data_5NPU
#
_model_server_result.job_id            LtYxfuu8pqZFB9Pl7uVP7g 
_model_server_result.datetime_utc      '2024-11-25 10:55:07' 
_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          5npu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":602}' 
#
_entry.id    5NPU 
#
_exptl.entry_id    5NPU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    4 
_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            5NPU 
_cell.length_a            108.33 
_cell.length_b            108.33 
_cell.length_c            322.651 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NPU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 software_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
PISA monomeric 1 software_defined_assembly 3 
PISA monomeric 1 software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,N 1 1 
B,G,H 2 1 
C,I,J,K 3 1 
D,L,M 4 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
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 M 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 441 A ASP 441 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc2 A OD1 ASN 468 A ASN 468 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc3 E MG MG . A MG 601 1_555 F O1A TPP . A TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc4 E MG MG . A MG 601 1_555 F O1B TPP . A TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc5 E MG MG . A MG 601 1_555 F O2B TPP . A TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc6 B OD1 ASP 441 B ASP 441 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? 
metalc ? metalc7 B OD1 ASN 468 B ASN 468 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc8 B O GLY 470 B GLY 470 1_555 G MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc9 G MG MG . B MG 601 1_555 H O2A TPP . B TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc10 C OD1 ASP 441 C ASP 441 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc11 C OD1 ASN 468 C ASN 468 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc12 C O GLY 470 C GLY 470 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc13 I MG MG . C MG 601 1_555 J O1B TPP . C TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? 
metalc ? metalc14 I MG MG . C MG 601 1_555 J O1A TPP . C TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? 
metalc ? metalc15 D OD1 ASP 441 D ASP 441 1_555 L MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc16 D OD1 ASN 468 D ASN 468 1_555 L MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc17 D O GLY 470 D GLY 470 1_555 L MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc18 L MG MG . D MG 601 1_555 M O2B TPP . D TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc19 L MG MG . D MG 601 1_555 M O2A TPP . D TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
#
_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 322 n y 
N1' C6' TPP sing 323 n y 
C2' CM2 TPP sing 324 n n 
C2' N3' TPP sing 325 n y 
CM2 HM21 TPP sing 326 n n 
CM2 HM22 TPP sing 327 n n 
CM2 HM23 TPP sing 328 n n 
N3' C4' TPP doub 329 n y 
C4' N4' TPP sing 330 n n 
C4' C5' TPP sing 331 n y 
N4' HN41 TPP sing 332 n n 
N4' HN42 TPP sing 333 n n 
C5' C6' TPP doub 334 n y 
C5' C7' TPP sing 335 n n 
C6' H6' TPP sing 336 n n 
C7' N3 TPP sing 337 n n 
C7' "H7'1" TPP sing 338 n n 
C7' "H7'2" TPP sing 339 n n 
N3 C2 TPP doub 340 n y 
N3 C4 TPP sing 341 n y 
C2 S1 TPP sing 342 n y 
C2 H2 TPP sing 343 n n 
S1 C5 TPP sing 344 n y 
C5 C4 TPP doub 345 n y 
C5 C6 TPP sing 346 n n 
C4 CM4 TPP sing 347 n n 
CM4 HM41 TPP sing 348 n n 
CM4 HM42 TPP sing 349 n n 
CM4 HM43 TPP sing 350 n n 
C6 C7 TPP sing 351 n n 
C6 H61 TPP sing 352 n n 
C6 H62 TPP sing 353 n n 
C7 O7 TPP sing 354 n n 
C7 H71 TPP sing 355 n n 
C7 H72 TPP sing 356 n n 
O7 PA TPP sing 357 n n 
PA O1A TPP doub 358 n n 
PA O2A TPP sing 359 n n 
PA O3A TPP sing 360 n n 
O2A HOA2 TPP sing 361 n n 
O3A PB TPP sing 362 n n 
PB O1B TPP doub 363 n n 
PB O2B TPP sing 364 n n 
PB O3B TPP sing 365 n n 
O2B HOB2 TPP sing 366 n n 
O3B HOB3 TPP sing 367 n n 
#
_atom_sites.entry_id                     5NPU 
_atom_sites.fract_transf_matrix[1][1]    0.009231 
_atom_sites.fract_transf_matrix[1][2]    0.00533 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010659 
_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]    0.003099 
_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
E 2 MG A 1 601 601 MG MG . 
F 3 TPP A 1 602 602 TPP TPP . 
G 2 MG B 1 601 601 MG MG . 
H 3 TPP B 1 602 602 TPP TPP . 
I 2 MG C 1 601 601 MG MG . 
J 3 TPP C 1 602 602 TPP TPP . 
K 4 PEG C 1 603 1 PEG PEG . 
L 2 MG D 1 601 601 MG MG . 
M 3 TPP D 1 602 602 TPP TPP . 
