data_8YS5
#
_model_server_result.job_id            dZKZHdoFk9J1p384Y2lRDA 
_model_server_result.datetime_utc      '2025-08-01 11:02:47' 
_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          8ys5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":303}' 
#
_entry.id    8YS5 
#
_exptl.entry_id    8YS5 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              425.314 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'THIAMINE DIPHOSPHATE' 
_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         90 
_cell.entry_id            8YS5 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YS5 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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
? 7 M N N 
? 7 R 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 SG CYS 19 D CYS 19 1_555 I FE1 SF4 . D SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc2 A SG CYS 22 D CYS 22 1_555 I FE4 SF4 . D SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc3 A SG CYS 25 D CYS 25 1_555 I FE2 SF4 . D SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc4 A SG CYS 29 D CYS 29 1_555 J FE3 SF4 . D SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc5 A SG CYS 56 D CYS 56 1_555 J FE2 SF4 . D SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc6 A O CYS 59 D CYS 59 1_555 J FE1 SF4 . D SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? 
metalc ? metalc7 A SG CYS 59 D CYS 59 1_555 J FE1 SF4 . D SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc8 A SG CYS 62 D CYS 62 1_555 J FE4 SF4 . D SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc9 A SG CYS 66 D CYS 66 1_555 I FE3 SF4 . D SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc10 C SG CYS 19 C CYS 19 1_555 K FE1 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc11 C SG CYS 22 C CYS 22 1_555 K FE2 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc12 C SG CYS 53 C CYS 53 1_555 K FE3 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc13 C OD1 ASP 95 C ASP 95 1_555 L MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? 
metalc ? metalc14 C OD1 ASN 123 C ASN 123 1_555 L MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? 
metalc ? metalc15 C SG CYS 202 C CYS 202 1_555 K FE4 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc16 L MG MG . C MG 302 1_555 M O2A TPP . C TPP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? 
metalc ? metalc17 L MG MG . C MG 302 1_555 M O3B TPP . C TPP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? 
metalc ? metalc18 L MG MG . C MG 302 1_555 M O1B TPP . C TPP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? 
metalc ? metalc19 E SG CYS 19 F CYS 19 1_555 N FE1 SF4 . F SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc20 E SG CYS 22 F CYS 22 1_555 N FE4 SF4 . F SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc21 E SG CYS 25 F CYS 25 1_555 N FE2 SF4 . F SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc22 E SG CYS 29 F CYS 29 1_555 O FE3 SF4 . F SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc23 E SG CYS 56 F CYS 56 1_555 O FE2 SF4 . F SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc24 E SG CYS 59 F CYS 59 1_555 O FE1 SF4 . F SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc25 E SG CYS 62 F CYS 62 1_555 O FE4 SF4 . F SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc26 E SG CYS 66 F CYS 66 1_555 N FE3 SF4 . F SF4 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc27 G SG CYS 19 H CYS 19 1_555 P FE1 SF4 . H SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc28 G SG CYS 22 H CYS 22 1_555 P FE2 SF4 . H SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc29 G SG CYS 53 H CYS 53 1_555 P FE3 SF4 . H SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc30 G OD1 ASP 95 H ASP 95 1_555 Q MG MG . H MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc31 G OD1 ASN 123 H ASN 123 1_555 Q MG MG . H MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc32 G ND2 ASN 123 H ASN 123 1_555 Q MG MG . H MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? 
metalc ? metalc33 G O ILE 125 H ILE 125 1_555 Q MG MG . H MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc34 G SG CYS 202 H CYS 202 1_555 P FE4 SF4 . H SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc35 Q MG MG . H MG 302 1_555 R O2B TPP . H TPP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? 
metalc ? metalc36 Q MG MG . H MG 302 1_555 R O3A TPP . H TPP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? 
#
_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 316 n y 
N1' C6' TPP sing 317 n y 
C2' CM2 TPP sing 318 n n 
C2' N3' TPP sing 319 n y 
CM2 HM21 TPP sing 320 n n 
CM2 HM22 TPP sing 321 n n 
CM2 HM23 TPP sing 322 n n 
N3' C4' TPP doub 323 n y 
C4' N4' TPP sing 324 n n 
C4' C5' TPP sing 325 n y 
N4' HN41 TPP sing 326 n n 
N4' HN42 TPP sing 327 n n 
C5' C6' TPP doub 328 n y 
C5' C7' TPP sing 329 n n 
C6' H6' TPP sing 330 n n 
C7' N3 TPP sing 331 n n 
C7' "H7'1" TPP sing 332 n n 
C7' "H7'2" TPP sing 333 n n 
N3 C2 TPP doub 334 n y 
N3 C4 TPP sing 335 n y 
C2 S1 TPP sing 336 n y 
C2 H2 TPP sing 337 n n 
S1 C5 TPP sing 338 n y 
C5 C4 TPP doub 339 n y 
C5 C6 TPP sing 340 n n 
C4 CM4 TPP sing 341 n n 
CM4 HM41 TPP sing 342 n n 
CM4 HM42 TPP sing 343 n n 
CM4 HM43 TPP sing 344 n n 
C6 C7 TPP sing 345 n n 
C6 H61 TPP sing 346 n n 
C6 H62 TPP sing 347 n n 
C7 O7 TPP sing 348 n n 
C7 H71 TPP sing 349 n n 
C7 H72 TPP sing 350 n n 
O7 PA TPP sing 351 n n 
PA O1A TPP doub 352 n n 
PA O2A TPP sing 353 n n 
PA O3A TPP sing 354 n n 
O2A HOA2 TPP sing 355 n n 
O3A PB TPP sing 356 n n 
PB O1B TPP doub 357 n n 
PB O2B TPP sing 358 n n 
PB O3B TPP sing 359 n n 
O2B HOB2 TPP sing 360 n n 
O3B HOB3 TPP sing 361 n n 
#
_atom_sites.entry_id                     8YS5 
_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
I 5 SF4 D 1 201 1 SF4 SF4 . 
