data_4D6U
#
_model_server_result.job_id            58iRDSiMIVLjLNuQNsAEAA 
_model_server_result.datetime_utc      '2024-11-05 16:23:00' 
_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          4d6u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":502}' 
#
_entry.id    4D6U 
#
_exptl.entry_id    4D6U 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          13 
_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            4D6U 
_cell.length_a            129.49 
_cell.length_b            129.49 
_cell.length_c            719.936 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D6U 
_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 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
? 13 U N N 
? 13 V N N 
? 13 JA N N 
? 13 KA 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf2 H SG CYS 53 H CYS 40 1_555 H SG CYS 67 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf3 O SG CYS 222 R CYS 144 1_555 O SG CYS 238 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf4 R SG CYS 37 U CYS 24 1_555 R SG CYS 81 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf5 R SG CYS 53 U CYS 40 1_555 R SG CYS 67 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
covale ? covale1 C NE2 HIS 201 C HIS 201 1_555 W O25 G8U . C G8U 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.258 ? 
covale ? covale2 M NE2 HIS 201 P HIS 201 1_555 LA O25 G8U . P G8U 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? 
metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
metalc ? metalc5 D NE2 HIS 125 D HIS 41 1_555 Z FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc6 D SD MET 244 D MET 160 1_555 Z FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc7 M NE2 HIS 83 P HIS 83 1_555 JA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc8 M NE2 HIS 97 P HIS 97 1_555 KA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc9 M NE2 HIS 182 P HIS 182 1_555 JA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc10 M NE2 HIS 196 P HIS 196 1_555 KA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc11 N NE2 HIS 125 Q HIS 41 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc12 N SD MET 244 Q MET 160 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc13 O SG CYS 236 R CYS 158 1_555 RA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
#
_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                     4D6U 
_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]    0.008917 
_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]    0.001389 
_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 13 HEM C 1 501 501 HEM HEM . 
V 13 HEM C 1 502 502 HEM HEM . 
W 14 G8U C 1 503 503 G8U G8U . 
X 15 PO4 C 1 504 504 PO4 PO4 . 
Y 16 PEE C 1 505 505 PEE PEE . 
Z 17 HEC D 1 501 501 HEC HEC . 
AA 15 PO4 D 1 502 502 PO4 PO4 . 
BA 15 PO4 D 1 503 503 PO4 PO4 . 
CA 15 PO4 D 1 504 504 PO4 PO4 . 
DA 18 CDL D 1 505 505 CDL CDL . 
EA 16 PEE D 1 506 506 PEE PEE . 
FA 15 PO4 E 1 501 501 PO4 PO4 . 
GA 15 PO4 F 1 501 501 PO4 PO4 . 
HA 18 CDL G 1 501 501 CDL CDL . 
IA 15 PO4 N 1 501 501 PO4 PO4 . 
JA 13 HEM P 1 501 501 HEM HEM . 
KA 13 HEM P 1 502 502 HEM HEM . 
LA 14 G8U P 1 503 503 G8U G8U . 
MA 15 PO4 P 1 504 504 PO4 PO4 . 
NA 16 PEE P 1 505 505 PEE PEE . 
OA 17 HEC Q 1 501 501 HEC HEC . 
PA 18 CDL Q 1 505 505 CDL CDL . 
QA 16 PEE Q 1 506 506 PEE PEE . 
RA 19 FES R 1 501 501 FES FES . 
SA 20 GOL R 1 502 502 GOL GOL . 
TA 15 PO4 S 1 501 501 PO4 PO4 . 