N 5 HOH A 1 701 1 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 N N1' TPP . . . H 3 -21.427 -17.067 2.944 1 61.78 ? N1' TPP 602 B 1 
HETATM 2 C C2' TPP . . . H 3 -21.4 -17.494 1.637 1 64.92 ? C2' TPP 602 B 1 
HETATM 3 C CM2 TPP . . . H 3 -20.175 -18.176 1.091 1 60.54 ? CM2 TPP 602 B 1 
HETATM 4 N N3' TPP . . . H 3 -22.507 -17.316 0.835 1 67.64 ? N3' TPP 602 B 1 
HETATM 5 C C4' TPP . . . H 3 -23.637 -16.686 1.312 1 62.48 ? C4' TPP 602 B 1 
HETATM 6 N N4' TPP . . . H 3 -24.68 -16.532 0.499 1 62.7 ? N4' TPP 602 B 1 
HETATM 7 C C5' TPP . . . H 3 -23.677 -16.256 2.633 1 63.8 ? C5' TPP 602 B 1 
HETATM 8 C C6' TPP . . . H 3 -22.555 -16.448 3.439 1 63.2 ? C6' TPP 602 B 1 
HETATM 9 C C7' TPP . . . H 3 -24.895 -15.556 3.208 1 65.96 ? C7' TPP 602 B 1 
HETATM 10 N N3 TPP . . . H 3 -24.941 -14.204 2.707 1 69.21 ? N3 TPP 602 B 1 
HETATM 11 C C2 TPP . . . H 3 -25.752 -13.77 1.683 1 88.51 ? C2 TPP 602 B 1 
HETATM 12 S S1 TPP . . . H 3 -25.58 -12.214 1.342 1 105.73 ? S1 TPP 602 B 1 
HETATM 13 C C5 TPP . . . H 3 -24.459 -12.041 2.447 1 100.98 ? C5 TPP 602 B 1 
HETATM 14 C C4 TPP . . . H 3 -24.184 -13.183 3.168 1 77.63 ? C4 TPP 602 B 1 
HETATM 15 C CM4 TPP . . . H 3 -23.165 -13.22 4.269 1 68.73 ? CM4 TPP 602 B 1 
HETATM 16 C C6 TPP . . . H 3 -23.892 -10.662 2.614 1 122.75 ? C6 TPP 602 B 1 
HETATM 17 C C7 TPP . . . H 3 -23.414 -10.015 1.314 1 129.26 ? C7 TPP 602 B 1 
HETATM 18 O O7 TPP . . . H 3 -22.594 -8.903 1.618 1 119.17 ? O7 TPP 602 B 1 
HETATM 19 P PA TPP . . . H 3 -22.379 -7.742 0.53 1 100.23 ? PA TPP 602 B 1 
HETATM 20 O O1A TPP . . . H 3 -22.025 -8.268 -0.844 1 93.69 ? O1A TPP 602 B 1 
HETATM 21 O O2A TPP . . . H 3 -21.371 -6.74 1.027 1 97.77 ? O2A TPP 602 B 1 
HETATM 22 O O3A TPP . . . H 3 -23.872 -7.142 0.528 1 90.79 ? O3A TPP 602 B 1 
HETATM 23 P PB TPP . . . H 3 -24.172 -5.625 0.109 1 74.07 ? PB TPP 602 B 1 
HETATM 24 O O1B TPP . . . H 3 -23.727 -5.459 -1.335 1 72.18 ? O1B TPP 602 B 1 
HETATM 25 O O2B TPP . . . H 3 -23.479 -4.661 1.036 1 73.58 ? O2B TPP 602 B 1 
HETATM 26 O O3B TPP . . . H 3 -25.654 -5.395 0.223 1 73.55 ? O3B TPP 602 B 1 
HETATM 27 H HM21 TPP . . . H 3 -19.795 -17.612 0.239 1 72.65 ? HM21 TPP 602 B 1 
HETATM 28 H HM22 TPP . . . H 3 -19.41 -18.223 1.866 1 72.65 ? HM22 TPP 602 B 1 
HETATM 29 H HM23 TPP . . . H 3 -20.433 -19.186 0.772 1 72.65 ? HM23 TPP 602 B 1 
HETATM 30 H HN41 TPP . . . H 3 -25.528 -16.092 0.841 1 75.24 ? HN41 TPP 602 B 1 
HETATM 31 H HN42 TPP . . . H 3 -24.628 -16.858 -0.46 1 75.24 ? HN42 TPP 602 B 1 
HETATM 32 H H6' TPP . . . H 3 -22.57 -16.104 4.473 1 75.84 ? H6' TPP 602 B 1 
HETATM 33 H "H7'1" TPP . . . H 3 -24.837 -15.546 4.297 1 79.15 ? "H7'1" TPP 602 B 1 
HETATM 34 H "H7'2" TPP . . . H 3 -25.8 -16.09 2.919 1 79.15 ? "H7'2" TPP 602 B 1 
HETATM 35 H H2 TPP . . . H 3 -25.946 -14.3 0.751 1 106.21 ? H2 TPP 602 B 1 
HETATM 36 H HM41 TPP . . . H 3 -23.446 -12.511 5.047 1 82.48 ? HM41 TPP 602 B 1 
HETATM 37 H HM42 TPP . . . H 3 -23.122 -14.225 4.69 1 82.48 ? HM42 TPP 602 B 1 
HETATM 38 H HM43 TPP . . . H 3 -22.188 -12.953 3.868 1 82.48 ? HM43 TPP 602 B 1 
HETATM 39 H H61 TPP . . . H 3 -24.651 -10.024 3.065 1 147.3 ? H61 TPP 602 B 1 
HETATM 40 H H62 TPP . . . H 3 -23.055 -10.71 3.31 1 147.3 ? H62 TPP 602 B 1 
HETATM 41 H H71 TPP . . . H 3 -24.273 -9.691 0.725 1 155.12 ? H71 TPP 602 B 1 
HETATM 42 H H72 TPP . . . H 3 -22.851 -10.74 0.726 1 155.12 ? H72 TPP 602 B 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           42 
#