data_3EXF
#
_model_server_result.job_id            8PCsru3UPOSGk_5Uxgb1tQ 
_model_server_result.datetime_utc      '2025-06-28 12:48:39' 
_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          3exf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1006}' 
#
_entry.id    3EXF 
#
_exptl.entry_id    3EXF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              425.314 
_entity.id                          4 
_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          109.15 
_cell.angle_gamma         90 
_cell.entry_id            3EXF 
_cell.length_a            103.389 
_cell.length_b            129.668 
_cell.length_c            144.946 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EXF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,I,J,K,L,M,N,U,V,W 1 1 
E,F,G,H,O,P,Q,R,S,T,X,Y,Z 2 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
? 4 J N N 
? 4 M N N 
? 4 P N N 
? 4 S 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 OD2 ASP 188 A ASP 167 1_555 I MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc2 A OD1 ASN 217 A ASN 196 1_555 I MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc3 A O TYR 219 A TYR 198 1_555 I MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc4 I MG MG . A MG 1001 1_555 J O1B TPP . A TPP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc5 I MG MG . A MG 1001 1_555 J O2A TPP . A TPP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? 
metalc ? metalc6 B O ALA 160 B ALA 160 1_555 K K K . B K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? 
metalc ? metalc7 B O ILE 161 B ILE 161 1_555 K K K . B K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? 
metalc ? metalc8 B O ASP 163 B ASP 163 1_555 K K K . B K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? 
metalc ? metalc9 C OD2 ASP 188 C ASP 167 1_555 L MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc10 C OD1 ASN 217 C ASN 196 1_555 L MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? 
metalc ? metalc11 C O TYR 219 C TYR 198 1_555 L MG MG . C MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc12 L MG MG . C MG 1004 1_555 M O1B TPP . C TPP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc13 L MG MG . C MG 1004 1_555 M O2A TPP . C TPP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc14 L MG MG . C MG 1004 1_555 V O HOH . C HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc15 D O ILE 161 D ILE 161 1_555 N K K . D K 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? 
metalc ? metalc16 E OD2 ASP 188 E ASP 167 1_555 O MG MG . E MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc17 E O TYR 219 E TYR 198 1_555 O MG MG . E MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc18 O MG MG . E MG 1007 1_555 P O2A TPP . E TPP 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc19 O MG MG . E MG 1007 1_555 P O1B TPP . E TPP 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.793 ? 
metalc ? metalc20 F O ILE 161 F ILE 161 1_555 Q K K . F K 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? 
metalc ? metalc21 F O ASP 163 F ASP 163 1_555 Q K K . F K 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? 
metalc ? metalc22 G OD2 ASP 188 G ASP 167 1_555 R MG MG . G MG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.883 ? 
metalc ? metalc23 G OD1 ASN 217 G ASN 196 1_555 R MG MG . G MG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? 
metalc ? metalc24 G O TYR 219 G TYR 198 1_555 R MG MG . G MG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
metalc ? metalc25 R MG MG . G MG 1010 1_555 S O2A TPP . G TPP 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc26 R MG MG . G MG 1010 1_555 S O1B TPP . G TPP 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc27 H O ASP 163 H ASP 163 1_555 T K K . H K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
#
_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                     3EXF 
_atom_sites.fract_transf_matrix[1][1]    0.009672 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003359 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007712 
_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]    0.007303 
_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
I 3 MG A 1 1001 1001 MG MG . 
J 4 TPP A 1 1003 1003 TPP TPP . 
K 5 K B 1 1005 1005 K K . 
L 3 MG C 1 1004 1004 MG MG . 
M 4 TPP C 1 1006 1006 TPP TPP . 
N 5 K D 1 1002 1002 K K . 
O 3 MG E 1 1007 1007 MG MG . 
P 4 TPP E 1 1009 1009 TPP TPP . 
Q 5 K F 1 1011 1011 K K . 
R 3 MG G 1 1010 1010 MG MG . 
S 4 TPP G 1 1012 1012 TPP TPP . 
T 5 K H 1 1008 1008 K K . 
U 6 HOH B 1 2004 2004 HOH HOH . 
V 6 HOH C 1 2002 2002 HOH HOH . 
V 6 HOH C 2 2006 2006 HOH HOH . 
V 6 HOH C 3 2009 2009 HOH HOH . 