UA 18 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 13 55.152 14.772 17.906 1 115.66 ? CHA HEM 502 C 1 
HETATM 2 C CHB HEM . . . V 13 50.562 13.554 18.657 1 114.97 ? CHB HEM 502 C 1 
HETATM 3 C CHC HEM . . . V 13 50.531 16.431 22.546 1 108.83 ? CHC HEM 502 C 1 
HETATM 4 C CHD HEM . . . V 13 54.743 18.294 21.157 1 103.03 ? CHD HEM 502 C 1 
HETATM 5 C C1A HEM . . . V 13 53.959 14.112 17.825 1 116.78 ? C1A HEM 502 C 1 
HETATM 6 C C2A HEM . . . V 13 53.752 12.894 17.101 1 118.21 ? C2A HEM 502 C 1 
HETATM 7 C C3A HEM . . . V 13 52.439 12.598 17.34 1 115.71 ? C3A HEM 502 C 1 
HETATM 8 C C4A HEM . . . V 13 51.86 13.596 18.154 1 114.16 ? C4A HEM 502 C 1 
HETATM 9 C CMA HEM . . . V 13 51.712 11.41 16.802 1 111.96 ? CMA HEM 502 C 1 
HETATM 10 C CAA HEM . . . V 13 54.733 12.064 16.25 1 111.69 ? CAA HEM 502 C 1 
HETATM 11 C CBA HEM . . . V 13 55.238 10.821 17.015 1 118.65 ? CBA HEM 502 C 1 
HETATM 12 C CGA HEM . . . V 13 56.238 11.263 18.053 1 140.14 ? CGA HEM 502 C 1 
HETATM 13 O O1A HEM . . . V 13 56.031 11.161 19.303 1 140.02 ? O1A HEM 502 C 1 
HETATM 14 O O2A HEM . . . V 13 57.297 11.748 17.595 1 147.85 ? O2A HEM 502 C 1 
HETATM 15 C C1B HEM . . . V 13 50.166 14.223 19.814 1 109.89 ? C1B HEM 502 C 1 
HETATM 16 C C2B HEM . . . V 13 48.899 13.963 20.444 1 112.04 ? C2B HEM 502 C 1 
HETATM 17 C C3B HEM . . . V 13 48.885 14.752 21.576 1 117.55 ? C3B HEM 502 C 1 
HETATM 18 C C4B HEM . . . V 13 50.185 15.498 21.568 1 112.55 ? C4B HEM 502 C 1 
HETATM 19 C CMB HEM . . . V 13 47.803 13.003 19.97 1 107.68 ? CMB HEM 502 C 1 
HETATM 20 C CAB HEM . . . V 13 47.761 15.043 22.499 1 120.98 ? CAB HEM 502 C 1 
HETATM 21 C CBB HEM . . . V 13 46.548 15.209 21.92 1 118.6 ? CBB HEM 502 C 1 
HETATM 22 C C1C HEM . . . V 13 51.681 17.202 22.519 1 100.33 ? C1C HEM 502 C 1 
HETATM 23 C C2C HEM . . . V 13 52.074 18.13 23.485 1 102.22 ? C2C HEM 502 C 1 
HETATM 24 C C3C HEM . . . V 13 53.298 18.651 23.092 1 99.99 ? C3C HEM 502 C 1 
HETATM 25 C C4C HEM . . . V 13 53.6 18.052 21.854 1 98.86 ? C4C HEM 502 C 1 
HETATM 26 C CMC HEM . . . V 13 51.296 18.448 24.739 1 109.64 ? CMC HEM 502 C 1 
HETATM 27 C CAC HEM . . . V 13 54.095 19.754 23.663 1 103.46 ? CAC HEM 502 C 1 
HETATM 28 C CBC HEM . . . V 13 53.508 20.709 24.409 1 103.86 ? CBC HEM 502 C 1 
HETATM 29 C C1D HEM . . . V 13 55.17 17.438 20.174 1 105.12 ? C1D HEM 502 C 1 
HETATM 30 C C2D HEM . . . V 13 56.509 17.574 19.605 1 108.1 ? C2D HEM 502 C 1 
HETATM 31 C C3D HEM . . . V 13 56.625 16.582 18.716 1 107.79 ? C3D HEM 502 C 1 
HETATM 32 C C4D HEM . . . V 13 55.36 15.848 18.746 1 108.19 ? C4D HEM 502 C 1 
HETATM 33 C CMD HEM . . . V 13 57.558 18.605 19.927 1 110.16 ? CMD HEM 502 C 1 
HETATM 34 C CAD HEM . . . V 13 57.81 16.295 17.826 1 104.51 ? CAD HEM 502 C 1 
HETATM 35 C CBD HEM . . . V 13 59.028 15.833 18.603 1 103 ? CBD HEM 502 C 1 
HETATM 36 C CGD HEM . . . V 13 59.764 14.729 17.915 1 98.25 ? CGD HEM 502 C 1 
HETATM 37 O O1D HEM . . . V 13 60.613 14.082 18.559 1 98.95 ? O1D HEM 502 C 1 
HETATM 38 O O2D HEM . . . V 13 59.546 14.449 16.719 1 96.94 ? O2D HEM 502 C 1 
HETATM 39 N NA HEM . . . V 13 52.81 14.51 18.483 1 110.7 ? NA HEM 502 C 1 
HETATM 40 N NB HEM . . . V 13 50.878 15.125 20.494 1 107.07 ? NB HEM 502 C 1 
HETATM 41 N NC HEM . . . V 13 52.61 17.175 21.546 1 97.56 ? NC HEM 502 C 1 
HETATM 42 N ND HEM . . . V 13 54.525 16.415 19.62 1 104.77 ? ND HEM 502 C 1 
HETATM 43 FE FE HEM . . . V 13 52.817 15.78 20.022 1 103.19 ? FE HEM 502 C 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           228 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#