J 5 SF4 D 1 202 2 SF4 SF4 . 
K 5 SF4 C 1 301 3 SF4 SF4 . 
L 6 MG C 1 302 4 MG MG . 
M 7 TPP C 1 303 5 TPP TPP . 
N 5 SF4 F 1 201 1 SF4 SF4 . 
O 5 SF4 F 1 202 2 SF4 SF4 . 
P 5 SF4 H 1 301 3 SF4 SF4 . 
Q 6 MG H 1 302 4 MG MG . 
R 7 TPP H 1 303 5 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 . . . M 7 130.086 130.533 149.944 1 38.43 ? N1' TPP 303 C 1 
HETATM 2 C C2' TPP . . . M 7 129.685 129.851 151.003 1 39.95 ? C2' TPP 303 C 1 
HETATM 3 C CM2 TPP . . . M 7 128.863 128.579 150.803 1 36.51 ? CM2 TPP 303 C 1 
HETATM 4 N N3' TPP . . . M 7 129.979 130.244 152.229 1 39.59 ? N3' TPP 303 C 1 
HETATM 5 C C4' TPP . . . M 7 130.689 131.341 152.429 1 37.64 ? C4' TPP 303 C 1 
HETATM 6 N N4' TPP . . . M 7 131.005 131.764 153.782 1 37.46 ? N4' TPP 303 C 1 
HETATM 7 C C5' TPP . . . M 7 131.13 132.089 151.349 1 40.85 ? C5' TPP 303 C 1 
HETATM 8 C C6' TPP . . . M 7 130.799 131.639 150.08 1 35.23 ? C6' TPP 303 C 1 
HETATM 9 C C7' TPP . . . M 7 131.954 133.364 151.547 1 43.75 ? C7' TPP 303 C 1 
HETATM 10 N N3 TPP . . . M 7 131.108 134.416 152.094 1 38.28 ? N3 TPP 303 C 1 
HETATM 11 C C2 TPP . . . M 7 129.865 134.176 152.471 1 32.37 ? C2 TPP 303 C 1 
HETATM 12 S S1 TPP . . . M 7 129.227 135.67 153.051 1 55.97 ? S1 TPP 303 C 1 
HETATM 13 C C5 TPP . . . M 7 130.666 136.577 152.766 1 30.11 ? C5 TPP 303 C 1 
HETATM 14 C C4 TPP . . . M 7 131.551 135.653 152.236 1 38.54 ? C4 TPP 303 C 1 
HETATM 15 C CM4 TPP . . . M 7 132.969 136.046 151.834 1 35.75 ? CM4 TPP 303 C 1 
HETATM 16 C C6 TPP . . . M 7 130.909 138.063 153.036 1 14.98 ? C6 TPP 303 C 1 
HETATM 17 C C7 TPP . . . M 7 130.044 138.963 152.155 1 28.3 ? C7 TPP 303 C 1 
HETATM 18 O O7 TPP . . . M 7 129.639 140.067 152.914 1 36.67 ? O7 TPP 303 C 1 
HETATM 19 P PA TPP . . . M 7 128.4 140.999 152.349 1 26.38 ? PA TPP 303 C 1 
HETATM 20 O O1A TPP . . . M 7 127.448 140.14 151.552 1 20.08 ? O1A TPP 303 C 1 
HETATM 21 O O2A TPP . . . M 7 128.953 142.091 151.465 1 24.68 ? O2A TPP 303 C 1 
HETATM 22 O O3A TPP . . . M 7 127.597 141.674 153.621 1 37.98 ? O3A TPP 303 C 1 
HETATM 23 P PB TPP . . . M 7 127.593 141.032 155.14 1 50.8 ? PB TPP 303 C 1 
HETATM 24 O O1B TPP . . . M 7 129.003 141.009 155.679 1 32.52 ? O1B TPP 303 C 1 
HETATM 25 O O2B TPP . . . M 7 127.051 139.623 155.087 1 37.27 ? O2B TPP 303 C 1 
HETATM 26 O O3B TPP . . . M 7 126.722 141.874 156.041 1 43.13 ? O3B TPP 303 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           26 
#