data_8P5U
#
_model_server_result.job_id            1zBj7y4a1EQ80NeZTdIpJw 
_model_server_result.datetime_utc      '2024-11-26 08:41:29' 
_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          8p5u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":1304}' 
#
_entry.id    8P5U 
#
_exptl.entry_id    8P5U 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              425.314 
_entity.id                          5 
_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            8P5U 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8P5U 
_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,Y,Z,AA,BA,CA,DA 
_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
? 5 J N N 
? 5 N N N 
? 5 R N N 
? 5 V N N 
? 5 Z N N 
? 5 DA 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc2 A OD1 ASN 680 A ASN 678 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc3 A O ILE 682 A ILE 680 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc4 G MG MG . A MG 1301 1_555 J O2B TPP . A TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc5 G MG MG . A MG 1301 1_555 J O1A TPP . A TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc6 B OD1 ASP 647 B ASP 645 1_555 K MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc7 B OD1 ASN 680 B ASN 678 1_555 K MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc8 B O ILE 682 B ILE 680 1_555 K MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc9 K MG MG . B MG 1301 1_555 N O2A TPP . B TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc10 K MG MG . B MG 1301 1_555 N O2B TPP . B TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc11 C OD1 ASP 647 C ASP 645 1_555 O MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc12 C OD1 ASN 680 C ASN 678 1_555 O MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc13 C O ILE 682 C ILE 680 1_555 O MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc14 O MG MG . C MG 1301 1_555 R O2B TPP . C TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc15 O MG MG . C MG 1301 1_555 R O1A TPP . C TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc16 D OD1 ASP 647 D ASP 645 1_555 S MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc17 D OD1 ASN 680 D ASN 678 1_555 S MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc18 D O ILE 682 D ILE 680 1_555 S MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc19 S MG MG . D MG 1301 1_555 V O2A TPP . D TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? 
metalc ? metalc20 S MG MG . D MG 1301 1_555 V O2B TPP . D TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc21 E OD1 ASP 647 E ASP 645 1_555 W MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? 
metalc ? metalc22 E OD1 ASN 680 E ASN 678 1_555 W MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc23 E O ILE 682 E ILE 680 1_555 W MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc24 W MG MG . E MG 1301 1_555 Z O2B TPP . E TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc25 W MG MG . E MG 1301 1_555 Z O1A TPP . E TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc26 F OD1 ASP 647 F ASP 645 1_555 AA MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc27 F OD1 ASN 680 F ASN 678 1_555 AA MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc28 F O ILE 682 F ILE 680 1_555 AA MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc29 AA MG MG . F MG 1301 1_555 DA O2B TPP . F TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc30 AA MG MG . F MG 1301 1_555 DA O2A TPP . F TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
#
_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 481 n y 
N1' C6' TPP sing 482 n y 
C2' CM2 TPP sing 483 n n 
C2' N3' TPP sing 484 n y 
CM2 HM21 TPP sing 485 n n 
CM2 HM22 TPP sing 486 n n 
CM2 HM23 TPP sing 487 n n 
N3' C4' TPP doub 488 n y 
C4' N4' TPP sing 489 n n 
C4' C5' TPP sing 490 n y 
N4' HN41 TPP sing 491 n n 
N4' HN42 TPP sing 492 n n 
C5' C6' TPP doub 493 n y 
C5' C7' TPP sing 494 n n 
C6' H6' TPP sing 495 n n 
C7' N3 TPP sing 496 n n 
C7' "H7'1" TPP sing 497 n n 
C7' "H7'2" TPP sing 498 n n 
N3 C2 TPP doub 499 n y 
N3 C4 TPP sing 500 n y 
C2 S1 TPP sing 501 n y 
C2 H2 TPP sing 502 n n 
S1 C5 TPP sing 503 n y 
C5 C4 TPP doub 504 n y 
C5 C6 TPP sing 505 n n 
C4 CM4 TPP sing 506 n n 
CM4 HM41 TPP sing 507 n n 
CM4 HM42 TPP sing 508 n n 
CM4 HM43 TPP sing 509 n n 
C6 C7 TPP sing 510 n n 
C6 H61 TPP sing 511 n n 
C6 H62 TPP sing 512 n n 
C7 O7 TPP sing 513 n n 
C7 H71 TPP sing 514 n n 
C7 H72 TPP sing 515 n n 
O7 PA TPP sing 516 n n 
PA O1A TPP doub 517 n n 
PA O2A TPP sing 518 n n 
PA O3A TPP sing 519 n n 
O2A HOA2 TPP sing 520 n n 
O3A PB TPP sing 521 n n 
PB O1B TPP doub 522 n n 
PB O2B TPP sing 523 n n 
PB O3B TPP sing 524 n n 
O2B HOB2 TPP sing 525 n n 
O3B HOB3 TPP sing 526 n n 
#
_atom_sites.entry_id                     8P5U 
_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 COA A 1 1302 1304 COA COA . 
I 4 ACO A 1 1303 1401 ACO ACO . 
