data_5EDL
#
_model_server_result.job_id            '_ArVD4gS0yNXVs_tDsmU_Q' 
_model_server_result.datetime_utc      '2024-12-01 00:07:55' 
_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          5edl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    5EDL 
#
_exptl.entry_id    5EDL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              265.355 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM 
_entity.pdbx_number_of_molecules    1 
_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            5EDL 
_cell.length_a            70.713 
_cell.length_b            70.713 
_cell.length_c            196.839 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EDL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C12 H17 N4 O S 1' 
_chem_comp.formula_weight    265.355 
_chem_comp.id                VIB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'THIAMIN;VITAMIN B1' 
#
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
CM2 C2A VIB sing 440 n n 
CM2 HM21 VIB sing 441 n n 
CM2 HM22 VIB sing 442 n n 
CM2 HM23 VIB sing 443 n n 
N4A C4A VIB sing 444 n n 
N4A H4A1 VIB sing 445 n n 
N4A H4A2 VIB sing 446 n n 
CM4 C4 VIB sing 447 n n 
CM4 HM41 VIB sing 448 n n 
CM4 HM42 VIB sing 449 n n 
CM4 HM43 VIB sing 450 n n 
O1 C7 VIB sing 451 n n 
O1 HO1 VIB sing 452 n n 
C7 C6 VIB sing 453 n n 
C7 HC71 VIB sing 454 n n 
C7 HC72 VIB sing 455 n n 
C6 C5 VIB sing 456 n n 
C6 HC61 VIB sing 457 n n 
C6 HC62 VIB sing 458 n n 
C2 S1 VIB sing 459 n y 
C2 N3 VIB doub 460 n y 
C2 HC2 VIB sing 461 n n 
S1 C5 VIB sing 462 n y 
C5 C4 VIB doub 463 n y 
C4 N3 VIB sing 464 n y 
N3 C7A VIB sing 465 n n 
C7A C5A VIB sing 466 n n 
C7A H7A1 VIB sing 467 n n 
C7A H7A2 VIB sing 468 n n 
C4A N3A VIB sing 469 n y 
C4A C5A VIB doub 470 n y 
N3A C2A VIB doub 471 n y 
C2A N1A VIB sing 472 n y 
N1A C6A VIB doub 473 n y 
C6A C5A VIB sing 474 n y 
C6A H6AC VIB sing 475 n n 
#
_atom_sites.entry_id                     5EDL 
_atom_sites.fract_transf_matrix[1][1]    0.014142 
_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]    0.014142 
_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]    0.00508 
_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
B 2 VIB A 1 201 1 VIB VIB . 
C 3 MPG A 1 202 1 MPG MPG . 
D 3 MPG A 1 203 2 MPG MPG . 
E 4 HOH A 1 301 44 HOH HOH . 
E 4 HOH A 2 302 14 HOH HOH . 
E 4 HOH A 3 303 22 HOH HOH . 
E 4 HOH A 4 304 32 HOH HOH . 
E 4 HOH A 5 305 16 HOH HOH . 
E 4 HOH A 6 306 28 HOH HOH . 
E 4 HOH A 7 307 72 HOH HOH . 
E 4 HOH A 8 308 13 HOH HOH . 
E 4 HOH A 9 309 15 HOH HOH . 
E 4 HOH A 10 310 3 HOH HOH . 
E 4 HOH A 11 311 55 HOH HOH . 
E 4 HOH A 12 312 2 HOH HOH . 
E 4 HOH A 13 313 29 HOH HOH . 
E 4 HOH A 14 314 51 HOH HOH . 
E 4 HOH A 15 315 52 HOH HOH . 
E 4 HOH A 16 316 11 HOH HOH . 
E 4 HOH A 17 317 70 HOH HOH . 
E 4 HOH A 18 318 40 HOH HOH . 
E 4 HOH A 19 319 6 HOH HOH . 
E 4 HOH A 20 320 56 HOH HOH . 
E 4 HOH A 21 321 17 HOH HOH . 
E 4 HOH A 22 322 23 HOH HOH . 
E 4 HOH A 23 323 35 HOH HOH . 
E 4 HOH A 24 324 20 HOH HOH . 
E 4 HOH A 25 325 12 HOH HOH . 
E 4 HOH A 26 326 50 HOH HOH . 
E 4 HOH A 27 327 39 HOH HOH . 
E 4 HOH A 28 328 64 HOH HOH . 
E 4 HOH A 29 329 38 HOH HOH . 
E 4 HOH A 30 330 31 HOH HOH . 
E 4 HOH A 31 331 41 HOH HOH . 
E 4 HOH A 32 332 9 HOH HOH . 
E 4 HOH A 33 333 5 HOH HOH . 
E 4 HOH A 34 334 10 HOH HOH . 
E 4 HOH A 35 335 60 HOH HOH . 
