data_4RJI
#
_model_server_result.job_id            yLH7Au1A6eiuJnkQX5nrbg 
_model_server_result.datetime_utc      '2025-02-26 12:20:30' 
_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          4rji 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1000}' 
#
_entry.id    4RJI 
#
_exptl.entry_id    4RJI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              425.314 
_entity.id                          2 
_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         90 
_cell.entry_id            4RJI 
_cell.length_a            140.647 
_cell.length_b            140.647 
_cell.length_c            238.877 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4RJI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,F,G,H,I,J,K,L,M,N,O,P,Q 
_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
? 2 E N N 
? 2 G N N 
? 2 J N N 
? 2 L 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 451 A ASP 451 1_555 F MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc2 A OD1 ASP 478 A ASP 478 1_555 F MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc3 A O THR 480 A THR 480 1_555 F MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc4 E O2A TPP . A TPP 1000 1_555 F MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? 
metalc ? metalc5 E O3B TPP . A TPP 1000 1_555 F MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? 
metalc ? metalc6 B OD1 ASP 451 B ASP 451 1_555 H MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? 
metalc ? metalc7 B OD1 ASP 478 B ASP 478 1_555 H MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc8 B O THR 480 B THR 480 1_555 H MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? 
metalc ? metalc9 G O2A TPP . B TPP 601 1_555 H MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
metalc ? metalc10 G O3B TPP . B TPP 601 1_555 H MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc11 C OD1 ASP 451 C ASP 451 1_555 K MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc12 C OD1 ASP 478 C ASP 478 1_555 K MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc13 C O THR 480 C THR 480 1_555 K MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc14 J O2A TPP . C TPP 1000 1_555 K MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc15 J O3B TPP . C TPP 1000 1_555 K MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? 
metalc ? metalc16 K MG MG . C MG 1001 1_555 P O HOH . C HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc17 D OD1 ASP 451 D ASP 451 1_555 M MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc18 D OD1 ASP 478 D ASP 478 1_555 M MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc19 D O THR 480 D THR 480 1_555 M MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? 
metalc ? metalc20 L O2A TPP . D TPP 1000 1_555 M MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc21 L O3B TPP . D TPP 1000 1_555 M MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
#
_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 336 n y 
N1' C6' TPP sing 337 n y 
C2' CM2 TPP sing 338 n n 
C2' N3' TPP sing 339 n y 
CM2 HM21 TPP sing 340 n n 
CM2 HM22 TPP sing 341 n n 
CM2 HM23 TPP sing 342 n n 
N3' C4' TPP doub 343 n y 
C4' N4' TPP sing 344 n n 
C4' C5' TPP sing 345 n y 
N4' HN41 TPP sing 346 n n 
N4' HN42 TPP sing 347 n n 
C5' C6' TPP doub 348 n y 
C5' C7' TPP sing 349 n n 
C6' H6' TPP sing 350 n n 
C7' N3 TPP sing 351 n n 
C7' "H7'1" TPP sing 352 n n 
C7' "H7'2" TPP sing 353 n n 
N3 C2 TPP doub 354 n y 
N3 C4 TPP sing 355 n y 
C2 S1 TPP sing 356 n y 
C2 H2 TPP sing 357 n n 
S1 C5 TPP sing 358 n y 
C5 C4 TPP doub 359 n y 
C5 C6 TPP sing 360 n n 
C4 CM4 TPP sing 361 n n 
CM4 HM41 TPP sing 362 n n 
CM4 HM42 TPP sing 363 n n 
CM4 HM43 TPP sing 364 n n 
C6 C7 TPP sing 365 n n 
C6 H61 TPP sing 366 n n 
C6 H62 TPP sing 367 n n 
C7 O7 TPP sing 368 n n 
C7 H71 TPP sing 369 n n 
C7 H72 TPP sing 370 n n 
O7 PA TPP sing 371 n n 
PA O1A TPP doub 372 n n 
PA O2A TPP sing 373 n n 
PA O3A TPP sing 374 n n 
O2A HOA2 TPP sing 375 n n 
O3A PB TPP sing 376 n n 
PB O1B TPP doub 377 n n 
PB O2B TPP sing 378 n n 
PB O3B TPP sing 379 n n 
O2B HOB2 TPP sing 380 n n 
O3B HOB3 TPP sing 381 n n 
#
_atom_sites.entry_id                     4RJI 
_atom_sites.fract_transf_matrix[1][1]    0.00711 
_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]    0.00711 
_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]    0.004186 
_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 TPP A 1 1000 1000 TPP TPP . 
F 3 MG A 1 1001 1001 MG MG . 
G 2 TPP B 1 601 1000 TPP TPP . 
H 3 MG B 1 602 1001 MG MG . 
I 4 PG4 B 1 603 1 PG4 PG4 . 
J 2 TPP C 1 1000 1000 TPP TPP . 
K 3 MG C 1 1001 1001 MG MG . 
L 2 TPP D 1 1000 1000 TPP TPP . 
M 3 MG D 1 1001 1001 MG MG . 
N 5 HOH A 1 1101 4 HOH HOH . 
