data_8P5X
#
_model_server_result.job_id            yniE7GoriV8rwl18O8DppQ 
_model_server_result.datetime_utc      '2024-10-20 01:34:06' 
_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          8p5x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":1301}' 
#
_entry.id    8P5X 
#
_exptl.entry_id    8P5X 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              425.314 
_entity.id                          3 
_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            8P5X 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8P5X 
_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    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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
? 3 M N N 
? 3 O N N 
? 3 R N N 
? 3 S N N 
? 3 U N N 
? 3 W 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 ASN 680 A ASN 678 1_555 N MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc2 A O ILE 682 A ILE 680 1_555 N MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
metalc ? metalc3 M O2A TPP . A TPP 1301 1_555 N MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? 
metalc ? metalc4 M O3B TPP . A TPP 1301 1_555 N MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? 
metalc ? metalc5 B OD1 ASN 680 B ASN 678 1_555 P MG MG . B MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? 
metalc ? metalc6 B O ILE 682 B ILE 680 1_555 P MG MG . B MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
metalc ? metalc7 O O1A TPP . B TPP 1301 1_555 P MG MG . B MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
metalc ? metalc8 O O1B TPP . B TPP 1301 1_555 P MG MG . B MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? 
metalc ? metalc9 C OD1 ASN 680 C ASN 678 1_555 Q MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc10 C O ILE 682 C ILE 680 1_555 Q MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? 
metalc ? metalc11 Q MG MG . C MG 1301 1_555 R O3B TPP . C TPP 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? 
metalc ? metalc12 Q MG MG . C MG 1301 1_555 R O2A TPP . C TPP 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc13 D OD1 ASN 680 D ASN 678 1_555 T MG MG . D MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc14 D O ILE 682 D ILE 680 1_555 T MG MG . D MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc15 S O1A TPP . D TPP 1301 1_555 T MG MG . D MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc16 S O1B TPP . D TPP 1301 1_555 T MG MG . D MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? 
metalc ? metalc17 E OD1 ASN 680 E ASN 678 1_555 V MG MG . E MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc18 E O ILE 682 E ILE 680 1_555 V MG MG . E MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? 
metalc ? metalc19 U O2A TPP . E TPP 1301 1_555 V MG MG . E MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? 
metalc ? metalc20 U O3B TPP . E TPP 1301 1_555 V MG MG . E MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? 
metalc ? metalc21 F OD1 ASN 680 F ASN 678 1_555 X MG MG . F MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc22 F O ILE 682 F ILE 680 1_555 X MG MG . F MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc23 W O1A TPP . F TPP 1301 1_555 X MG MG . F MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? 
metalc ? metalc24 W O1B TPP . F TPP 1301 1_555 X MG MG . F MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.938 ? 
#
_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                     8P5X 
_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
M 3 TPP A 1 1301 1302 TPP TPP . 
N 4 MG A 1 1302 1303 MG MG . 
O 3 TPP B 1 1301 1302 TPP TPP . 
P 4 MG B 1 1302 1303 MG MG . 
Q 4 MG C 1 1301 1303 MG MG . 
R 3 TPP C 1 1302 1302 TPP TPP . 
S 3 TPP D 1 1301 1302 TPP TPP . 
T 4 MG D 1 1302 1303 MG MG . 
U 3 TPP E 1 1301 1302 TPP TPP . 
V 4 MG E 1 1302 1303 MG MG . 
W 3 TPP F 1 1301 1302 TPP TPP . 
X 4 MG F 1 1302 1303 MG MG . 
#
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 . . . W 3 102.029 197.841 154.385 1 157.87 ? N1' TPP 1301 F 1 
HETATM 2 C C2' TPP . . . W 3 101.209 197.01 155.041 1 158.58 ? C2' TPP 1301 F 1 
HETATM 3 C CM2 TPP . . . W 3 101.208 197.082 156.535 1 161.27 ? CM2 TPP 1301 F 1 
HETATM 4 N N3' TPP . . . W 3 100.385 196.12 154.472 1 156.85 ? N3' TPP 1301 F 1 
HETATM 5 C C4' TPP . . . W 3 100.362 196.048 153.128 1 153.95 ? C4' TPP 1301 F 1 
HETATM 6 N N4' TPP . . . W 3 99.526 195.158 152.582 1 153.77 ? N4' TPP 1301 F 1 
HETATM 7 C C5' TPP . . . W 3 101.193 196.898 152.335 1 155.3 ? C5' TPP 1301 F 1 
HETATM 8 C C6' TPP . . . W 3 102.001 197.762 153.047 1 156.4 ? C6' TPP 1301 F 1 
HETATM 9 C C7' TPP . . . W 3 101.145 196.938 150.829 1 154.22 ? C7' TPP 1301 F 1 
HETATM 10 N N3 TPP . . . W 3 101.604 195.685 150.17 1 150.58 ? N3 TPP 1301 F 1 
HETATM 11 C C2 TPP . . . W 3 100.781 194.764 149.706 1 155.95 ? C2 TPP 1301 F 1 
HETATM 12 S S1 TPP . . . W 3 101.59 193.51 148.944 1 155.97 ? S1 TPP 1301 F 1 
HETATM 13 C C5 TPP . . . W 3 103.116 194.249 149.26 1 136.58 ? C5 TPP 1301 F 1 
HETATM 14 C C4 TPP . . . W 3 102.953 195.415 149.93 1 137.05 ? C4 TPP 1301 F 1 
HETATM 15 C CM4 TPP . . . W 3 104.016 196.354 150.386 1 114.53 ? CM4 TPP 1301 F 1 
HETATM 16 C C6 TPP . . . W 3 104.397 193.598 148.811 1 122.54 ? C6 TPP 1301 F 1 
HETATM 17 C C7 TPP . . . W 3 104.914 192.567 149.789 1 109.41 ? C7 TPP 1301 F 1 
HETATM 18 O O7 TPP . . . W 3 106.079 191.924 149.213 1 91.69 ? O7 TPP 1301 F 1 
HETATM 19 P PA TPP . . . W 3 106.773 190.649 149.937 1 71.24 ? PA TPP 1301 F 1 
HETATM 20 O O1A TPP . . . W 3 108.224 190.611 149.473 1 78.24 ? O1A TPP 1301 F 1 
HETATM 21 O O2A TPP . . . W 3 106.635 190.733 151.402 1 76.02 ? O2A TPP 1301 F 1 
HETATM 22 O O3A TPP . . . W 3 106.061 189.348 149.345 1 76.02 ? O3A TPP 1301 F 1 
HETATM 23 P PB TPP . . . W 3 105.502 188.805 147.944 1 63.49 ? PB TPP 1301 F 1 
HETATM 24 O O1B TPP . . . W 3 106.312 189.296 146.794 1 72.98 ? O1B TPP 1301 F 1 
HETATM 25 O O2B TPP . . . W 3 104.045 189.27 147.904 1 71.69 ? O2B TPP 1301 F 1 
HETATM 26 O O3B TPP . . . W 3 105.517 187.285 148.089 1 69.66 ? O3B TPP 1301 F 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    337 
_model_server_stats.query_time_ms           255 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           26 
#