data_8P5R
#
_model_server_result.job_id            WtzyKD_bLgHbseT5E8z3kA 
_model_server_result.datetime_utc      '2025-09-30 16:24:17' 
_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          8p5r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DA","auth_seq_id":1303}' 
#
_entry.id    8P5R 
#
_exptl.entry_id    8P5R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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         120 
_cell.entry_id            8P5R 
_cell.length_a            325.75 
_cell.length_b            325.75 
_cell.length_c            396.944 
_cell.Z_PDB               60 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8P5R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexadecameric 
_pdbx_struct_assembly.oligomeric_count      16 
_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,EA,FA,GA,HA,IA,JA 
_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    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
? 5 S N N 
? 5 W N N 
? 5 AA N N 
? 5 DA N N 
? 5 GA N N 
? 5 JA 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 OE2 GLU 311 A GLU 288 1_555 T CA CA . A CA 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.985 ? 
metalc ? metalc2 Q MG MG . A MG 1301 1_555 S O3A TPP . A TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? 
metalc ? metalc3 Q MG MG . A MG 1301 1_555 S O1B TPP . A TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc4 T CA CA . A CA 1304 1_555 C OE2 GLU 311 C GLU 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? 
metalc ? metalc5 T CA CA . A CA 1304 1_555 E OE2 GLU 311 E GLU 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.182 ? 
metalc ? metalc6 B OE2 GLU 311 B GLU 288 1_555 X CA CA . B CA 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? 
metalc ? metalc7 B OD1 ASP 668 B ASP 645 1_555 U MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? 
metalc ? metalc8 B OD1 ASN 701 B ASN 678 1_555 U MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc9 B O ILE 703 B ILE 680 1_555 U MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc10 U MG MG . B MG 1301 1_555 W O2A TPP . B TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc11 U MG MG . B MG 1301 1_555 W O1B TPP . B TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? 
metalc ? metalc12 X CA CA . B CA 1304 1_555 D OE2 GLU 311 D GLU 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? 
metalc ? metalc13 X CA CA . B CA 1304 1_555 F OE2 GLU 311 F GLU 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? 
metalc ? metalc14 C OD1 ASP 668 C ASP 645 1_555 Y MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? 
metalc ? metalc15 Y MG MG . C MG 1301 1_555 AA O1A TPP . C TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc16 Y MG MG . C MG 1301 1_555 AA O3A TPP . C TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc17 Y MG MG . C MG 1301 1_555 AA O1B TPP . C TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? 
metalc ? metalc18 Y MG MG . C MG 1301 1_555 AA O2B TPP . C TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? 
metalc ? metalc19 D OD1 ASP 668 D ASP 645 1_555 BA MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc20 D OD1 ASN 701 D ASN 678 1_555 BA MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
metalc ? metalc21 BA MG MG . D MG 1301 1_555 DA O1B TPP . D TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? 
metalc ? metalc22 BA MG MG . D MG 1301 1_555 DA O3B TPP . D TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? 
metalc ? metalc23 BA MG MG . D MG 1301 1_555 DA O2A TPP . D TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc24 E OD1 ASP 668 E ASP 645 1_555 EA MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? 
metalc ? metalc25 E OD1 ASN 701 E ASN 678 1_555 EA MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc26 E O ILE 703 E ILE 680 1_555 EA MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
metalc ? metalc27 EA MG MG . E MG 1301 1_555 GA O1A TPP . E TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? 
metalc ? metalc28 EA MG MG . E MG 1301 1_555 GA O3B TPP . E TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc29 HA MG MG . F MG 1301 1_555 JA O1A TPP . F TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
metalc ? metalc30 HA MG MG . F MG 1301 1_555 JA O3A TPP . F TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc31 HA MG MG . F MG 1301 1_555 JA O3B TPP . F TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? 
#
_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 304 n y 
N1' C6' TPP sing 305 n y 
C2' CM2 TPP sing 306 n n 
C2' N3' TPP sing 307 n y 
CM2 HM21 TPP sing 308 n n 
CM2 HM22 TPP sing 309 n n 
CM2 HM23 TPP sing 310 n n 
N3' C4' TPP doub 311 n y 
C4' N4' TPP sing 312 n n 
C4' C5' TPP sing 313 n y 
N4' HN41 TPP sing 314 n n 
N4' HN42 TPP sing 315 n n 
C5' C6' TPP doub 316 n y 
C5' C7' TPP sing 317 n n 
C6' H6' TPP sing 318 n n 
C7' N3 TPP sing 319 n n 
C7' "H7'1" TPP sing 320 n n 
C7' "H7'2" TPP sing 321 n n 
N3 C2 TPP doub 322 n y 
N3 C4 TPP sing 323 n y 
C2 S1 TPP sing 324 n y 
C2 H2 TPP sing 325 n n 
S1 C5 TPP sing 326 n y 
C5 C4 TPP doub 327 n y 
C5 C6 TPP sing 328 n n 
C4 CM4 TPP sing 329 n n 
CM4 HM41 TPP sing 330 n n 
CM4 HM42 TPP sing 331 n n 
CM4 HM43 TPP sing 332 n n 
C6 C7 TPP sing 333 n n 
C6 H61 TPP sing 334 n n 
C6 H62 TPP sing 335 n n 
C7 O7 TPP sing 336 n n 
C7 H71 TPP sing 337 n n 
C7 H72 TPP sing 338 n n 
O7 PA TPP sing 339 n n 
PA O1A TPP doub 340 n n 
PA O2A TPP sing 341 n n 
PA O3A TPP sing 342 n n 
O2A HOA2 TPP sing 343 n n 
O3A PB TPP sing 344 n n 
PB O1B TPP doub 345 n n 
PB O2B TPP sing 346 n n 
PB O3B TPP sing 347 n n 
O2B HOB2 TPP sing 348 n n 
O3B HOB3 TPP sing 349 n n 
#
_atom_sites.entry_id                     8P5R 
_atom_sites.fract_transf_matrix[1][1]    0.00307 
_atom_sites.fract_transf_matrix[1][2]    0.001772 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.003545 
_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]    0.002519 
_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
Q 3 MG A 1 1301 2002 MG MG . 
