data_4D6U
#
_model_server_result.job_id            6ldAiDOUp1GjhflboNAKkg 
_model_server_result.datetime_utc      '2024-11-05 16:43:05' 
_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          4d6u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":501}' 
#
_entry.id    4D6U 
#
_exptl.entry_id    4D6U 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              618.503 
_entity.id                          17 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'HEME C' 
_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            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
? 17 Z N N 
? 17 OA 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 H34 Fe N4 O4' 
_chem_comp.formula_weight    618.503 
_chem_comp.id                HEC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'HEME C' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
FE NA HEC sing 447 n n 
FE NB HEC sing 448 n n 
FE NC HEC sing 449 n n 
FE ND HEC sing 450 n n 
CHA C1A HEC doub 451 n n 
CHA C4D HEC sing 452 n n 
CHA HHA HEC sing 453 n n 
CHB C4A HEC doub 454 n n 
CHB C1B HEC sing 455 n n 
CHB HHB HEC sing 456 n n 
CHC C4B HEC doub 457 n n 
CHC C1C HEC sing 458 n n 
CHC HHC HEC sing 459 n n 
CHD C4C HEC doub 460 n n 
CHD C1D HEC sing 461 n n 
CHD HHD HEC sing 462 n n 
NA C1A HEC sing 463 n y 
NA C4A HEC sing 464 n y 
C1A C2A HEC sing 465 n y 
C2A C3A HEC doub 466 n y 
C2A CAA HEC sing 467 n n 
C3A C4A HEC sing 468 n y 
C3A CMA HEC sing 469 n n 
CMA HMA1 HEC sing 470 n n 
CMA HMA2 HEC sing 471 n n 
CMA HMA3 HEC sing 472 n n 
CAA CBA HEC sing 473 n n 
CAA HAA1 HEC sing 474 n n 
CAA HAA2 HEC sing 475 n n 
CBA CGA HEC sing 476 n n 
CBA HBA1 HEC sing 477 n n 
CBA HBA2 HEC sing 478 n n 
CGA O1A HEC doub 479 n n 
CGA O2A HEC sing 480 n n 
O2A H2A HEC sing 481 n n 
NB C1B HEC sing 482 n y 
NB C4B HEC sing 483 n y 
C1B C2B HEC doub 484 n y 
C2B C3B HEC sing 485 n y 
C2B CMB HEC sing 486 n n 
C3B C4B HEC sing 487 n y 
C3B CAB HEC doub 488 e n 
CMB HMB1 HEC sing 489 n n 
CMB HMB2 HEC sing 490 n n 
CMB HMB3 HEC sing 491 n n 
CAB CBB HEC sing 492 n n 
CAB HAB HEC sing 493 n n 
CBB HBB1 HEC sing 494 n n 
CBB HBB2 HEC sing 495 n n 
CBB HBB3 HEC sing 496 n n 
NC C1C HEC sing 497 n y 
NC C4C HEC sing 498 n y 
C1C C2C HEC doub 499 n y 
C2C C3C HEC sing 500 n y 
C2C CMC HEC sing 501 n n 
C3C C4C HEC sing 502 n y 
C3C CAC HEC doub 503 e n 
CMC HMC1 HEC sing 504 n n 
CMC HMC2 HEC sing 505 n n 
CMC HMC3 HEC sing 506 n n 
CAC CBC HEC sing 507 n n 
CAC HAC HEC sing 508 n n 
CBC HBC1 HEC sing 509 n n 
CBC HBC2 HEC sing 510 n n 
CBC HBC3 HEC sing 511 n n 
ND C1D HEC sing 512 n y 
ND C4D HEC sing 513 n y 
C1D C2D HEC doub 514 n y 
C2D C3D HEC sing 515 n y 
C2D CMD HEC sing 516 n n 
C3D C4D HEC doub 517 n y 
C3D CAD HEC sing 518 n n 
CMD HMD1 HEC sing 519 n n 
CMD HMD2 HEC sing 520 n n 
CMD HMD3 HEC sing 521 n n 
CAD CBD HEC sing 522 n n 
CAD HAD1 HEC sing 523 n n 
CAD HAD2 HEC sing 524 n n 
CBD CGD HEC sing 525 n n 
CBD HBD1 HEC sing 526 n n 
CBD HBD2 HEC sing 527 n n 
CGD O1D HEC doub 528 n n 
CGD O2D HEC sing 529 n n 
O2D H2D HEC sing 530 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 FE FE HEC . . . Z 17 24.622 1.805 60.484 1 134.62 ? FE HEC 501 D 1 
HETATM 2 C CHA HEC . . . Z 17 26.588 4.622 59.83 1 133.92 ? CHA HEC 501 D 1 
HETATM 3 C CHB HEC . . . Z 17 26.718 -0.101 58.512 1 134.15 ? CHB HEC 501 D 1 
