data_6XVF
#
_model_server_result.job_id            iRqFcEu-TudHP9AM-AE7QA 
_model_server_result.datetime_utc      '2025-02-17 09:03:05' 
_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          6xvf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":402}' 
#
_entry.id    6XVF 
#
_exptl.entry_id    6XVF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          15 
_entity.src_method                  syn 
_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            6XVF 
_cell.length_a            209.869 
_cell.length_b            209.869 
_cell.length_c            342.418 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XVF 
_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    eicosameric 
_pdbx_struct_assembly.oligomeric_count      20 
_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,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA 
_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' 10_445 -y-1,-x-1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -104.9345 -181.751885 57.069667 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 15 P N N 
? 15 Q 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 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 H SG CYS 11 H CYS 24 1_555 H SG CYS 55 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf3 H SG CYS 27 H CYS 40 1_555 H SG CYS 41 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc1 C NE2 HIS 82 C HIS 83 1_555 P FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc2 C NE2 HIS 96 C HIS 97 1_555 Q FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc3 C NE2 HIS 181 C HIS 182 1_555 P FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc4 C NE2 HIS 195 C HIS 196 1_555 Q FE HEM . C HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc5 D NE2 HIS 40 D HIS 41 1_555 Y FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
metalc ? metalc6 D SD MET 159 D MET 160 1_555 Y FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc7 E SG CYS 158 E CYS 158 1_555 BA FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
#
_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 531 n n 
CHA C4D HEM doub 532 n n 
CHA HHA HEM sing 533 n n 
CHB C4A HEM sing 534 n n 
CHB C1B HEM doub 535 n n 
CHB HHB HEM sing 536 n n 
CHC C4B HEM sing 537 n n 
CHC C1C HEM doub 538 n n 
CHC HHC HEM sing 539 n n 
CHD C4C HEM doub 540 n n 
CHD C1D HEM sing 541 n n 
CHD HHD HEM sing 542 n n 
C1A C2A HEM doub 543 n y 
C1A NA HEM sing 544 n y 
C2A C3A HEM sing 545 n y 
C2A CAA HEM sing 546 n n 
C3A C4A HEM doub 547 n y 
C3A CMA HEM sing 548 n n 
C4A NA HEM sing 549 n y 
CMA HMA HEM sing 550 n n 
CMA HMAA HEM sing 551 n n 
CMA HMAB HEM sing 552 n n 
CAA CBA HEM sing 553 n n 
CAA HAA HEM sing 554 n n 
CAA HAAA HEM sing 555 n n 
CBA CGA HEM sing 556 n n 
CBA HBA HEM sing 557 n n 
CBA HBAA HEM sing 558 n n 
CGA O1A HEM doub 559 n n 
CGA O2A HEM sing 560 n n 
C1B C2B HEM sing 561 n n 
C1B NB HEM sing 562 n n 
C2B C3B HEM doub 563 n n 
C2B CMB HEM sing 564 n n 
C3B C4B HEM sing 565 n n 
C3B CAB HEM sing 566 n n 
C4B NB HEM doub 567 n n 
CMB HMB HEM sing 568 n n 
CMB HMBA HEM sing 569 n n 
CMB HMBB HEM sing 570 n n 
CAB CBB HEM doub 571 n n 
CAB HAB HEM sing 572 n n 
CBB HBB HEM sing 573 n n 
CBB HBBA HEM sing 574 n n 
C1C C2C HEM sing 575 n y 
C1C NC HEM sing 576 n y 
C2C C3C HEM doub 577 n y 
C2C CMC HEM sing 578 n n 
C3C C4C HEM sing 579 n y 
C3C CAC HEM sing 580 n n 
C4C NC HEM sing 581 n y 
CMC HMC HEM sing 582 n n 
CMC HMCA HEM sing 583 n n 
CMC HMCB HEM sing 584 n n 
CAC CBC HEM doub 585 n n 
CAC HAC HEM sing 586 n n 
CBC HBC HEM sing 587 n n 
CBC HBCA HEM sing 588 n n 
C1D C2D HEM sing 589 n n 
C1D ND HEM doub 590 n n 
C2D C3D HEM doub 591 n n 
C2D CMD HEM sing 592 n n 
C3D C4D HEM sing 593 n n 
C3D CAD HEM sing 594 n n 
C4D ND HEM sing 595 n n 
CMD HMD HEM sing 596 n n 
CMD HMDA HEM sing 597 n n 
CMD HMDB HEM sing 598 n n 
CAD CBD HEM sing 599 n n 
CAD HAD HEM sing 600 n n 
CAD HADA HEM sing 601 n n 
CBD CGD HEM sing 602 n n 
CBD HBD HEM sing 603 n n 
CBD HBDA HEM sing 604 n n 
CGD O1D HEM doub 605 n n 
CGD O2D HEM sing 606 n n 
O2A H2A HEM sing 607 n n 
O2D H2D HEM sing 608 n n 
FE NA HEM sing 609 n n 
FE NB HEM sing 610 n n 
FE NC HEM sing 611 n n 
FE ND HEM sing 612 n n 
#
_atom_sites.entry_id                     6XVF 
_atom_sites.fract_transf_matrix[1][1]    0.004765 
_atom_sites.fract_transf_matrix[1][2]    0.002751 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005502 
_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]    0.00292 
_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
K 11 PG4 A 1 501 501 PG4 PG4 . 
