data_4QQ8
#
_model_server_result.job_id            vuXJiCpMwkEM62NvSTupZg 
_model_server_result.datetime_utc      '2024-11-06 15:38:28' 
_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          4qq8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":602}' 
#
_entry.id    4QQ8 
#
_exptl.entry_id    4QQ8 
_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         90 
_cell.entry_id            4QQ8 
_cell.length_a            144.742 
_cell.length_b            144.742 
_cell.length_c            269.553 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4QQ8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 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,R,S,T 
_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
? 3 F N N 
? 3 J N N 
? 3 L N N 
? 3 O 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 448 A ASP 448 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc2 A OD1 ASN 475 A ASN 475 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc3 A O SER 477 A SER 477 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc4 E MG MG . A MG 601 1_555 F O1A TPP . A TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? 
metalc ? metalc5 E MG MG . A MG 601 1_555 F O1B TPP . A TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc6 E MG MG . A MG 601 1_555 Q O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc7 Q O HOH . A HOH 704 1_555 K MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc8 Q O HOH . A HOH 705 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc9 B OD1 ASP 448 B ASP 448 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc10 B OD1 ASN 475 B ASN 475 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc11 B O SER 477 B SER 477 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc12 I MG MG . B MG 601 1_555 J O1A TPP . B TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc13 I MG MG . B MG 601 1_555 J O3B TPP . B TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc14 C OD1 ASP 448 C ASP 448 1_555 K MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc15 C OD1 ASN 475 C ASN 475 1_555 K MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc16 C O SER 477 C SER 477 1_555 K MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc17 K MG MG . C MG 601 1_555 L O1A TPP . C TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc18 K MG MG . C MG 601 1_555 L O3B TPP . C TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc19 D OD1 ASP 448 D ASP 448 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc20 D OD1 ASN 475 D ASN 475 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc21 D O SER 477 D SER 477 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc22 N MG MG . D MG 601 1_555 O O1A TPP . D TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc23 N MG MG . D MG 601 1_555 O O3B TPP . D TPP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
#
_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 315 n y 
N1' C6' TPP sing 316 n y 
C2' CM2 TPP sing 317 n n 
C2' N3' TPP sing 318 n y 
CM2 HM21 TPP sing 319 n n 
CM2 HM22 TPP sing 320 n n 
CM2 HM23 TPP sing 321 n n 
N3' C4' TPP doub 322 n y 
C4' N4' TPP sing 323 n n 
C4' C5' TPP sing 324 n y 
N4' HN41 TPP sing 325 n n 
N4' HN42 TPP sing 326 n n 
C5' C6' TPP doub 327 n y 
C5' C7' TPP sing 328 n n 
C6' H6' TPP sing 329 n n 
C7' N3 TPP sing 330 n n 
C7' "H7'1" TPP sing 331 n n 
C7' "H7'2" TPP sing 332 n n 
N3 C2 TPP doub 333 n y 
N3 C4 TPP sing 334 n y 
C2 S1 TPP sing 335 n y 
C2 H2 TPP sing 336 n n 
S1 C5 TPP sing 337 n y 
C5 C4 TPP doub 338 n y 
C5 C6 TPP sing 339 n n 
C4 CM4 TPP sing 340 n n 
CM4 HM41 TPP sing 341 n n 
CM4 HM42 TPP sing 342 n n 
CM4 HM43 TPP sing 343 n n 
C6 C7 TPP sing 344 n n 
C6 H61 TPP sing 345 n n 
C6 H62 TPP sing 346 n n 
C7 O7 TPP sing 347 n n 
C7 H71 TPP sing 348 n n 
C7 H72 TPP sing 349 n n 
O7 PA TPP sing 350 n n 
PA O1A TPP doub 351 n n 
PA O2A TPP sing 352 n n 
PA O3A TPP sing 353 n n 
O2A HOA2 TPP sing 354 n n 
O3A PB TPP sing 355 n n 
PB O1B TPP doub 356 n n 
PB O2B TPP sing 357 n n 
PB O3B TPP sing 358 n n 
O2B HOB2 TPP sing 359 n n 
O3B HOB3 TPP sing 360 n n 
#
_atom_sites.entry_id                     4QQ8 
_atom_sites.fract_transf_matrix[1][1]    0.006909 
_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]    0.006909 
_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]    0.00371 
_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 4 EDO A 1 603 4 EDO EDO . 
