data_4D6T
#
_model_server_result.job_id            Th764aVcBLXtqava3ZqZTQ 
_model_server_result.datetime_utc      '2024-11-05 13:38:37' 
_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          4d6t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":502}' 
#
_entry.id    4D6T 
#
_exptl.entry_id    4D6T 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          12 
_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            4D6T 
_cell.length_a            129.896 
_cell.length_b            129.896 
_cell.length_c            722.152 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D6T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 65' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PQS decameric 10 software_defined_assembly 1 
PQS decameric 10 software_defined_assembly 2 
#
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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA 1 1 
K,L,M,N,O,P,Q,R,S,T,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA 2 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
? 12 U N N 
? 12 V N N 
? 12 KA N N 
? 12 LA 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 H SG CYS 37 H CYS 24 1_555 H SG CYS 81 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf2 H SG CYS 53 H CYS 40 1_555 H SG CYS 67 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
disulf ? disulf3 O SG CYS 222 R CYS 144 1_555 O SG CYS 238 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf4 R SG CYS 37 U CYS 24 1_555 R SG CYS 81 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf5 R SG CYS 53 U CYS 40 1_555 R SG CYS 67 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc5 D NE2 HIS 65 D HIS 41 1_555 Z FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc6 D SD MET 184 D MET 160 1_555 Z FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc7 M NE2 HIS 83 P HIS 83 1_555 KA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc8 M NE2 HIS 97 P HIS 97 1_555 LA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc9 M NE2 HIS 182 P HIS 182 1_555 KA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc10 M NE2 HIS 196 P HIS 196 1_555 LA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc11 N NE2 HIS 65 Q HIS 41 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? 
metalc ? metalc12 N SD MET 184 Q MET 160 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
metalc ? metalc13 O SG CYS 236 R CYS 158 1_555 TA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
#
_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 530 n n 
CHA C4D HEM doub 531 n n 
CHA HHA HEM sing 532 n n 
CHB C4A HEM sing 533 n n 
CHB C1B HEM doub 534 n n 
CHB HHB HEM sing 535 n n 
CHC C4B HEM sing 536 n n 
CHC C1C HEM doub 537 n n 
CHC HHC HEM sing 538 n n 
CHD C4C HEM doub 539 n n 
CHD C1D HEM sing 540 n n 
CHD HHD HEM sing 541 n n 
C1A C2A HEM doub 542 n y 
C1A NA HEM sing 543 n y 
C2A C3A HEM sing 544 n y 
C2A CAA HEM sing 545 n n 
C3A C4A HEM doub 546 n y 
C3A CMA HEM sing 547 n n 
C4A NA HEM sing 548 n y 
CMA HMA HEM sing 549 n n 
CMA HMAA HEM sing 550 n n 
CMA HMAB HEM sing 551 n n 
CAA CBA HEM sing 552 n n 
CAA HAA HEM sing 553 n n 
CAA HAAA HEM sing 554 n n 
CBA CGA HEM sing 555 n n 
CBA HBA HEM sing 556 n n 
CBA HBAA HEM sing 557 n n 
CGA O1A HEM doub 558 n n 
CGA O2A HEM sing 559 n n 
C1B C2B HEM sing 560 n n 
C1B NB HEM sing 561 n n 
C2B C3B HEM doub 562 n n 
C2B CMB HEM sing 563 n n 
C3B C4B HEM sing 564 n n 
C3B CAB HEM sing 565 n n 
C4B NB HEM doub 566 n n 
CMB HMB HEM sing 567 n n 
CMB HMBA HEM sing 568 n n 
CMB HMBB HEM sing 569 n n 
CAB CBB HEM doub 570 n n 
CAB HAB HEM sing 571 n n 
CBB HBB HEM sing 572 n n 
CBB HBBA HEM sing 573 n n 
C1C C2C HEM sing 574 n y 
C1C NC HEM sing 575 n y 
C2C C3C HEM doub 576 n y 
C2C CMC HEM sing 577 n n 
C3C C4C HEM sing 578 n y 
C3C CAC HEM sing 579 n n 
C4C NC HEM sing 580 n y 
CMC HMC HEM sing 581 n n 
CMC HMCA HEM sing 582 n n 
CMC HMCB HEM sing 583 n n 
CAC CBC HEM doub 584 n n 
CAC HAC HEM sing 585 n n 
CBC HBC HEM sing 586 n n 
CBC HBCA HEM sing 587 n n 
C1D C2D HEM sing 588 n n 
C1D ND HEM doub 589 n n 
C2D C3D HEM doub 590 n n 
C2D CMD HEM sing 591 n n 
C3D C4D HEM sing 592 n n 
C3D CAD HEM sing 593 n n 
C4D ND HEM sing 594 n n 
CMD HMD HEM sing 595 n n 
CMD HMDA HEM sing 596 n n 
CMD HMDB HEM sing 597 n n 
CAD CBD HEM sing 598 n n 
CAD HAD HEM sing 599 n n 
CAD HADA HEM sing 600 n n 
CBD CGD HEM sing 601 n n 
CBD HBD HEM sing 602 n n 
CBD HBDA HEM sing 603 n n 
CGD O1D HEM doub 604 n n 
CGD O2D HEM sing 605 n n 
O2A H2A HEM sing 606 n n 
O2D H2D HEM sing 607 n n 
FE NA HEM sing 608 n n 
FE NB HEM sing 609 n n 
FE NC HEM sing 610 n n 
FE ND HEM sing 611 n n 
#
_atom_sites.entry_id                     4D6T 
_atom_sites.fract_transf_matrix[1][1]    0.007698 
_atom_sites.fract_transf_matrix[1][2]    0.004445 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008889 
_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]    0.001385 
_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
U 12 HEM C 1 501 501 HEM HEM . 
