033 37.452 1 89.75 ? NA HEM 502 C 1 
HETATM 40 N NB HEM . . . O 13 -65.266 -69.052 38.114 1 86.47 ? NB HEM 502 C 1 
HETATM 41 N NC HEM . . . O 13 -65.793 -68.682 40.899 1 86.05 ? NC HEM 502 C 1 
HETATM 42 N ND HEM . . . O 13 -67.587 -66.633 40.188 1 100.54 ? ND HEM 502 C 1 
HETATM 43 FE FE HEM . . . O 13 -66.471 -67.762 39.182 1 86.88 ? FE HEM 502 C 1 
#
_model_server_stats.io_time_ms              42 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           347 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#