N 5 HOH A 2 1102 5 HOH HOH . 
N 5 HOH A 3 1103 29 HOH HOH . 
O 5 HOH B 1 701 2 HOH HOH . 
O 5 HOH B 2 702 3 HOH HOH . 
O 5 HOH B 3 703 6 HOH HOH . 
O 5 HOH B 4 704 7 HOH HOH . 
O 5 HOH B 5 705 13 HOH HOH . 
O 5 HOH B 6 706 28 HOH HOH . 
P 5 HOH C 1 1101 8 HOH HOH . 
P 5 HOH C 2 1102 9 HOH HOH . 
P 5 HOH C 3 1103 11 HOH HOH . 
P 5 HOH C 4 1104 15 HOH HOH . 
P 5 HOH C 5 1105 16 HOH HOH . 
P 5 HOH C 6 1106 20 HOH HOH . 
P 5 HOH C 7 1107 27 HOH HOH . 
Q 5 HOH D 1 1101 14 HOH HOH . 
Q 5 HOH D 2 1102 17 HOH HOH . 
Q 5 HOH D 3 1103 21 HOH HOH . 
Q 5 HOH D 4 1104 22 HOH HOH . 
Q 5 HOH D 5 1105 23 HOH HOH . 
Q 5 HOH D 6 1106 24 HOH HOH . 
Q 5 HOH D 7 1107 25 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 . . . J 2 34.406 -27.058 -19.734 1 56.64 ? N1' TPP 1000 C 1 
HETATM 2 C C2' TPP . . . J 2 33.294 -27.734 -19.286 1 57.96 ? C2' TPP 1000 C 1 
HETATM 3 C CM2 TPP . . . J 2 33.332 -29.238 -19.088 1 53.94 ? CM2 TPP 1000 C 1 
HETATM 4 N N3' TPP . . . J 2 32.146 -27.028 -19.019 1 62.34 ? N3' TPP 1000 C 1 
HETATM 5 C C4' TPP . . . J 2 32.096 -25.667 -19.188 1 64.09 ? C4' TPP 1000 C 1 
HETATM 6 N N4' TPP . . . J 2 30.849 -24.97 -18.881 1 63.33 ? N4' TPP 1000 C 1 
HETATM 7 C C5' TPP . . . J 2 33.237 -24.987 -19.643 1 61.74 ? C5' TPP 1000 C 1 
HETATM 8 C C6' TPP . . . J 2 34.39 -25.705 -19.912 1 56.75 ? C6' TPP 1000 C 1 
HETATM 9 C C7' TPP . . . J 2 33.25 -23.459 -19.868 1 67.03 ? C7' TPP 1000 C 1 
HETATM 10 N N3 TPP . . . J 2 32.543 -23.117 -21.105 1 68.17 ? N3 TPP 1000 C 1 
HETATM 11 C C2 TPP . . . J 2 31.3 -22.748 -21.08 1 69.08 ? C2 TPP 1000 C 1 
HETATM 12 S S1 TPP . . . J 2 30.718 -22.42 -22.693 1 79.97 ? S1 TPP 1000 C 1 
HETATM 13 C C5 TPP . . . J 2 32.274 -22.825 -23.36 1 73.95 ? C5 TPP 1000 C 1 
HETATM 14 C C4 TPP . . . J 2 33.112 -23.177 -22.312 1 70.09 ? C4 TPP 1000 C 1 
HETATM 15 C CM4 TPP . . . J 2 34.563 -23.592 -22.559 1 72.95 ? CM4 TPP 1000 C 1 
HETATM 16 C C6 TPP . . . J 2 32.627 -22.794 -24.853 1 75.47 ? C6 TPP 1000 C 1 
HETATM 17 C C7 TPP . . . J 2 31.474 -23.311 -25.721 1 73.5 ? C7 TPP 1000 C 1 
HETATM 18 O O7 TPP . . . J 2 31.928 -23.585 -26.997 1 72.84 ? O7 TPP 1000 C 1 
HETATM 19 P PA TPP . . . J 2 30.894 -23.914 -28.114 1 76.98 ? PA TPP 1000 C 1 
HETATM 20 O O1A TPP . . . J 2 30.371 -25.328 -27.912 1 69.55 ? O1A TPP 1000 C 1 
HETATM 21 O O2A TPP . . . J 2 31.552 -23.843 -29.471 1 78.96 -1 O2A TPP 1000 C 1 
HETATM 22 O O3A TPP . . . J 2 29.657 -22.896 -28.06 1 81.16 ? O3A TPP 1000 C 1 
HETATM 23 P PB TPP . . . J 2 29.709 -21.351 -28.349 1 75.18 ? PB TPP 1000 C 1 
HETATM 24 O O1B TPP . . . J 2 30.238 -20.581 -27.169 1 72.75 ? O1B TPP 1000 C 1 
HETATM 25 O O2B TPP . . . J 2 28.288 -20.882 -28.62 1 70.5 -1 O2B TPP 1000 C 1 
HETATM 26 O O3B TPP . . . J 2 30.58 -21.072 -29.544 1 77.33 -1 O3B TPP 1000 C 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#