data_9E9B
#
_model_server_result.job_id            39P5Gbl4JlPb8fpaRKK5lg 
_model_server_result.datetime_utc      '2025-08-03 01:59:37' 
_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          9e9b 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
#
_entry.id    9E9B 
#
_exptl.entry_id    9E9B 
_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    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            9E9B 
_cell.length_a            176.025 
_cell.length_b            176.025 
_cell.length_c            100.144 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9E9B 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        181 
_symmetry.space_group_name_Hall    'P 64 2 (x,y,z+1/6)' 
_symmetry.space_group_name_H-M     'P 64 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 
_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_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -176.025 0 0 
3 'crystal symmetry operation' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
4 'crystal symmetry operation' 11_455 -x+y-1,y,-z -1 0 0 0 1 0 0 0 -1 -176.025 0 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 
#
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 462 A ASP 459 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? 
metalc ? metalc2 A OD1 ASN 489 A ASN 486 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
metalc ? metalc3 A O GLY 491 A GLY 488 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? 
metalc ? metalc4 B O2A TPP . A TPP 601 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc5 B O3B TPP . A TPP 601 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
#
_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 306 n y 
N1' C6' TPP sing 307 n y 
C2' CM2 TPP sing 308 n n 
C2' N3' TPP sing 309 n y 
CM2 HM21 TPP sing 310 n n 
CM2 HM22 TPP sing 311 n n 
CM2 HM23 TPP sing 312 n n 
N3' C4' TPP doub 313 n y 
C4' N4' TPP sing 314 n n 
C4' C5' TPP sing 315 n y 
N4' HN41 TPP sing 316 n n 
N4' HN42 TPP sing 317 n n 
C5' C6' TPP doub 318 n y 
C5' C7' TPP sing 319 n n 
C6' H6' TPP sing 320 n n 
C7' N3 TPP sing 321 n n 
C7' "H7'1" TPP sing 322 n n 
C7' "H7'2" TPP sing 323 n n 
N3 C2 TPP doub 324 n y 
N3 C4 TPP sing 325 n y 
C2 S1 TPP sing 326 n y 
C2 H2 TPP sing 327 n n 
S1 C5 TPP sing 328 n y 
C5 C4 TPP doub 329 n y 
C5 C6 TPP sing 330 n n 
C4 CM4 TPP sing 331 n n 
CM4 HM41 TPP sing 332 n n 
CM4 HM42 TPP sing 333 n n 
CM4 HM43 TPP sing 334 n n 
C6 C7 TPP sing 335 n n 
C6 H61 TPP sing 336 n n 
C6 H62 TPP sing 337 n n 
C7 O7 TPP sing 338 n n 
C7 H71 TPP sing 339 n n 
C7 H72 TPP sing 340 n n 
O7 PA TPP sing 341 n n 
PA O1A TPP doub 342 n n 
PA O2A TPP sing 343 n n 
PA O3A TPP sing 344 n n 
O2A HOA2 TPP sing 345 n n 
O3A PB TPP sing 346 n n 
PB O1B TPP doub 347 n n 
PB O2B TPP sing 348 n n 
PB O3B TPP sing 349 n n 
O2B HOB2 TPP sing 350 n n 
O3B HOB3 TPP sing 351 n n 
#
_atom_sites.entry_id                     9E9B 
_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]    0.00656 
_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]    0.009986 
_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 TPP A 1 601 601 TPP TPP . 
C 3 MG A 1 602 1 MG MG . 
D 4 HOH A 1 701 46 HOH HOH . 
D 4 HOH A 2 702 47 HOH HOH . 
D 4 HOH A 3 703 52 HOH HOH . 
D 4 HOH A 4 704 69 HOH HOH . 
D 4 HOH A 5 705 75 HOH HOH . 
D 4 HOH A 6 706 85 HOH HOH . 
D 4 HOH A 7 707 51 HOH HOH . 
D 4 HOH A 8 708 50 HOH HOH . 
D 4 HOH A 9 709 78 HOH HOH . 
D 4 HOH A 10 710 93 HOH HOH . 
D 4 HOH A 11 711 88 HOH HOH . 
D 4 HOH A 12 712 74 HOH HOH . 
D 4 HOH A 13 713 62 HOH HOH . 
D 4 HOH A 14 714 65 HOH HOH . 
D 4 HOH A 15 715 56 HOH HOH . 
D 4 HOH A 16 716 70 HOH HOH . 
D 4 HOH A 17 717 17 HOH HOH . 
D 4 HOH A 18 718 23 HOH HOH . 
D 4 HOH A 19 719 76 HOH HOH . 
D 4 HOH A 20 720 49 HOH HOH . 
D 4 HOH A 21 721 2 HOH HOH . 
D 4 HOH A 22 722 82 HOH HOH . 
D 4 HOH A 23 723 45 HOH HOH . 
D 4 HOH A 24 724 64 HOH HOH . 
D 4 HOH A 25 725 79 HOH HOH . 
D 4 HOH A 26 726 53 HOH HOH . 
D 4 HOH A 27 727 60 HOH HOH . 
D 4 HOH A 28 728 18 HOH HOH . 
D 4 HOH A 29 729 89 HOH HOH . 
D 4 HOH A 30 730 87 HOH HOH . 
D 4 HOH A 31 731 26 HOH HOH . 
D 4 HOH A 32 732 63 HOH HOH . 
D 4 HOH A 33 733 15 HOH HOH . 
D 4 HOH A 34 734 72 HOH HOH . 
D 4 HOH A 35 735 59 HOH HOH . 
