data_6DEK
#
_model_server_result.job_id            slyEiT7pa60K-mU_9t8y1w 
_model_server_result.datetime_utc      '2024-11-28 22:21:25' 
_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          6dek 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":704}' 
#
_entry.id    6DEK 
#
_exptl.entry_id    6DEK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              425.314 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'THIAMINE DIPHOSPHATE' 
_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         120 
_cell.entry_id            6DEK 
_cell.length_a            176.039 
_cell.length_b            176.039 
_cell.length_c            177.626 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DEK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        180 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 62 2 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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_785 -x+2,-y+3,z -1 0 0 0 -1 0 0 0 1 88.0195 457.362738 0 
3 'crystal symmetry operation' 9_765 -x+2,-x+y+1,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 264.0585 152.454246 59.208667 
4 'crystal symmetry operation' 12_575 x,x-y+2,-z+1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -176.039 304.908492 59.208667 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OE1 GLN 338 A GLN 339 1_555 C K K . A K 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? 
metalc ? metalc2 A OD1 ASP 345 A ASP 346 1_555 C K K . A K 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? 
metalc ? metalc3 A O GLN 501 A GLN 502 1_555 C K K . A K 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? 
metalc ? metalc4 A O PHE 503 A PHE 504 1_555 C K K . A K 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? 
metalc ? metalc5 A OD1 ASP 545 A ASP 546 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc6 A OD1 ASN 572 A ASN 573 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc7 A O GLU 574 A GLU 575 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc8 C K K . A K 702 1_555 F O HOH . A HOH 817 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? 
metalc ? metalc9 C K K . A K 702 1_555 F O HOH . A HOH 884 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? 
metalc ? metalc10 D MG MG . A MG 703 1_555 E O2A TPP . A TPP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc11 D MG MG . A MG 703 1_555 E O1B TPP . A TPP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc12 D MG MG . A MG 703 1_555 F O HOH . A HOH 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
#
_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 397 n y 
N1' C6' TPP sing 398 n y 
C2' CM2 TPP sing 399 n n 
C2' N3' TPP sing 400 n y 
CM2 HM21 TPP sing 401 n n 
CM2 HM22 TPP sing 402 n n 
CM2 HM23 TPP sing 403 n n 
N3' C4' TPP doub 404 n y 
C4' N4' TPP sing 405 n n 
C4' C5' TPP sing 406 n y 
N4' HN41 TPP sing 407 n n 
N4' HN42 TPP sing 408 n n 
C5' C6' TPP doub 409 n y 
C5' C7' TPP sing 410 n n 
C6' H6' TPP sing 411 n n 
C7' N3 TPP sing 412 n n 
C7' "H7'1" TPP sing 413 n n 
C7' "H7'2" TPP sing 414 n n 
N3 C2 TPP doub 415 n y 
N3 C4 TPP sing 416 n y 
C2 S1 TPP sing 417 n y 
C2 H2 TPP sing 418 n n 
S1 C5 TPP sing 419 n y 
C5 C4 TPP doub 420 n y 
C5 C6 TPP sing 421 n n 
C4 CM4 TPP sing 422 n n 
CM4 HM41 TPP sing 423 n n 
CM4 HM42 TPP sing 424 n n 
CM4 HM43 TPP sing 425 n n 
C6 C7 TPP sing 426 n n 
C6 H61 TPP sing 427 n n 
C6 H62 TPP sing 428 n n 
C7 O7 TPP sing 429 n n 
C7 H71 TPP sing 430 n n 
C7 H72 TPP sing 431 n n 
O7 PA TPP sing 432 n n 
PA O1A TPP doub 433 n n 
PA O2A TPP sing 434 n n 
PA O3A TPP sing 435 n n 
O2A HOA2 TPP sing 436 n n 
O3A PB TPP sing 437 n n 
PB O1B TPP doub 438 n n 
PB O2B TPP sing 439 n n 
PB O3B TPP sing 440 n n 
O2B HOB2 TPP sing 441 n n 
O3B HOB3 TPP sing 442 n n 
#
_atom_sites.entry_id                     6DEK 
_atom_sites.fract_transf_matrix[1][1]    0.005681 
_atom_sites.fract_transf_matrix[1][2]    0.00328 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006559 
_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]    0.00563 
_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 FAD A 1 701 701 FAD FAD . 
C 3 K A 1 702 1696 K K . 
D 4 MG A 1 703 1699 MG MG . 