L 12 6PE A 1 502 502 6PE 6PE . 
M 13 PO4 A 1 503 503 PO4 PO4 . 
N 14 CDL A 1 504 401 CDL CDL . 
O 13 PO4 B 1 501 501 PO4 PO4 . 
P 15 HEM C 1 401 402 HEM HEM . 
Q 15 HEM C 1 402 403 HEM HEM . 
R 16 LMT C 1 403 405 LMT LMT . 
S 11 PG4 C 1 404 406 PG4 PG4 . 
T 11 PG4 C 1 405 407 PG4 PG4 . 
U 14 CDL C 1 406 408 CDL CDL . 
V 17 PEE C 1 407 409 PEE PEE . 
W 18 JAG C 1 408 404 JAG JAG . 
X 13 PO4 C 1 409 410 PO4 PO4 . 
Y 19 HEC D 1 501 501 HEC HEC . 
Z 13 PO4 D 1 502 502 PO4 PO4 . 
AA 14 CDL D 1 503 503 CDL CDL . 
BA 20 FES E 1 201 201 FES FES . 
CA 21 PX4 E 1 202 202 PX4 PX4 . 
DA 13 PO4 E 1 203 203 PO4 PO4 . 
EA 17 PEE E 1 204 204 PEE PEE . 
FA 14 CDL E 1 205 205 CDL CDL . 
GA 13 PO4 F 1 501 501 PO4 PO4 . 
HA 13 PO4 G 1 101 101 PO4 PO4 . 
IA 13 PO4 G 1 102 102 PO4 PO4 . 
JA 13 PO4 G 1 103 103 PO4 PO4 . 
KA 22 HOH A 1 601 504 HOH HOH . 
KA 22 HOH A 2 602 508 HOH HOH . 
KA 22 HOH A 3 603 507 HOH HOH . 
KA 22 HOH A 4 604 505 HOH HOH . 
KA 22 HOH A 5 605 509 HOH HOH . 
KA 22 HOH A 6 606 506 HOH HOH . 
LA 22 HOH B 1 601 502 HOH HOH . 
LA 22 HOH B 2 602 503 HOH HOH . 
MA 22 HOH C 1 501 412 HOH HOH . 
MA 22 HOH C 2 502 414 HOH HOH . 
MA 22 HOH C 3 503 411 HOH HOH . 
MA 22 HOH C 4 504 413 HOH HOH . 
NA 22 HOH D 1 601 505 HOH HOH . 
NA 22 HOH D 2 602 504 HOH HOH . 
OA 22 HOH F 1 601 502 HOH HOH . 
PA 22 HOH G 1 201 104 HOH HOH . 
QA 22 HOH I 1 101 101 HOH HOH . 
QA 22 HOH I 2 102 102 HOH HOH . 
RA 22 HOH J 1 101 101 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 . . . Q 15 -68.401 -65.058 38.063 1 118.72 ? CHA HEM 402 C 1 
HETATM 2 C CHB HEM . . . Q 15 -65.923 -68.376 35.561 1 118.48 ? CHB HEM 402 C 1 
HETATM 3 C CHC HEM . . . Q 15 -64.014 -70.02 39.696 1 118.79 ? CHC HEM 402 C 1 
HETATM 4 C CHD HEM . . . Q 15 -67.172 -67.331 42.168 1 118.88 ? CHD HEM 402 C 1 
HETATM 5 C C1A HEM . . . Q 15 -67.781 -65.754 37.041 1 118.6 ? C1A HEM 402 C 1 
HETATM 6 C C2A HEM . . . Q 15 -67.818 -65.372 35.68 1 118.68 ? C2A HEM 402 C 1 
HETATM 7 C C3A HEM . . . Q 15 -67.127 -66.306 34.971 1 118.51 ? C3A HEM 402 C 1 
HETATM 8 C C4A HEM . . . Q 15 -66.659 -67.263 35.893 1 118.36 ? C4A HEM 402 C 1 
HETATM 9 C CMA HEM . . . Q 15 -66.888 -66.339 33.476 1 118.57 ? CMA HEM 402 C 1 
HETATM 10 C CAA HEM . . . Q 15 -68.496 -64.142 35.127 1 119.1 ? CAA HEM 402 C 1 
HETATM 11 C CBA HEM . . . Q 15 -67.477 -63.016 34.911 1 120.41 ? CBA HEM 402 C 1 
HETATM 12 C CGA HEM . . . Q 15 -66.924 -62.486 36.206 1 120.91 ? CGA HEM 402 C 1 
HETATM 13 O O1A HEM . . . Q 15 -65.745 -62.746 36.511 1 121.19 ? O1A HEM 402 C 1 
HETATM 14 O O2A HEM . . . Q 15 -67.622 -61.781 36.964 1 121.12 ? O2A HEM 402 C 1 