D 4 HOH A 36 736 67 HOH HOH . 
D 4 HOH A 37 737 83 HOH HOH . 
D 4 HOH A 38 738 68 HOH HOH . 
D 4 HOH A 39 739 35 HOH HOH . 
D 4 HOH A 40 740 21 HOH HOH . 
D 4 HOH A 41 741 58 HOH HOH . 
D 4 HOH A 42 742 33 HOH HOH . 
D 4 HOH A 43 743 41 HOH HOH . 
D 4 HOH A 44 744 86 HOH HOH . 
D 4 HOH A 45 745 57 HOH HOH . 
D 4 HOH A 46 746 66 HOH HOH . 
D 4 HOH A 47 747 71 HOH HOH . 
D 4 HOH A 48 748 19 HOH HOH . 
D 4 HOH A 49 749 30 HOH HOH . 
D 4 HOH A 50 750 10 HOH HOH . 
D 4 HOH A 51 751 44 HOH HOH . 
D 4 HOH A 52 752 55 HOH HOH . 
D 4 HOH A 53 753 54 HOH HOH . 
D 4 HOH A 54 754 80 HOH HOH . 
D 4 HOH A 55 755 7 HOH HOH . 
D 4 HOH A 56 756 73 HOH HOH . 
D 4 HOH A 57 757 77 HOH HOH . 
D 4 HOH A 58 758 92 HOH HOH . 
D 4 HOH A 59 759 13 HOH HOH . 
D 4 HOH A 60 760 22 HOH HOH . 
D 4 HOH A 61 761 91 HOH HOH . 
D 4 HOH A 62 762 90 HOH HOH . 
D 4 HOH A 63 763 40 HOH HOH . 
D 4 HOH A 64 764 81 HOH HOH . 
D 4 HOH A 65 765 61 HOH HOH . 
D 4 HOH A 66 766 48 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 . . . B 2 -77.586 2.6 -22.366 1 55.34 ? N1' TPP 601 A 1 
HETATM 2 C C2' TPP . . . B 2 -78.168 3.745 -21.97 1 55.12 ? C2' TPP 601 A 1 
HETATM 3 C CM2 TPP . . . B 2 -79.654 3.739 -21.819 1 51.51 ? CM2 TPP 601 A 1 
HETATM 4 N N3' TPP . . . B 2 -77.531 4.889 -21.701 1 54.57 ? N3' TPP 601 A 1 
HETATM 5 C C4' TPP . . . B 2 -76.192 4.907 -21.83 1 58.77 ? C4' TPP 601 A 1 
HETATM 6 N N4' TPP . . . B 2 -75.574 6.061 -21.558 1 54.25 ? N4' TPP 601 A 1 
HETATM 7 C C5' TPP . . . B 2 -75.478 3.742 -22.245 1 56.18 ? C5' TPP 601 A 1 
HETATM 8 C C6' TPP . . . B 2 -76.254 2.632 -22.49 1 51.41 ? C6' TPP 601 A 1 
HETATM 9 C C7' TPP . . . B 2 -73.98 3.702 -22.41 1 57.37 ? C7' TPP 601 A 1 
HETATM 10 N N3 TPP . . . B 2 -73.492 4.567 -23.51 1 58.19 ? N3 TPP 601 A 1 
HETATM 11 C C2 TPP . . . B 2 -73.019 5.784 -23.33 1 60.57 ? C2 TPP 601 A 1 
HETATM 12 S S1 TPP . . . B 2 -72.554 6.509 -24.767 1 60.88 ? S1 TPP 601 A 1 
HETATM 13 C C5 TPP . . . B 2 -73.01 5.11 -25.67 1 59.2 ? C5 TPP 601 A 1 
HETATM 14 C C4 TPP . . . B 2 -73.501 4.152 -24.842 1 58.66 ? C4 TPP 601 A 1 
HETATM 15 C CM4 TPP . . . B 2 -74.005 2.8 -25.214 1 54.28 ? CM4 TPP 601 A 1 
HETATM 16 C C6 TPP . . . B 2 -72.863 5.067 -27.165 1 54.65 ? C6 TPP 601 A 1 
HETATM 17 C C7 TPP . . . B 2 -74.058 5.642 -27.89 1 52.45 ? C7 TPP 601 A 1 
HETATM 18 O O7 TPP . . . B 2 -73.748 5.734 -29.303 1 50.27 ? O7 TPP 601 A 1 
HETATM 19 P PA TPP . . . B 2 -74.324 6.84 -30.272 1 47.82 ? PA TPP 601 A 1 
HETATM 20 O O1A TPP . . . B 2 -75.66 7.316 -29.849 1 46.48 ? O1A TPP 601 A 1 
HETATM 21 O O2A TPP . . . B 2 -74.294 6.295 -31.698 1 47.82 ? O2A TPP 601 A 1 
HETATM 22 O O3A TPP . . . B 2 -73.219 7.991 -30.19 1 51.25 ? O3A TPP 601 A 1 
HETATM 23 P PB TPP . . . B 2 -71.86 8.415 -30.891 1 62.64 ? PB TPP 601 A 1 
HETATM 24 O O1B TPP . . . B 2 -72.008 9.694 -31.649 1 70.04 ? O1B TPP 601 A 1 
HETATM 25 O O2B TPP . . . B 2 -70.847 8.475 -29.753 1 56.1 ? O2B TPP 601 A 1 
HETATM 26 O O3B TPP . . . B 2 -71.511 7.218 -31.785 1 63.7 ? O3B TPP 601 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           26 
#