E 4 HOH A 36 336 7 HOH HOH . 
E 4 HOH A 37 337 37 HOH HOH . 
E 4 HOH A 38 338 1 HOH HOH . 
E 4 HOH A 39 339 19 HOH HOH . 
E 4 HOH A 40 340 4 HOH HOH . 
E 4 HOH A 41 341 18 HOH HOH . 
E 4 HOH A 42 342 68 HOH HOH . 
E 4 HOH A 43 343 34 HOH HOH . 
E 4 HOH A 44 344 67 HOH HOH . 
E 4 HOH A 45 345 8 HOH HOH . 
E 4 HOH A 46 346 62 HOH HOH . 
E 4 HOH A 47 347 76 HOH HOH . 
E 4 HOH A 48 348 46 HOH HOH . 
E 4 HOH A 49 349 63 HOH HOH . 
E 4 HOH A 50 350 65 HOH HOH . 
E 4 HOH A 51 351 49 HOH HOH . 
E 4 HOH A 52 352 30 HOH HOH . 
E 4 HOH A 53 353 36 HOH HOH . 
E 4 HOH A 54 354 33 HOH HOH . 
E 4 HOH A 55 355 61 HOH HOH . 
E 4 HOH A 56 356 57 HOH HOH . 
E 4 HOH A 57 357 84 HOH HOH . 
E 4 HOH A 58 358 80 HOH HOH . 
E 4 HOH A 59 359 43 HOH HOH . 
E 4 HOH A 60 360 74 HOH HOH . 
E 4 HOH A 61 361 54 HOH HOH . 
E 4 HOH A 62 362 21 HOH HOH . 
E 4 HOH A 63 363 24 HOH HOH . 
E 4 HOH A 64 364 77 HOH HOH . 
E 4 HOH A 65 365 53 HOH HOH . 
E 4 HOH A 66 366 73 HOH HOH . 
E 4 HOH A 67 367 25 HOH HOH . 
E 4 HOH A 68 368 66 HOH HOH . 
E 4 HOH A 69 369 69 HOH HOH . 
E 4 HOH A 70 370 58 HOH HOH . 
E 4 HOH A 71 371 26 HOH HOH . 
E 4 HOH A 72 372 47 HOH HOH . 
E 4 HOH A 73 373 27 HOH HOH . 
E 4 HOH A 74 374 79 HOH HOH . 
#
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 C CM2 VIB . . . B 2 5.677 19.182 62.907 1 21.79 ? CM2 VIB 201 A 1 
HETATM 2 N N4A VIB . . . B 2 9.987 17.727 61.102 1 17.01 ? N4A VIB 201 A 1 
HETATM 3 C CM4 VIB . . . B 2 12.396 19.369 57.248 1 19.99 ? CM4 VIB 201 A 1 
HETATM 4 O O1 VIB . . . B 2 13.367 15.629 57.307 1 32.11 ? O1 VIB 201 A 1 
HETATM 5 C C7 VIB . . . B 2 12.615 15.314 56.152 1 25.25 ? C7 VIB 201 A 1 
HETATM 6 C C6 VIB . . . B 2 12.155 16.607 55.524 1 27.23 ? C6 VIB 201 A 1 
HETATM 7 C C2 VIB . . . B 2 8.98 17.553 57.693 1 27.58 ? C2 VIB 201 A 1 
HETATM 8 S S1 VIB . . . B 2 9.681 16.565 56.701 1 29.14 ? S1 VIB 201 A 1 
HETATM 9 C C5 VIB . . . B 2 11.076 17.182 56.424 1 28.09 ? C5 VIB 201 A 1 
HETATM 10 C C4 VIB . . . B 2 11.211 18.398 57.189 1 22.07 ? C4 VIB 201 A 1 
HETATM 11 N N3 VIB . . . B 2 9.879 18.633 57.985 1 21.6 ? N3 VIB 201 A 1 
HETATM 12 C C7A VIB . . . B 2 9.695 19.811 58.827 1 19.46 ? C7A VIB 201 A 1 
HETATM 13 C C4A VIB . . . B 2 8.823 18.582 61.016 1 21.35 ? C4A VIB 201 A 1 
HETATM 14 N N3A VIB . . . B 2 7.851 18.502 61.927 1 22.46 ? N3A VIB 201 A 1 
HETATM 15 C C2A VIB . . . B 2 6.765 19.317 61.828 1 23.11 ? C2A VIB 201 A 1 
HETATM 16 N N1A VIB . . . B 2 6.678 20.228 60.807 1 20.99 ? N1A VIB 201 A 1 
HETATM 17 C C6A VIB . . . B 2 7.659 20.325 59.873 1 18.53 ? C6A VIB 201 A 1 
HETATM 18 C C5A VIB . . . B 2 8.742 19.491 59.993 1 21.7 ? C5A VIB 201 A 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           18 
#