E 5 TPP A 1 704 1 TPP TPP . 
F 6 HOH A 1 801 37 HOH HOH . 
F 6 HOH A 2 802 71 HOH HOH . 
F 6 HOH A 3 803 66 HOH HOH . 
F 6 HOH A 4 804 85 HOH HOH . 
F 6 HOH A 5 805 61 HOH HOH . 
F 6 HOH A 6 806 41 HOH HOH . 
F 6 HOH A 7 807 73 HOH HOH . 
F 6 HOH A 8 808 55 HOH HOH . 
F 6 HOH A 9 809 84 HOH HOH . 
F 6 HOH A 10 810 38 HOH HOH . 
F 6 HOH A 11 811 28 HOH HOH . 
F 6 HOH A 12 812 65 HOH HOH . 
F 6 HOH A 13 813 20 HOH HOH . 
F 6 HOH A 14 814 1 HOH HOH . 
F 6 HOH A 15 815 60 HOH HOH . 
F 6 HOH A 16 816 13 HOH HOH . 
F 6 HOH A 17 817 32 HOH HOH . 
F 6 HOH A 18 818 77 HOH HOH . 
F 6 HOH A 19 819 56 HOH HOH . 
F 6 HOH A 20 820 59 HOH HOH . 
F 6 HOH A 21 821 19 HOH HOH . 
F 6 HOH A 22 822 2 HOH HOH . 
F 6 HOH A 23 823 76 HOH HOH . 
F 6 HOH A 24 824 9 HOH HOH . 
F 6 HOH A 25 825 17 HOH HOH . 
F 6 HOH A 26 826 34 HOH HOH . 
F 6 HOH A 27 827 44 HOH HOH . 
F 6 HOH A 28 828 15 HOH HOH . 
F 6 HOH A 29 829 75 HOH HOH . 
F 6 HOH A 30 830 3 HOH HOH . 
F 6 HOH A 31 831 11 HOH HOH . 
F 6 HOH A 32 832 52 HOH HOH . 
F 6 HOH A 33 833 7 HOH HOH . 
F 6 HOH A 34 834 67 HOH HOH . 
F 6 HOH A 35 835 68 HOH HOH . 
F 6 HOH A 36 836 25 HOH HOH . 
F 6 HOH A 37 837 91 HOH HOH . 
F 6 HOH A 38 838 53 HOH HOH . 
F 6 HOH A 39 839 23 HOH HOH . 
F 6 HOH A 40 840 81 HOH HOH . 
F 6 HOH A 41 841 6 HOH HOH . 
F 6 HOH A 42 842 43 HOH HOH . 
F 6 HOH A 43 843 64 HOH HOH . 
F 6 HOH A 44 844 42 HOH HOH . 
F 6 HOH A 45 845 57 HOH HOH . 
F 6 HOH A 46 846 22 HOH HOH . 
F 6 HOH A 47 847 16 HOH HOH . 
F 6 HOH A 48 848 48 HOH HOH . 
F 6 HOH A 49 849 78 HOH HOH . 
F 6 HOH A 50 850 8 HOH HOH . 
F 6 HOH A 51 851 80 HOH HOH . 
F 6 HOH A 52 852 40 HOH HOH . 
F 6 HOH A 53 853 63 HOH HOH . 
F 6 HOH A 54 854 24 HOH HOH . 
F 6 HOH A 55 855 47 HOH HOH . 
F 6 HOH A 56 856 4 HOH HOH . 
F 6 HOH A 57 857 27 HOH HOH . 
F 6 HOH A 58 858 54 HOH HOH . 
F 6 HOH A 59 859 21 HOH HOH . 
F 6 HOH A 60 860 50 HOH HOH . 
F 6 HOH A 61 861 33 HOH HOH . 
F 6 HOH A 62 862 72 HOH HOH . 
F 6 HOH A 63 863 29 HOH HOH . 
F 6 HOH A 64 864 49 HOH HOH . 
F 6 HOH A 65 865 70 HOH HOH . 
F 6 HOH A 66 866 79 HOH HOH . 
F 6 HOH A 67 867 69 HOH HOH . 
F 6 HOH A 68 868 31 HOH HOH . 
F 6 HOH A 69 869 51 HOH HOH . 
F 6 HOH A 70 870 88 HOH HOH . 
F 6 HOH A 71 871 89 HOH HOH . 
F 6 HOH A 72 872 62 HOH HOH . 
