data_8P5T
#
_model_server_result.job_id            g5qcdyQNDn3g1PBk3A5jJQ 
_model_server_result.datetime_utc      '2024-10-19 07:37:02' 
_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          8p5t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":1303}' 
#
_entry.id    8P5T 
#
_exptl.entry_id    8P5T 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              425.314 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'THIAMINE DIPHOSPHATE' 
_entity.pdbx_number_of_molecules    6 
_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         90 
_cell.entry_id            8P5T 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8P5T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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
? 4 I N N 
? 4 L N N 
? 4 O N N 
? 4 R N N 
? 4 U N N 
? 4 X 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
metalc ? metalc1 A OD1 ASP 647 A ASP 645 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc2 A OD1 ASN 680 A ASN 678 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc3 A O ILE 682 A ILE 680 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc4 G MG MG . A MG 1301 1_555 I O2B TPP . A TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc5 G MG MG . A MG 1301 1_555 I O1A TPP . A TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc6 B OD1 ASP 647 B ASP 645 1_555 J MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc7 B OD1 ASN 680 B ASN 678 1_555 J MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc8 B O ILE 682 B ILE 680 1_555 J MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc9 J MG MG . B MG 1301 1_555 L O2A TPP . B TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc10 J MG MG . B MG 1301 1_555 L O2B TPP . B TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? 
metalc ? metalc11 C OD1 ASP 647 C ASP 645 1_555 M MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc12 C OD1 ASN 680 C ASN 678 1_555 M MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc13 C O ILE 682 C ILE 680 1_555 M MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc14 M MG MG . C MG 1301 1_555 O O2B TPP . C TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc15 M MG MG . C MG 1301 1_555 O O1A TPP . C TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc16 D OD1 ASP 647 D ASP 645 1_555 P MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc17 D OD1 ASN 680 D ASN 678 1_555 P MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc18 D O ILE 682 D ILE 680 1_555 P MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc19 P MG MG . D MG 1301 1_555 R O2A TPP . D TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc20 P MG MG . D MG 1301 1_555 R O2B TPP . D TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc21 E OD1 ASP 647 E ASP 645 1_555 S MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc22 E OD1 ASN 680 E ASN 678 1_555 S MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc23 E O ILE 682 E ILE 680 1_555 S MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc24 S MG MG . E MG 1301 1_555 U O2B TPP . E TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc25 S MG MG . E MG 1301 1_555 U O1A TPP . E TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc26 F OD1 ASP 647 F ASP 645 1_555 V MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc27 F OD1 ASN 680 F ASN 678 1_555 V MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc28 F O ILE 682 F ILE 680 1_555 V MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
metalc ? metalc29 V MG MG . F MG 1301 1_555 X O2B TPP . F TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc30 V MG MG . F MG 1301 1_555 X O2A TPP . F TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
#
_chem_comp.formula           'C12 H19 N4 O7 P2 S 1' 
_chem_comp.formula_weight    425.314 
_chem_comp.id                TPP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'THIAMINE DIPHOSPHATE' 
_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
N1' C2' TPP doub 395 n y 
N1' C6' TPP sing 396 n y 
C2' CM2 TPP sing 397 n n 
C2' N3' TPP sing 398 n y 
CM2 HM21 TPP sing 399 n n 
CM2 HM22 TPP sing 400 n n 
CM2 HM23 TPP sing 401 n n 
N3' C4' TPP doub 402 n y 
C4' N4' TPP sing 403 n n 
C4' C5' TPP sing 404 n y 
N4' HN41 TPP sing 405 n n 
N4' HN42 TPP sing 406 n n 
C5' C6' TPP doub 407 n y 
C5' C7' TPP sing 408 n n 
C6' H6' TPP sing 409 n n 
C7' N3 TPP sing 410 n n 
C7' "H7'1" TPP sing 411 n n 
C7' "H7'2" TPP sing 412 n n 
N3 C2 TPP doub 413 n y 
N3 C4 TPP sing 414 n y 
C2 S1 TPP sing 415 n y 
C2 H2 TPP sing 416 n n 
S1 C5 TPP sing 417 n y 
C5 C4 TPP doub 418 n y 
C5 C6 TPP sing 419 n n 
C4 CM4 TPP sing 420 n n 
CM4 HM41 TPP sing 421 n n 
CM4 HM42 TPP sing 422 n n 
CM4 HM43 TPP sing 423 n n 
C6 C7 TPP sing 424 n n 
C6 H61 TPP sing 425 n n 
C6 H62 TPP sing 426 n n 
C7 O7 TPP sing 427 n n 
C7 H71 TPP sing 428 n n 
C7 H72 TPP sing 429 n n 
O7 PA TPP sing 430 n n 
PA O1A TPP doub 431 n n 
PA O2A TPP sing 432 n n 
PA O3A TPP sing 433 n n 
O2A HOA2 TPP sing 434 n n 
O3A PB TPP sing 435 n n 
PB O1B TPP doub 436 n n 
PB O2B TPP sing 437 n n 
PB O3B TPP sing 438 n n 
O2B HOB2 TPP sing 439 n n 
O3B HOB3 TPP sing 440 n n 
#
_atom_sites.entry_id                     8P5T 
_atom_sites.fract_transf_matrix[1][1]    1 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    1 
_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]    1 
_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
G 2 MG A 1 1301 3 MG MG . 
