data_4D6T
#
_model_server_result.job_id            -jxqgBbbzMcTCYl9efs1UA 
_model_server_result.datetime_utc      '2024-11-24 02:40:21' 
_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":"Z","auth_seq_id":501}' 
#
_entry.id    4D6T 
#
_exptl.entry_id    4D6T 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              618.503 
_entity.id                          16 
_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            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
? 16 Z N N 
? 16 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
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 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 446 n n 
FE NB HEC sing 447 n n 
FE NC HEC sing 448 n n 
FE ND HEC sing 449 n n 
CHA C1A HEC doub 450 n n 
CHA C4D HEC sing 451 n n 
CHA HHA HEC sing 452 n n 
CHB C4A HEC doub 453 n n 
CHB C1B HEC sing 454 n n 
CHB HHB HEC sing 455 n n 
CHC C4B HEC doub 456 n n 
CHC C1C HEC sing 457 n n 
CHC HHC HEC sing 458 n n 
CHD C4C HEC doub 459 n n 
CHD C1D HEC sing 460 n n 
CHD HHD HEC sing 461 n n 
NA C1A HEC sing 462 n y 
NA C4A HEC sing 463 n y 
C1A C2A HEC sing 464 n y 
C2A C3A HEC doub 465 n y 
C2A CAA HEC sing 466 n n 
C3A C4A HEC sing 467 n y 
C3A CMA HEC sing 468 n n 
CMA HMA1 HEC sing 469 n n 
CMA HMA2 HEC sing 470 n n 
CMA HMA3 HEC sing 471 n n 
CAA CBA HEC sing 472 n n 
CAA HAA1 HEC sing 473 n n 
CAA HAA2 HEC sing 474 n n 
CBA CGA HEC sing 475 n n 
CBA HBA1 HEC sing 476 n n 
CBA HBA2 HEC sing 477 n n 
CGA O1A HEC doub 478 n n 
CGA O2A HEC sing 479 n n 
O2A H2A HEC sing 480 n n 
NB C1B HEC sing 481 n y 
NB C4B HEC sing 482 n y 
C1B C2B HEC doub 483 n y 
C2B C3B HEC sing 484 n y 
C2B CMB HEC sing 485 n n 
C3B C4B HEC sing 486 n y 
C3B CAB HEC doub 487 e n 
CMB HMB1 HEC sing 488 n n 
CMB HMB2 HEC sing 489 n n 
CMB HMB3 HEC sing 490 n n 
CAB CBB HEC sing 491 n n 
CAB HAB HEC sing 492 n n 
CBB HBB1 HEC sing 493 n n 
CBB HBB2 HEC sing 494 n n 
CBB HBB3 HEC sing 495 n n 
NC C1C HEC sing 496 n y 
NC C4C HEC sing 497 n y 
C1C C2C HEC doub 498 n y 
C2C C3C HEC sing 499 n y 
C2C CMC HEC sing 500 n n 
C3C C4C HEC sing 501 n y 
C3C CAC HEC doub 502 e n 
CMC HMC1 HEC sing 503 n n 
CMC HMC2 HEC sing 504 n n 
CMC HMC3 HEC sing 505 n n 
CAC CBC HEC sing 506 n n 
CAC HAC HEC sing 507 n n 
CBC HBC1 HEC sing 508 n n 
CBC HBC2 HEC sing 509 n n 
CBC HBC3 HEC sing 510 n n 
ND C1D HEC sing 511 n y 
ND C4D HEC sing 512 n y 
C1D C2D HEC doub 513 n y 
C2D C3D HEC sing 514 n y 
C2D CMD HEC sing 515 n n 
C3D C4D HEC doub 516 n y 
C3D CAD HEC sing 517 n n 
CMD HMD1 HEC sing 518 n n 
CMD HMD2 HEC sing 519 n n 
CMD HMD3 HEC sing 520 n n 
CAD CBD HEC sing 521 n n 
CAD HAD1 HEC sing 522 n n 
CAD HAD2 HEC sing 523 n n 
CBD CGD HEC sing 524 n n 
CBD HBD1 HEC sing 525 n n 
CBD HBD2 HEC sing 526 n n 
CGD O1D HEC doub 527 n n 
CGD O2D HEC sing 528 n n 
O2D H2D HEC sing 529 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 FE FE HEC . . . Z 16 24.5 1.605 60.643 1 112.97 ? FE HEC 501 D 1 
HETATM 2 C CHA HEC . . . Z 16 26.436 4.439 60.414 1 101.81 ? CHA HEC 501 D 1 
HETATM 3 C CHB HEC . . . Z 16 26.715 -0.079 58.644 1 93.63 ? CHB HEC 501 D 1 
HETATM 4 C CHC HEC . . . Z 16 22.917 -1.355 61.479 1 123.83 ? CHC HEC 501 D 1 