F 6 HOH A 73 873 26 HOH HOH . 
F 6 HOH A 74 874 14 HOH HOH . 
F 6 HOH A 75 875 82 HOH HOH . 
F 6 HOH A 76 876 83 HOH HOH . 
F 6 HOH A 77 877 35 HOH HOH . 
F 6 HOH A 78 878 86 HOH HOH . 
F 6 HOH A 79 879 18 HOH HOH . 
F 6 HOH A 80 880 74 HOH HOH . 
F 6 HOH A 81 881 90 HOH HOH . 
F 6 HOH A 82 882 45 HOH HOH . 
F 6 HOH A 83 883 87 HOH HOH . 
F 6 HOH A 84 884 30 HOH HOH . 
F 6 HOH A 85 885 36 HOH HOH . 
F 6 HOH A 86 886 5 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 . . . E 5 68.35 235.834 38.896 1 35.94 ? N1' TPP 704 A 1 
HETATM 2 C C2' TPP . . . E 5 67.445 236.843 38.978 1 39.41 ? C2' TPP 704 A 1 
HETATM 3 C CM2 TPP . . . E 5 67.009 237.553 37.753 1 28.51 ? CM2 TPP 704 A 1 
HETATM 4 N N3' TPP . . . E 5 66.944 237.197 40.186 1 43.27 ? N3' TPP 704 A 1 
HETATM 5 C C4' TPP . . . E 5 67.33 236.565 41.305 1 40.25 ? C4' TPP 704 A 1 
HETATM 6 N N4' TPP . . . E 5 66.768 236.978 42.542 1 54.26 ? N4' TPP 704 A 1 
HETATM 7 C C5' TPP . . . E 5 68.257 235.529 41.225 1 45.01 ? C5' TPP 704 A 1 
HETATM 8 C C6' TPP . . . E 5 68.753 235.181 39.997 1 43.43 ? C6' TPP 704 A 1 
HETATM 9 C C7' TPP . . . E 5 68.738 234.773 42.44 1 53.41 ? C7' TPP 704 A 1 
HETATM 10 N N3 TPP . . . E 5 69.56 235.651 43.282 1 50.92 ? N3 TPP 704 A 1 
HETATM 11 C C2 TPP . . . E 5 69.005 236.23 44.334 1 44.34 ? C2 TPP 704 A 1 
HETATM 12 S S1 TPP . . . E 5 70.166 237.223 45.174 1 49.93 ? S1 TPP 704 A 1 
HETATM 13 C C5 TPP . . . E 5 71.411 236.796 44.02 1 48.87 ? C5 TPP 704 A 1 
HETATM 14 C C4 TPP . . . E 5 70.85 235.917 43.072 1 51.91 ? C4 TPP 704 A 1 
HETATM 15 C CM4 TPP . . . E 5 71.657 235.351 41.936 1 43.7 ? CM4 TPP 704 A 1 
HETATM 16 C C6 TPP . . . E 5 72.842 237.295 44.06 1 48.66 ? C6 TPP 704 A 1 
HETATM 17 C C7 TPP . . . E 5 72.958 238.778 43.776 1 39.95 ? C7 TPP 704 A 1 
HETATM 18 O O7 TPP . . . E 5 74.303 239.12 43.875 1 51.94 ? O7 TPP 704 A 1 
HETATM 19 P PA TPP . . . E 5 74.523 240.652 44.113 1 43.6 ? PA TPP 704 A 1 
HETATM 20 O O1A TPP . . . E 5 73.727 241.463 43.112 1 35.09 ? O1A TPP 704 A 1 
HETATM 21 O O2A TPP . . . E 5 75.968 240.977 43.905 1 44 ? O2A TPP 704 A 1 
HETATM 22 O O3A TPP . . . E 5 74.011 241.001 45.561 1 54.25 ? O3A TPP 704 A 1 
HETATM 23 P PB TPP . . . E 5 74.92 240.645 46.789 1 47.42 ? PB TPP 704 A 1 
HETATM 24 O O1B TPP . . . E 5 76.354 240.318 46.407 1 40.39 ? O1B TPP 704 A 1 
HETATM 25 O O2B TPP . . . E 5 74.906 241.807 47.732 1 42.96 ? O2B TPP 704 A 1 
HETATM 26 O O3B TPP . . . E 5 74.341 239.437 47.51 1 35.03 ? O3B TPP 704 A 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           26 
#