H 4 EDO A 1 604 5 EDO EDO . 
I 2 MG B 1 601 601 MG MG . 
J 3 TPP B 1 602 602 TPP TPP . 
K 2 MG C 1 601 601 MG MG . 
L 3 TPP C 1 602 602 TPP TPP . 
M 4 EDO C 1 603 7 EDO EDO . 
N 2 MG D 1 601 601 MG MG . 
O 3 TPP D 1 602 602 TPP TPP . 
P 4 EDO D 1 603 8 EDO EDO . 
Q 5 HOH A 1 701 1 HOH HOH . 
Q 5 HOH A 2 702 5 HOH HOH . 
Q 5 HOH A 3 703 9 HOH HOH . 
Q 5 HOH A 4 704 25 HOH HOH . 
Q 5 HOH A 5 705 26 HOH HOH . 
Q 5 HOH A 6 706 27 HOH HOH . 
Q 5 HOH A 7 707 28 HOH HOH . 
Q 5 HOH A 8 708 30 HOH HOH . 
Q 5 HOH A 9 709 31 HOH HOH . 
Q 5 HOH A 10 710 32 HOH HOH . 
Q 5 HOH A 11 711 33 HOH HOH . 
Q 5 HOH A 12 712 34 HOH HOH . 
Q 5 HOH A 13 713 35 HOH HOH . 
Q 5 HOH A 14 714 36 HOH HOH . 
Q 5 HOH A 15 715 37 HOH HOH . 
Q 5 HOH A 16 716 38 HOH HOH . 
Q 5 HOH A 17 717 39 HOH HOH . 
Q 5 HOH A 18 718 40 HOH HOH . 
Q 5 HOH A 19 719 41 HOH HOH . 
Q 5 HOH A 20 720 42 HOH HOH . 
Q 5 HOH A 21 721 43 HOH HOH . 
Q 5 HOH A 22 722 44 HOH HOH . 
Q 5 HOH A 23 723 45 HOH HOH . 
Q 5 HOH A 24 724 46 HOH HOH . 
Q 5 HOH A 25 725 47 HOH HOH . 
Q 5 HOH A 26 726 48 HOH HOH . 
Q 5 HOH A 27 727 49 HOH HOH . 
Q 5 HOH A 28 728 51 HOH HOH . 
Q 5 HOH A 29 729 55 HOH HOH . 
Q 5 HOH A 30 730 68 HOH HOH . 
Q 5 HOH A 31 731 69 HOH HOH . 
Q 5 HOH A 32 732 75 HOH HOH . 
Q 5 HOH A 33 733 81 HOH HOH . 
R 5 HOH B 1 701 57 HOH HOH . 
R 5 HOH B 2 702 65 HOH HOH . 
R 5 HOH B 3 703 74 HOH HOH . 
R 5 HOH B 4 704 80 HOH HOH . 
S 5 HOH C 1 701 56 HOH HOH . 
S 5 HOH C 2 702 61 HOH HOH . 
S 5 HOH C 3 703 62 HOH HOH . 
S 5 HOH C 4 704 63 HOH HOH . 
S 5 HOH C 5 705 70 HOH HOH . 
S 5 HOH C 6 706 72 HOH HOH . 
S 5 HOH C 7 707 73 HOH HOH . 
S 5 HOH C 8 708 77 HOH HOH . 
S 5 HOH C 9 709 79 HOH HOH . 