V 12 HEM C 1 502 502 HEM HEM . 
W 13 4X9 C 1 503 503 4X9 4X9 . 
X 14 PO4 C 1 504 504 PO4 PO4 . 
Y 15 PEE C 1 505 505 PEE PEE . 
Z 16 HEC D 1 501 501 HEC HEC . 
AA 14 PO4 D 1 502 502 PO4 PO4 . 
BA 14 PO4 D 1 503 503 PO4 PO4 . 
CA 14 PO4 D 1 504 504 PO4 PO4 . 
DA 17 CDL D 1 505 505 CDL CDL . 
EA 15 PEE D 1 506 506 PEE PEE . 
FA 14 PO4 E 1 501 501 PO4 PO4 . 
GA 14 PO4 F 1 501 501 PO4 PO4 . 
HA 17 CDL G 1 501 501 CDL CDL . 
IA 14 PO4 N 1 501 501 PO4 PO4 . 
JA 14 PO4 N 1 1001 1001 PO4 PO4 . 
KA 12 HEM P 1 501 501 HEM HEM . 
LA 12 HEM P 1 502 502 HEM HEM . 
MA 13 4X9 P 1 503 503 4X9 4X9 . 
NA 15 PEE P 1 505 505 PEE PEE . 
OA 16 HEC Q 1 501 501 HEC HEC . 
PA 17 CDL Q 1 505 505 CDL CDL . 
QA 15 PEE Q 1 506 506 PEE PEE . 
RA 14 PO4 Q 1 1001 1001 PO4 PO4 . 
SA 14 PO4 Q 1 1002 1002 PO4 PO4 . 
TA 18 FES R 1 501 501 FES FES . 
UA 19 GOL R 1 502 502 GOL GOL . 
VA 14 PO4 S 1 501 501 PO4 PO4 . 
WA 17 CDL T 1 501 501 CDL CDL . 
#
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 . . . V 12 55.384 14.586 17.973 1 71.84 ? CHA HEM 502 C 1 
HETATM 2 C CHB HEM . . . V 12 50.859 13.309 18.926 1 81.25 ? CHB HEM 502 C 1 
HETATM 3 C CHC HEM . . . V 12 50.719 16.573 22.47 1 86.87 ? CHC HEM 502 C 1 
HETATM 4 C CHD HEM . . . V 12 55.093 18.103 21.208 1 83.24 ? CHD HEM 502 C 1 
HETATM 5 C C1A HEM . . . V 12 54.192 13.937 17.982 1 78.82 ? C1A HEM 502 C 1 
HETATM 6 C C2A HEM . . . V 12 53.939 12.738 17.293 1 84.66 ? C2A HEM 502 C 1 
HETATM 7 C C3A HEM . . . V 12 52.666 12.382 17.568 1 83.06 ? C3A HEM 502 C 1 
HETATM 8 C C4A HEM . . . V 12 52.124 13.359 18.411 1 80.65 ? C4A HEM 502 C 1 
HETATM 9 C CMA HEM . . . V 12 51.954 11.175 17.025 1 87.49 ? CMA HEM 502 C 1 
HETATM 10 C CAA HEM . . . V 12 54.907 11.968 16.433 1 97.19 ? CAA HEM 502 C 1 
HETATM 11 C CBA HEM . . . V 12 55.614 10.902 17.307 1 102.93 ? CBA HEM 502 C 1 
HETATM 12 C CGA HEM . . . V 12 56.72 11.449 18.198 1 105.55 ? CGA HEM 502 C 1 
HETATM 13 O O1A HEM . . . V 12 56.642 11.231 19.445 1 106.06 ? O1A HEM 502 C 1 
HETATM 14 O O2A HEM . . . V 12 57.702 12.086 17.703 1 89.83 ? O2A HEM 502 C 1 
HETATM 15 C C1B HEM . . . V 12 50.439 14.094 19.985 1 87.89 ? C1B HEM 502 C 1 
HETATM 16 C C2B HEM . . . V 12 49.144 13.933 20.564 1 97.02 ? C2B HEM 502 C 1 