HETATM 5 C CHD HEC . . . Z 16 22.012 3.429 62.189 1 126 ? CHD HEC 501 D 1 
HETATM 6 N NA HEC . . . Z 16 26.29 2.08 59.683 1 96.82 ? NA HEC 501 D 1 
HETATM 7 C C1A HEC . . . Z 16 26.922 3.248 59.715 1 97.72 ? C1A HEC 501 D 1 
HETATM 8 C C2A HEC . . . Z 16 28.149 3.321 58.915 1 95.11 ? C2A HEC 501 D 1 
HETATM 9 C C3A HEC . . . Z 16 28.269 1.96 58.375 1 86.63 ? C3A HEC 501 D 1 
HETATM 10 C C4A HEC . . . Z 16 27.043 1.317 58.903 1 88.93 ? C4A HEC 501 D 1 
HETATM 11 C CMA HEC . . . Z 16 29.344 1.387 57.49 1 80.97 ? CMA HEC 501 D 1 
HETATM 12 C CAA HEC . . . Z 16 29.061 4.519 58.884 1 101.79 ? CAA HEC 501 D 1 
HETATM 13 C CBA HEC . . . Z 16 29.524 5.178 57.609 1 105.65 ? CBA HEC 501 D 1 
HETATM 14 C CGA HEC . . . Z 16 30.916 5.691 57.929 1 114.39 ? CGA HEC 501 D 1 
HETATM 15 O O1A HEC . . . Z 16 31.714 5.862 56.993 1 131.11 ? O1A HEC 501 D 1 
HETATM 16 O O2A HEC . . . Z 16 31.258 5.92 59.114 1 105.81 ? O2A HEC 501 D 1 
HETATM 17 N NB HEC . . . Z 16 24.785 -0.4 60.148 1 99.23 ? NB HEC 501 D 1 
HETATM 18 C C1B HEC . . . Z 16 25.693 -0.899 59.309 1 96.46 ? C1B HEC 501 D 1 
HETATM 19 C C2B HEC . . . Z 16 25.67 -2.38 59.124 1 102.41 ? C2B HEC 501 D 1 
HETATM 20 C C3B HEC . . . Z 16 24.553 -2.748 59.982 1 103.25 ? C3B HEC 501 D 1 
HETATM 21 C C4B HEC . . . Z 16 24.08 -1.463 60.563 1 111.42 ? C4B HEC 501 D 1 
HETATM 22 C CMB HEC . . . Z 16 26.579 -3.235 58.271 1 104.03 ? CMB HEC 501 D 1 
HETATM 23 C CAB HEC . . . Z 16 24.011 -4.106 60.232 1 102.06 ? CAB HEC 501 D 1 
HETATM 24 C CBB HEC . . . Z 16 24.587 -5.349 59.597 1 102.18 ? CBB HEC 501 D 1 
HETATM 25 N NC HEC . . . Z 16 22.753 1.114 61.687 1 116.62 ? NC HEC 501 D 1 
HETATM 26 C C1C HEC . . . Z 16 22.254 -0.109 61.929 1 118.81 ? C1C HEC 501 D 1 
HETATM 27 C C2C HEC . . . Z 16 20.969 -0.131 62.668 1 118.82 ? C2C HEC 501 D 1 
HETATM 28 C C3C HEC . . . Z 16 20.713 1.308 62.866 1 117.92 ? C3C HEC 501 D 1 
HETATM 29 C C4C HEC . . . Z 16 21.856 1.964 62.206 1 119.68 ? C4C HEC 501 D 1 
HETATM 30 C CMC HEC . . . Z 16 20.203 -1.352 63.085 1 127.94 ? CMC HEC 501 D 1 
HETATM 31 C CAC HEC . . . Z 16 19.592 2.046 63.533 1 118.16 ? CAC HEC 501 D 1 
HETATM 32 C CBC HEC . . . Z 16 18.41 1.389 64.218 1 130.12 ? CBC HEC 501 D 1 
HETATM 33 N ND HEC . . . Z 16 24.273 3.618 61.219 1 115.09 ? ND HEC 501 D 1 
HETATM 34 C C1D HEC . . . Z 16 23.207 4.187 61.795 1 118.85 ? C1D HEC 501 D 1 
HETATM 35 C C2D HEC . . . Z 16 23.331 5.642 62.07 1 118.03 ? C2D HEC 501 D 1 
HETATM 36 C C3D HEC . . . Z 16 24.659 5.956 61.551 1 111.93 ? C3D HEC 501 D 1 
HETATM 37 C C4D HEC . . . Z 16 25.132 4.638 61.046 1 109.23 ? C4D HEC 501 D 1 
HETATM 38 C CMD HEC . . . Z 16 22.362 6.605 62.714 1 118.3 ? CMD HEC 501 D 1 
HETATM 39 C CAD HEC . . . Z 16 25.254 7.336 61.589 1 109.2 ? CAD HEC 501 D 1 
HETATM 40 C CBD HEC . . . Z 16 26.736 7.375 61.313 1 112.39 ? CBD HEC 501 D 1 
HETATM 41 C CGD HEC . . . Z 16 27.257 8.639 61.915 1 118.89 ? CGD HEC 501 D 1 
HETATM 42 O O1D HEC . . . Z 16 27.562 8.604 63.115 1 122.01 ? O1D HEC 501 D 1 
HETATM 43 O O2D HEC . . . Z 16 27.349 9.661 61.208 1 138.51 ? O2D HEC 501 D 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    44 
_model_server_stats.query_time_ms           401 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           43 
#