H 3 ACO A 1 1302 1401 ACO ACO . 
I 4 TPP A 1 1303 1501 TPP TPP . 
J 2 MG B 1 1301 6 MG MG . 
K 3 ACO B 1 1302 1401 ACO ACO . 
L 4 TPP B 1 1303 1501 TPP TPP . 
M 2 MG C 1 1301 2 MG MG . 
N 3 ACO C 1 1302 1401 ACO ACO . 
O 4 TPP C 1 1303 1501 TPP TPP . 
P 2 MG D 1 1301 4 MG MG . 
Q 3 ACO D 1 1302 1401 ACO ACO . 
R 4 TPP D 1 1303 1501 TPP TPP . 
S 2 MG E 1 1301 1 MG MG . 
T 3 ACO E 1 1302 1401 ACO ACO . 
U 4 TPP E 1 1303 1501 TPP TPP . 
V 2 MG F 1 1301 5 MG MG . 
W 3 ACO F 1 1302 1401 ACO ACO . 
X 4 TPP F 1 1303 1501 TPP TPP . 
#
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 N N1' TPP . . . R 4 105.162 203.442 176.06 1 46.79 ? N1' TPP 1303 D 1 
HETATM 2 C C2' TPP . . . R 4 105.544 204.49 175.335 1 44.75 ? C2' TPP 1303 D 1 
HETATM 3 C CM2 TPP . . . R 4 105.532 204.344 173.851 1 48.38 ? CM2 TPP 1303 D 1 
HETATM 4 N N3' TPP . . . R 4 105.94 205.656 175.84 1 47.22 ? N3' TPP 1303 D 1 
HETATM 5 C C4' TPP . . . R 4 105.95 205.79 177.171 1 42.99 ? C4' TPP 1303 D 1 
HETATM 6 N N4' TPP . . . R 4 106.345 206.98 177.641 1 47.24 ? N4' TPP 1303 D 1 
HETATM 7 C C5' TPP . . . R 4 105.573 204.739 178.022 1 41.81 ? C5' TPP 1303 D 1 
HETATM 8 C C6' TPP . . . R 4 105.176 203.581 177.39 1 45.01 ? C6' TPP 1303 D 1 
HETATM 9 C C7' TPP . . . R 4 105.579 204.841 179.533 1 41.36 ? C7' TPP 1303 D 1 
HETATM 10 N N3 TPP . . . R 4 106.922 204.897 180.115 1 39.38 ? N3 TPP 1303 D 1 
HETATM 11 C C2 TPP . . . R 4 107.525 206.053 180.485 1 38.21 ? C2 TPP 1303 D 1 
HETATM 12 S S1 TPP . . . R 4 109.023 205.736 181.084 1 33.82 ? S1 TPP 1303 D 1 
HETATM 13 C C5 TPP . . . R 4 108.962 204.119 180.933 1 32.05 ? C5 TPP 1303 D 1 
HETATM 14 C C4 TPP . . . R 4 107.734 203.788 180.382 1 38.53 ? C4 TPP 1303 D 1 
HETATM 15 C CM4 TPP . . . R 4 107.276 202.4 180.056 1 46.67 ? CM4 TPP 1303 D 1 
HETATM 16 C C6 TPP . . . R 4 110.151 203.35 181.373 1 30.6 ? C6 TPP 1303 D 1 
HETATM 17 C C7 TPP . . . R 4 111.296 203.561 180.454 1 30.11 ? C7 TPP 1303 D 1 
HETATM 18 O O7 TPP . . . R 4 112.394 202.726 180.873 1 29.15 ? O7 TPP 1303 D 1 
HETATM 19 P PA TPP . . . R 4 113.847 202.995 180.272 1 21.28 ? PA TPP 1303 D 1 
HETATM 20 O O1A TPP . . . R 4 113.769 203.015 178.796 1 31.02 ? O1A TPP 1303 D 1 
HETATM 21 O O2A TPP . . . R 4 114.797 202.051 180.907 1 31.99 ? O2A TPP 1303 D 1 
HETATM 22 O O3A TPP . . . R 4 114.152 204.448 180.85 1 27.96 ? O3A TPP 1303 D 1 
HETATM 23 P PB TPP . . . R 4 114.893 205.013 182.149 1 19.62 ? PB TPP 1303 D 1 
HETATM 24 O O1B TPP . . . R 4 115.801 206.087 181.704 1 29.54 ? O1B TPP 1303 D 1 
HETATM 25 O O2B TPP . . . R 4 115.605 203.845 182.689 1 29.18 ? O2B TPP 1303 D 1 
HETATM 26 O O3B TPP . . . R 4 113.824 205.512 183.026 1 28.01 ? O3B TPP 1303 D 1 
#
_model_server_stats.io_time_ms              35 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    93 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           26 
#