J 5 TPP A 1 1304 1501 TPP TPP . 
K 2 MG B 1 1301 6 MG MG . 
L 3 COA B 1 1302 1304 COA COA . 
M 4 ACO B 1 1303 1401 ACO ACO . 
N 5 TPP B 1 1304 1501 TPP TPP . 
O 2 MG C 1 1301 2 MG MG . 
P 3 COA C 1 1302 1304 COA COA . 
Q 4 ACO C 1 1303 1401 ACO ACO . 
R 5 TPP C 1 1304 1501 TPP TPP . 
S 2 MG D 1 1301 4 MG MG . 
T 3 COA D 1 1302 1304 COA COA . 
U 4 ACO D 1 1303 1401 ACO ACO . 
V 5 TPP D 1 1304 1501 TPP TPP . 
W 2 MG E 1 1301 1 MG MG . 
X 3 COA E 1 1302 1304 COA COA . 
Y 4 ACO E 1 1303 1401 ACO ACO . 
Z 5 TPP E 1 1304 1501 TPP TPP . 
AA 2 MG F 1 1301 5 MG MG . 
BA 3 COA F 1 1302 1304 COA COA . 
CA 4 ACO F 1 1303 1401 ACO ACO . 
DA 5 TPP F 1 1304 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 . . . V 5 105.136 203.417 175.225 1 46.43 ? N1' TPP 1304 D 1 
HETATM 2 C C2' TPP . . . V 5 105.548 204.465 174.51 1 43.9 ? C2' TPP 1304 D 1 
HETATM 3 C CM2 TPP . . . V 5 105.573 204.314 173.025 1 47.81 ? CM2 TPP 1304 D 1 
HETATM 4 N N3' TPP . . . V 5 105.972 205.625 175.012 1 46.28 ? N3' TPP 1304 D 1 
HETATM 5 C C4' TPP . . . V 5 105.99 205.765 176.345 1 42.12 ? C4' TPP 1304 D 1 
HETATM 6 N N4' TPP . . . V 5 106.313 206.969 176.814 1 46.68 ? N4' TPP 1304 D 1 
HETATM 7 C C5' TPP . . . V 5 105.58 204.702 177.196 1 41.56 ? C5' TPP 1304 D 1 
HETATM 8 C C6' TPP . . . V 5 105.162 203.565 176.552 1 44.73 ? C6' TPP 1304 D 1 
HETATM 9 C C7' TPP . . . V 5 105.605 204.777 178.701 1 41.4 ? C7' TPP 1304 D 1 
HETATM 10 N N3 TPP . . . V 5 106.973 204.881 179.276 1 39.14 ? N3 TPP 1304 D 1 
HETATM 11 C C2 TPP . . . V 5 107.535 206.022 179.602 1 38.27 ? C2 TPP 1304 D 1 
HETATM 12 S S1 TPP . . . V 5 109.075 205.815 180.217 1 35.79 ? S1 TPP 1304 D 1 
HETATM 13 C C5 TPP . . . V 5 108.966 204.159 180.041 1 31.91 ? C5 TPP 1304 D 1 
HETATM 14 C C4 TPP . . . V 5 107.779 203.773 179.523 1 38.71 ? C4 TPP 1304 D 1 
HETATM 15 C CM4 TPP . . . V 5 107.31 202.394 179.212 1 46.66 ? CM4 TPP 1304 D 1 
HETATM 16 C C6 TPP . . . V 5 110.143 203.314 180.425 1 29.85 ? C6 TPP 1304 D 1 
HETATM 17 C C7 TPP . . . V 5 111.349 203.576 179.563 1 29.43 ? C7 TPP 1304 D 1 
HETATM 18 O O7 TPP . . . V 5 112.432 202.729 179.997 1 28.43 ? O7 TPP 1304 D 1 
HETATM 19 P PA TPP . . . V 5 113.887 202.989 179.427 1 21.61 ? PA TPP 1304 D 1 
HETATM 20 O O1A TPP . . . V 5 113.801 203.027 177.963 1 31.31 ? O1A TPP 1304 D 1 
HETATM 21 O O2A TPP . . . V 5 114.848 202.062 180.05 1 32.32 ? O2A TPP 1304 D 1 
HETATM 22 O O3A TPP . . . V 5 114.176 204.441 180.02 1 27.77 ? O3A TPP 1304 D 1 
HETATM 23 P PB TPP . . . V 5 114.919 205.009 181.3 1 19.23 ? PB TPP 1304 D 1 
HETATM 24 O O1B TPP . . . V 5 115.736 206.177 180.824 1 29.75 ? O1B TPP 1304 D 1 
HETATM 25 O O2B TPP . . . V 5 115.755 203.842 181.754 1 27.86 ? O2B TPP 1304 D 1 
HETATM 26 O O3B TPP . . . V 5 113.856 205.406 182.286 1 27.89 ? O3B TPP 1304 D 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    76 
_model_server_stats.query_time_ms           396 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           26 
#