T 5 HOH D 1 701 64 HOH HOH . 
T 5 HOH D 2 702 66 HOH HOH . 
T 5 HOH D 3 703 71 HOH HOH . 
T 5 HOH D 4 704 76 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 . . . O 3 2.952 -74.16 23.343 1 51.95 ? N1' TPP 602 D 1 
HETATM 2 C C2' TPP . . . O 3 4.053 -73.871 22.664 1 53.35 ? C2' TPP 602 D 1 
HETATM 3 C CM2 TPP . . . O 3 4.004 -73.605 21.173 1 52.58 ? CM2 TPP 602 D 1 
HETATM 4 N N3' TPP . . . O 3 5.225 -73.791 23.271 1 54.37 ? N3' TPP 602 D 1 
HETATM 5 C C4' TPP . . . O 3 5.352 -74.022 24.581 1 53.12 ? C4' TPP 602 D 1 
HETATM 6 N N4' TPP . . . O 3 6.629 -73.913 25.13 1 57.68 ? N4' TPP 602 D 1 
HETATM 7 C C5' TPP . . . O 3 4.231 -74.362 25.374 1 53.83 ? C5' TPP 602 D 1 
HETATM 8 C C6' TPP . . . O 3 2.992 -74.408 24.679 1 53.45 ? C6' TPP 602 D 1 
HETATM 9 C C7' TPP . . . O 3 4.346 -74.631 26.928 1 53.95 ? C7' TPP 602 D 1 
HETATM 10 N N3 TPP . . . O 3 4.96 -75.927 27.271 1 54.87 ? N3 TPP 602 D 1 
HETATM 11 C C2 TPP . . . O 3 6.229 -76.063 27.756 1 54.76 ? C2 TPP 602 D 1 
HETATM 12 S S1 TPP . . . O 3 6.508 -77.758 27.999 1 54.72 ? S1 TPP 602 D 1 
HETATM 13 C C5 TPP . . . O 3 4.986 -78.314 27.535 1 52.54 ? C5 TPP 602 D 1 
HETATM 14 C C4 TPP . . . O 3 4.257 -77.144 27.146 1 54.58 ? C4 TPP 602 D 1 
HETATM 15 C CM4 TPP . . . O 3 2.83 -77.238 26.645 1 55.05 ? CM4 TPP 602 D 1 
HETATM 16 C C6 TPP . . . O 3 4.561 -79.786 27.538 1 51.19 ? C6 TPP 602 D 1 
HETATM 17 C C7 TPP . . . O 3 5.023 -80.604 26.31 1 49.25 ? C7 TPP 602 D 1 
HETATM 18 O O7 TPP . . . O 3 4.596 -81.96 26.539 1 46.03 ? O7 TPP 602 D 1 
HETATM 19 P PA TPP . . . O 3 5.251 -83.122 25.7 1 42.74 ? PA TPP 602 D 1 
HETATM 20 O O1A TPP . . . O 3 4.272 -84.251 25.808 1 43.52 ? O1A TPP 602 D 1 
HETATM 21 O O2A TPP . . . O 3 5.658 -82.678 24.317 1 40.69 ? O2A TPP 602 D 1 
HETATM 22 O O3A TPP . . . O 3 6.552 -83.654 26.386 1 43.35 ? O3A TPP 602 D 1 
HETATM 23 P PB TPP . . . O 3 6.676 -83.914 27.945 1 42.98 ? PB TPP 602 D 1 
HETATM 24 O O1B TPP . . . O 3 8.104 -84.343 28.036 1 42.43 ? O1B TPP 602 D 1 
HETATM 25 O O2B TPP . . . O 3 6.534 -82.631 28.699 1 42.44 ? O2B TPP 602 D 1 
HETATM 26 O O3B TPP . . . O 3 5.627 -84.856 28.474 1 42.47 ? O3B TPP 602 D 1 
#
_model_server_stats.io_time_ms              39 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#