HETATM 15 C C1B HEM . . . Q 15 -65.172 -69.094 36.491 1 118.21 ? C1B HEM 402 C 1 
HETATM 16 C C2B HEM . . . Q 15 -64.242 -70.099 36.085 1 118.03 ? C2B HEM 402 C 1 
HETATM 17 C C3B HEM . . . Q 15 -63.697 -70.574 37.249 1 118.23 ? C3B HEM 402 C 1 
HETATM 18 C C4B HEM . . . Q 15 -64.337 -69.815 38.352 1 118.41 ? C4B HEM 402 C 1 
HETATM 19 C CMB HEM . . . Q 15 -63.96 -70.511 34.649 1 117.66 ? CMB HEM 402 C 1 
HETATM 20 C CAB HEM . . . Q 15 -62.67 -71.605 37.488 1 118.55 ? CAB HEM 402 C 1 
HETATM 21 C CBB HEM . . . Q 15 -62.265 -72.459 36.562 1 118.98 ? CBB HEM 402 C 1 
HETATM 22 C C1C HEM . . . Q 15 -64.665 -69.401 40.76 1 118.85 ? C1C HEM 402 C 1 
HETATM 23 C C2C HEM . . . Q 15 -64.324 -69.531 42.125 1 119.13 ? C2C HEM 402 C 1 
HETATM 24 C C3C HEM . . . Q 15 -65.241 -68.749 42.839 1 119.24 ? C3C HEM 402 C 1 
HETATM 25 C C4C HEM . . . Q 15 -66.116 -68.155 41.874 1 118.77 ? C4C HEM 402 C 1 
HETATM 26 C CMC HEM . . . Q 15 -63.179 -70.374 42.654 1 119.01 ? CMC HEM 402 C 1 
HETATM 27 C CAC HEM . . . Q 15 -65.355 -68.523 44.306 1 119.86 ? CAC HEM 402 C 1 
HETATM 28 C CBC HEM . . . Q 15 -64.788 -69.263 45.259 1 120.42 ? CBC HEM 402 C 1 
HETATM 29 C C1D HEM . . . Q 15 -67.753 -66.483 41.224 1 118.97 ? C1D HEM 402 C 1 
HETATM 30 C C2D HEM . . . Q 15 -68.716 -65.429 41.61 1 119.02 ? C2D HEM 402 C 1 
HETATM 31 C C3D HEM . . . Q 15 -69.061 -64.785 40.481 1 118.84 ? C3D HEM 402 C 1 
HETATM 32 C C4D HEM . . . Q 15 -68.31 -65.461 39.395 1 118.88 ? C4D HEM 402 C 1 
HETATM 33 C CMD HEM . . . Q 15 -69.216 -65.123 43.003 1 119.28 ? CMD HEM 402 C 1 
HETATM 34 C CAD HEM . . . Q 15 -70.029 -63.626 40.39 1 118.82 ? CAD HEM 402 C 1 
HETATM 35 C CBD HEM . . . Q 15 -69.285 -62.295 40.287 1 119.76 ? CBD HEM 402 C 1 
HETATM 36 C CGD HEM . . . Q 15 -70.171 -61.068 40.216 1 120.26 ? CGD HEM 402 C 1 
HETATM 37 O O1D HEM . . . Q 15 -69.785 -60.013 40.761 1 120.73 ? O1D HEM 402 C 1 
HETATM 38 O O2D HEM . . . Q 15 -71.277 -61.051 39.625 1 120.67 ? O2D HEM 402 C 1 
HETATM 39 N NA HEM . . . Q 15 -67.057 -66.923 37.155 1 118.26 ? NA HEM 402 C 1 
HETATM 40 N NB HEM . . . Q 15 -65.206 -68.952 37.823 1 118.24 ? NB HEM 402 C 1 
HETATM 41 N NC HEM . . . Q 15 -65.731 -68.556 40.626 1 118.53 ? NC HEM 402 C 1 
HETATM 42 N ND HEM . . . Q 15 -67.544 -66.47 39.892 1 118.72 ? ND HEM 402 C 1 
HETATM 43 FE FE HEM . . . Q 15 -66.422 -67.615 38.9 1 118.11 ? FE HEM 402 C 1 
#
_model_server_stats.io_time_ms              41 
_model_server_stats.parse_time_ms           35 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           43 
#