R 4 CA A 1 1302 2003 CA CA . 
S 5 TPP A 1 1303 2301 TPP TPP . 
T 4 CA A 1 1304 2 CA CA . 
U 3 MG B 1 1301 2002 MG MG . 
V 4 CA B 1 1302 2003 CA CA . 
W 5 TPP B 1 1303 2301 TPP TPP . 
X 4 CA B 1 1304 1 CA CA . 
Y 3 MG C 1 1301 2002 MG MG . 
Z 4 CA C 1 1302 2003 CA CA . 
AA 5 TPP C 1 1303 2301 TPP TPP . 
BA 3 MG D 1 1301 2002 MG MG . 
CA 4 CA D 1 1302 2003 CA CA . 
DA 5 TPP D 1 1303 2301 TPP TPP . 
EA 3 MG E 1 1301 2002 MG MG . 
FA 4 CA E 1 1302 2003 CA CA . 
GA 5 TPP E 1 1303 2301 TPP TPP . 
HA 3 MG F 1 1301 2002 MG MG . 
IA 4 CA F 1 1302 2003 CA CA . 
JA 5 TPP F 1 1303 2301 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 . . . DA 5 189.399 -116.243 -18.987 1 223.11 ? N1' TPP 1303 D 1 
HETATM 2 C C2' TPP . . . DA 5 188.751 -117.004 -19.88 1 223.11 ? C2' TPP 1303 D 1 
HETATM 3 C CM2 TPP . . . DA 5 188.739 -116.536 -21.298 1 223.11 ? CM2 TPP 1303 D 1 
HETATM 4 N N3' TPP . . . DA 5 188.123 -118.153 -19.612 1 223.11 ? N3' TPP 1303 D 1 
HETATM 5 C C4' TPP . . . DA 5 188.142 -118.602 -18.346 1 223.11 ? C4' TPP 1303 D 1 
HETATM 6 N N4' TPP . . . DA 5 187.584 -119.796 -18.116 1 223.11 ? N4' TPP 1303 D 1 
HETATM 7 C C5' TPP . . . DA 5 188.796 -117.859 -17.319 1 223.11 ? C5' TPP 1303 D 1 
HETATM 8 C C6' TPP . . . DA 5 189.404 -116.695 -17.73 1 223.11 ? C6' TPP 1303 D 1 
HETATM 9 C C7' TPP . . . DA 5 188.826 -118.286 -15.876 1 223.11 ? C7' TPP 1303 D 1 
HETATM 10 N N3 TPP . . . DA 5 187.479 -118.381 -15.257 1 223.11 ? N3 TPP 1303 D 1 
HETATM 11 C C2 TPP . . . DA 5 186.873 -119.527 -15.014 1 223.11 ? C2 TPP 1303 D 1 
HETATM 12 S S1 TPP . . . DA 5 185.32 -119.318 -14.425 1 223.11 ? S1 TPP 1303 D 1 
HETATM 13 C C5 TPP . . . DA 5 185.485 -117.581 -14.493 1 223.11 ? C5 TPP 1303 D 1 
HETATM 14 C C4 TPP . . . DA 5 186.721 -117.253 -14.935 1 223.11 ? C4 TPP 1303 D 1 
HETATM 15 C CM4 TPP . . . DA 5 187.312 -115.884 -14.977 1 223.11 ? CM4 TPP 1303 D 1 
HETATM 16 C C6 TPP . . . DA 5 184.348 -116.654 -14.14 1 223.11 ? C6 TPP 1303 D 1 
HETATM 17 C C7 TPP . . . DA 5 182.994 -117.159 -14.595 1 223.11 ? C7 TPP 1303 D 1 
HETATM 18 O O7 TPP . . . DA 5 182.309 -116.102 -15.319 1 223.11 ? O7 TPP 1303 D 1 
HETATM 19 P PA TPP . . . DA 5 180.98 -116.409 -16.199 1 223.11 ? PA TPP 1303 D 1 
HETATM 20 O O1A TPP . . . DA 5 181.292 -116.368 -17.638 1 223.11 ? O1A TPP 1303 D 1 
HETATM 21 O O2A TPP . . . DA 5 179.919 -115.425 -15.745 1 223.11 ? O2A TPP 1303 D 1 
HETATM 22 O O3A TPP . . . DA 5 180.494 -117.865 -15.77 1 223.11 ? O3A TPP 1303 D 1 
HETATM 23 P PB TPP . . . DA 5 179.624 -118.471 -14.579 1 223.11 ? PB TPP 1303 D 1 
HETATM 24 O O1B TPP . . . DA 5 178.234 -118.648 -15.176 1 223.11 ? O1B TPP 1303 D 1 
HETATM 25 O O2B TPP . . . DA 5 180.216 -119.743 -14.093 1 223.11 ? O2B TPP 1303 D 1 
HETATM 26 O O3B TPP . . . DA 5 179.569 -117.394 -13.493 1 223.11 ? O3B TPP 1303 D 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    102 
_model_server_stats.query_time_ms           364 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           26 
#