W 6 HOH D 1 2001 2001 HOH HOH . 
X 6 HOH E 1 2007 2007 HOH HOH . 
Y 6 HOH F 1 2005 2005 HOH HOH . 
Y 6 HOH F 2 2008 2008 HOH HOH . 
Z 6 HOH H 1 2003 2003 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 . . . M 4 -28.97 -19.323 -7.5 1 18.46 ? N1' TPP 1006 C 1 
HETATM 2 C C2' TPP . . . M 4 -28.835 -18.781 -6.232 1 17.49 ? C2' TPP 1006 C 1 
HETATM 3 C CM2 TPP . . . M 4 -27.821 -17.697 -5.967 1 17.2 ? CM2 TPP 1006 C 1 
HETATM 4 N N3' TPP . . . M 4 -29.6 -19.267 -5.21 1 16.53 ? N3' TPP 1006 C 1 
HETATM 5 C C4' TPP . . . M 4 -30.521 -20.258 -5.471 1 18.86 ? C4' TPP 1006 C 1 
HETATM 6 N N4' TPP . . . M 4 -31.213 -20.658 -4.406 1 15.99 ? N4' TPP 1006 C 1 
HETATM 7 C C5' TPP . . . M 4 -30.692 -20.79 -6.785 1 21.28 ? C5' TPP 1006 C 1 
HETATM 8 C C6' TPP . . . M 4 -29.878 -20.315 -7.798 1 19.49 ? C6' TPP 1006 C 1 
HETATM 9 C C7' TPP . . . M 4 -31.663 -21.906 -7.183 1 26.03 ? C7' TPP 1006 C 1 
HETATM 10 N N3 TPP . . . M 4 -31.087 -23.138 -6.689 1 33.58 ? N3 TPP 1006 C 1 
HETATM 11 C C2 TPP . . . M 4 -31.253 -23.501 -5.355 1 35.86 ? C2 TPP 1006 C 1 
HETATM 12 S S1 TPP . . . M 4 -30.522 -24.883 -4.973 1 40.55 ? S1 TPP 1006 C 1 
HETATM 13 C C5 TPP . . . M 4 -29.934 -25.096 -6.478 1 34.95 ? C5 TPP 1006 C 1 
HETATM 14 C C4 TPP . . . M 4 -30.304 -24.075 -7.366 1 34.85 ? C4 TPP 1006 C 1 
HETATM 15 C CM4 TPP . . . M 4 -29.902 -24.065 -8.813 1 33.68 ? CM4 TPP 1006 C 1 
HETATM 16 C C6 TPP . . . M 4 -29.111 -26.35 -6.676 1 31.03 ? C6 TPP 1006 C 1 
HETATM 17 C C7 TPP . . . M 4 -27.899 -26.36 -5.725 1 26.68 ? C7 TPP 1006 C 1 
HETATM 18 O O7 TPP . . . M 4 -26.996 -27.428 -5.978 1 23.06 ? O7 TPP 1006 C 1 
HETATM 19 P PA TPP . . . M 4 -26.084 -28.092 -4.832 1 20.89 ? PA TPP 1006 C 1 
HETATM 20 O O1A TPP . . . M 4 -25.042 -27.117 -4.372 1 21.97 ? O1A TPP 1006 C 1 
HETATM 21 O O2A TPP . . . M 4 -25.431 -29.373 -5.246 1 21.41 ? O2A TPP 1006 C 1 
HETATM 22 O O3A TPP . . . M 4 -27.135 -28.367 -3.661 1 22.16 ? O3A TPP 1006 C 1 
HETATM 23 P PB TPP . . . M 4 -27.562 -29.839 -3.234 1 23.49 ? PB TPP 1006 C 1 
HETATM 24 O O1B TPP . . . M 4 -27.645 -30.827 -4.402 1 25.24 ? O1B TPP 1006 C 1 
HETATM 25 O O2B TPP . . . M 4 -26.556 -30.306 -2.21 1 22.21 ? O2B TPP 1006 C 1 
HETATM 26 O O3B TPP . . . M 4 -28.951 -29.713 -2.652 1 22.58 ? O3B TPP 1006 C 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           94 
_model_server_stats.create_model_time_ms    100 
_model_server_stats.query_time_ms           357 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           26 
#