HETATM 17 C C3B HEM . . . V 12 49.073 14.841 21.586 1 99.82 ? C3B HEM 502 C 1 
HETATM 18 C C4B HEM . . . V 12 50.384 15.56 21.581 1 95.27 ? C4B HEM 502 C 1 
HETATM 19 C CMB HEM . . . V 12 48.078 12.94 20.132 1 97.06 ? CMB HEM 502 C 1 
HETATM 20 C CAB HEM . . . V 12 47.93 15.157 22.47 1 98.47 ? CAB HEM 502 C 1 
HETATM 21 C CBB HEM . . . V 12 46.672 14.816 22.193 1 93.59 ? CBB HEM 502 C 1 
HETATM 22 C C1C HEM . . . V 12 51.919 17.26 22.475 1 77.13 ? C1C HEM 502 C 1 
HETATM 23 C C2C HEM . . . V 12 52.313 18.183 23.441 1 76.38 ? C2C HEM 502 C 1 
HETATM 24 C C3C HEM . . . V 12 53.559 18.625 23.079 1 77.54 ? C3C HEM 502 C 1 
HETATM 25 C C4C HEM . . . V 12 53.91 17.961 21.88 1 77.66 ? C4C HEM 502 C 1 
HETATM 26 C CMC HEM . . . V 12 51.514 18.612 24.647 1 78.84 ? CMC HEM 502 C 1 
HETATM 27 C CAC HEM . . . V 12 54.404 19.623 23.752 1 85.9 ? CAC HEM 502 C 1 
HETATM 28 C CBC HEM . . . V 12 54.069 20.316 24.839 1 90.98 ? CBC HEM 502 C 1 
HETATM 29 C C1D HEM . . . V 12 55.488 17.235 20.214 1 81.69 ? C1D HEM 502 C 1 
HETATM 30 C C2D HEM . . . V 12 56.818 17.339 19.616 1 85.69 ? C2D HEM 502 C 1 
HETATM 31 C C3D HEM . . . V 12 56.912 16.346 18.72 1 84.62 ? C3D HEM 502 C 1 
HETATM 32 C C4D HEM . . . V 12 55.62 15.664 18.785 1 74.11 ? C4D HEM 502 C 1 
HETATM 33 C CMD HEM . . . V 12 57.89 18.344 19.941 1 92.11 ? CMD HEM 502 C 1 
HETATM 34 C CAD HEM . . . V 12 58.08 15.988 17.796 1 93.61 ? CAD HEM 502 C 1 
HETATM 35 C CBD HEM . . . V 12 59.481 15.959 18.44 1 94.71 ? CBD HEM 502 C 1 
HETATM 36 C CGD HEM . . . V 12 60.338 14.771 18.02 1 89.24 ? CGD HEM 502 C 1 
HETATM 37 O O1D HEM . . . V 12 61.159 14.232 18.808 1 79.54 ? O1D HEM 502 C 1 
HETATM 38 O O2D HEM . . . V 12 60.227 14.325 16.858 1 89.14 ? O2D HEM 502 C 1 
HETATM 39 N NA HEM . . . V 12 53.069 14.305 18.667 1 81.06 ? NA HEM 502 C 1 
HETATM 40 N NB HEM . . . V 12 51.119 15.054 20.601 1 87.52 ? NB HEM 502 C 1 
HETATM 41 N NC HEM . . . V 12 52.893 17.14 21.553 1 74.91 ? NC HEM 502 C 1 
HETATM 42 N ND HEM . . . V 12 54.8 16.234 19.679 1 78.57 ? ND HEM 502 C 1 
HETATM 43 FE FE HEM . . . V 12 53.059 15.641 20.13 1 83.13 ? FE HEM 502 C 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    58 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           43 
#