HETATM 4 C CHC HEC . . . Z 17 22.87 -1.055 61.416 1 141.67 ? CHC HEC 501 D 1 
HETATM 5 C CHD HEC . . . Z 17 22.348 3.796 62.182 1 137.61 ? CHD HEC 501 D 1 
HETATM 6 N NA HEC . . . Z 17 26.353 2.191 59.369 1 127.76 ? NA HEC 501 D 1 
HETATM 7 C C1A HEC . . . Z 17 27.016 3.356 59.216 1 130.83 ? C1A HEC 501 D 1 
HETATM 8 C C2A HEC . . . Z 17 28.216 3.289 58.353 1 134.89 ? C2A HEC 501 D 1 
HETATM 9 C C3A HEC . . . Z 17 28.246 1.883 57.95 1 133.66 ? C3A HEC 501 D 1 
HETATM 10 C C4A HEC . . . Z 17 27.054 1.323 58.632 1 128.81 ? C4A HEC 501 D 1 
HETATM 11 C CMA HEC . . . Z 17 29.252 1.2 57.063 1 139.55 ? CMA HEC 501 D 1 
HETATM 12 C CAA HEC . . . Z 17 29.17 4.372 57.922 1 141.34 ? CAA HEC 501 D 1 
HETATM 13 C CBA HEC . . . Z 17 30.059 4.927 59.018 1 143.47 ? CBA HEC 501 D 1 
HETATM 14 C CGA HEC . . . Z 17 31.075 5.772 58.289 1 142.29 ? CGA HEC 501 D 1 
HETATM 15 O O1A HEC . . . Z 17 30.826 6.987 58.13 1 141.4 ? O1A HEC 501 D 1 
HETATM 16 O O2A HEC . . . Z 17 32.102 5.216 57.836 1 140.35 ? O2A HEC 501 D 1 
HETATM 17 N NB HEC . . . Z 17 24.766 -0.242 60.038 1 130.39 ? NB HEC 501 D 1 
HETATM 18 C C1B HEC . . . Z 17 25.658 -0.834 59.219 1 132.16 ? C1B HEC 501 D 1 
HETATM 19 C C2B HEC . . . Z 17 25.561 -2.311 59.072 1 130.2 ? C2B HEC 501 D 1 
HETATM 20 C C3B HEC . . . Z 17 24.422 -2.586 59.941 1 127.22 ? C3B HEC 501 D 1 
HETATM 21 C C4B HEC . . . Z 17 24.007 -1.259 60.487 1 131.9 ? C4B HEC 501 D 1 
HETATM 22 C CMB HEC . . . Z 17 26.429 -3.22 58.233 1 130.16 ? CMB HEC 501 D 1 
HETATM 23 C CAB HEC . . . Z 17 23.832 -3.918 60.205 1 127.21 ? CAB HEC 501 D 1 
HETATM 24 C CBB HEC . . . Z 17 24.382 -5.176 59.571 1 125.66 ? CBB HEC 501 D 1 
HETATM 25 N NC HEC . . . Z 17 22.895 1.435 61.615 1 138.37 ? NC HEC 501 D 1 
HETATM 26 C C1C HEC . . . Z 17 22.331 0.241 61.905 1 145.31 ? C1C HEC 501 D 1 
HETATM 27 C C2C HEC . . . Z 17 21.098 0.311 62.748 1 153.06 ? C2C HEC 501 D 1 
HETATM 28 C C3C HEC . . . Z 17 20.968 1.764 62.952 1 151.55 ? C3C HEC 501 D 1 
HETATM 29 C C4C HEC . . . Z 17 22.106 2.345 62.211 1 141.43 ? C4C HEC 501 D 1 
HETATM 30 C CMC HEC . . . Z 17 20.247 -0.832 63.243 1 157.66 ? CMC HEC 501 D 1 
HETATM 31 C CAC HEC . . . Z 17 19.952 2.56 63.705 1 158.73 ? CAC HEC 501 D 1 
HETATM 32 C CBC HEC . . . Z 17 18.79 1.959 64.463 1 161.37 ? CBC HEC 501 D 1 
HETATM 33 N ND HEC . . . Z 17 24.497 3.853 60.938 1 134.02 ? ND HEC 501 D 1 
HETATM 34 C C1D HEC . . . Z 17 23.509 4.485 61.605 1 133.5 ? C1D HEC 501 D 1 
HETATM 35 C C2D HEC . . . Z 17 23.694 5.949 61.764 1 132.8 ? C2D HEC 501 D 1 
HETATM 36 C C3D HEC . . . Z 17 24.966 6.199 61.068 1 132.74 ? C3D HEC 501 D 1 
HETATM 37 C C4D HEC . . . Z 17 25.356 4.842 60.609 1 134.05 ? C4D HEC 501 D 1 
HETATM 38 C CMD HEC . . . Z 17 22.787 6.928 62.466 1 135.16 ? CMD HEC 501 D 1 
HETATM 39 C CAD HEC . . . Z 17 25.685 7.514 60.866 1 134.65 ? CAD HEC 501 D 1 
HETATM 40 C CBD HEC . . . Z 17 26.218 8.042 62.188 1 135.19 ? CBD HEC 501 D 1 
HETATM 41 C CGD HEC . . . Z 17 27.181 9.184 61.936 1 133.15 ? CGD HEC 501 D 1 
HETATM 42 O O1D HEC . . . Z 17 26.741 10.35 61.791 1 128.79 ? O1D HEC 501 D 1 
HETATM 43 O O2D HEC . . . Z 17 28.398 8.91 61.889 1 133.3 ? O2D HEC 501 D 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    158 
_model_server_stats.query_time_ms           452 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#