data_3MEL
#
_model_server_result.job_id            P3kW03uSoEnTBXWTDTeBuA 
_model_server_result.datetime_utc      '2025-04-06 21:09:02' 
_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          3mel 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":902}' 
#
_entry.id    3MEL 
#
_exptl.entry_id    3MEL 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          98.13 
_cell.angle_gamma         90 
_cell.entry_id            3MEL 
_cell.length_a            62.286 
_cell.length_b            102.112 
_cell.length_c            94.277 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3MEL 
_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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,E,F,G,H,I,J,K,L,M,T,U 1 1 
C,D,N,O,P,Q,R,S,V,W 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
? 2 E N N 
? 2 Q 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
covale ? covale1 A C GLU 95 A GLU 95 1_555 A N MSE 96 A MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale2 A C MSE 96 A MSE 96 1_555 A N THR 97 A THR 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? 
covale ? covale3 A C GLY 204 A GLY 204 1_555 A N MSE 205 A MSE 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale4 A C MSE 205 A MSE 205 1_555 A N ILE 206 A ILE 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale5 B C GLU 95 B GLU 95 1_555 B N MSE 96 B MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale6 B C MSE 96 B MSE 96 1_555 B N THR 97 B THR 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale7 B C GLY 204 B GLY 204 1_555 B N MSE 205 B MSE 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale8 B C MSE 205 B MSE 205 1_555 B N ILE 206 B ILE 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? 
covale ? covale9 C C MSE 1 C MSE 1 1_555 C N SER 2 C SER 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? 
covale ? covale10 C C GLU 95 C GLU 95 1_555 C N MSE 96 C MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale11 C C MSE 96 C MSE 96 1_555 C N THR 97 C THR 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale12 C C GLY 204 C GLY 204 1_555 C N MSE 205 C MSE 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale13 C C MSE 205 C MSE 205 1_555 C N ILE 206 C ILE 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale14 D C GLU 95 D GLU 95 1_555 D N MSE 96 D MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale15 D C MSE 96 D MSE 96 1_555 D N THR 97 D THR 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale16 D C GLY 204 D GLY 204 1_555 D N MSE 205 D MSE 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale17 D C MSE 205 D MSE 205 1_555 D N ILE 206 D ILE 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
metalc ? metalc1 A OD2 ASP 30 A ASP 30 1_555 F MG MG . A MG 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? 
metalc ? metalc2 A OD1 ASP 49 A ASP 49 1_555 F MG MG . A MG 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
metalc ? metalc3 F MG MG . A MG 223 1_555 E O2A TPP . A TPP 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? 
metalc ? metalc4 B OD2 ASP 30 B ASP 30 1_555 K MG MG . B MG 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? 
metalc ? metalc5 B OD1 ASP 49 B ASP 49 1_555 K MG MG . B MG 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? 
metalc ? metalc6 B O PHE 50 B PHE 50 1_555 L MG MG . B MG 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? 
metalc ? metalc7 C OD2 ASP 30 C ASP 30 1_555 O MG MG . C MG 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? 
metalc ? metalc8 C OD1 ASP 49 C ASP 49 1_555 O MG MG . C MG 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
metalc ? metalc9 D OD2 ASP 30 D ASP 30 1_555 R MG MG . D MG 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? 
metalc ? metalc10 D OD1 ASP 49 D ASP 49 1_555 R MG MG . D MG 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? 
metalc ? metalc11 D OD2 ASP 79 D ASP 79 1_555 R MG MG . D MG 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? 
metalc ? metalc12 R MG MG . D MG 223 1_555 Q O2A TPP . D TPP 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
#
_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 310 n y 
N1' C6' TPP sing 311 n y 
C2' CM2 TPP sing 312 n n 
C2' N3' TPP sing 313 n y 
CM2 HM21 TPP sing 314 n n 
CM2 HM22 TPP sing 315 n n 
CM2 HM23 TPP sing 316 n n 
N3' C4' TPP doub 317 n y 
C4' N4' TPP sing 318 n n 
C4' C5' TPP sing 319 n y 
N4' HN41 TPP sing 320 n n 
N4' HN42 TPP sing 321 n n 
C5' C6' TPP doub 322 n y 
C5' C7' TPP sing 323 n n 
C6' H6' TPP sing 324 n n 
C7' N3 TPP sing 325 n n 
C7' "H7'1" TPP sing 326 n n 
C7' "H7'2" TPP sing 327 n n 
N3 C2 TPP doub 328 n y 
N3 C4 TPP sing 329 n y 
C2 S1 TPP sing 330 n y 
C2 H2 TPP sing 331 n n 
S1 C5 TPP sing 332 n y 
C5 C4 TPP doub 333 n y 
C5 C6 TPP sing 334 n n 
C4 CM4 TPP sing 335 n n 
CM4 HM41 TPP sing 336 n n 
CM4 HM42 TPP sing 337 n n 
CM4 HM43 TPP sing 338 n n 
C6 C7 TPP sing 339 n n 
C6 H61 TPP sing 340 n n 
C6 H62 TPP sing 341 n n 
C7 O7 TPP sing 342 n n 
C7 H71 TPP sing 343 n n 
C7 H72 TPP sing 344 n n 
O7 PA TPP sing 345 n n 
PA O1A TPP doub 346 n n 
PA O2A TPP sing 347 n n 
PA O3A TPP sing 348 n n 
O2A HOA2 TPP sing 349 n n 
O3A PB TPP sing 350 n n 
PB O1B TPP doub 351 n n 
PB O2B TPP sing 352 n n 
PB O3B TPP sing 353 n n 
O2B HOB2 TPP sing 354 n n 
O3B HOB3 TPP sing 355 n n 
#
_atom_sites.entry_id                     3MEL 
_atom_sites.fract_transf_matrix[1][1]    0.016055 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002294 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009793 
_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]    0.010715 
_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 1 902 902 TPP TPP . 
F 3 MG A 1 223 2 MG MG . 
G 3 MG A 1 224 7 MG MG . 
H 3 MG A 1 225 9 MG MG . 
I 3 MG A 1 226 10 MG MG . 
J 4 PO4 B 1 223 2 PO4 PO4 . 
K 3 MG B 1 224 3 MG MG . 
L 3 MG B 1 225 6 MG MG . 
M 3 MG B 1 226 8 MG MG . 
N 4 PO4 C 1 223 1 PO4 PO4 . 
O 3 MG C 1 224 4 MG MG . 
P 3 MG C 1 225 5 MG MG . 
Q 2 TPP D 1 902 902 TPP TPP . 
R 3 MG D 1 223 1 MG MG . 
S 3 MG D 1 224 11 MG MG . 
T 5 HOH A 1 227 4 HOH HOH . 
T 5 HOH A 2 228 6 HOH HOH . 
U 5 HOH B 1 227 3 HOH HOH . 
V 5 HOH C 1 226 1 HOH HOH . 
V 5 HOH C 2 227 2 HOH HOH . 
W 5 HOH D 1 225 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 . . . Q 2 -0.824 13.054 59.889 1 46.95 ? N1' TPP 902 D 1 
HETATM 2 C C2' TPP . . . Q 2 0.161 13.477 60.908 1 42.31 ? C2' TPP 902 D 1 
HETATM 3 C CM2 TPP . . . Q 2 1.501 13.906 60.295 1 38.88 ? CM2 TPP 902 D 1 
HETATM 4 N N3' TPP . . . Q 2 0.261 12.556 62.032 1 44.58 ? N3' TPP 902 D 1 
HETATM 5 C C4' TPP . . . Q 2 -0.987 12.049 62.636 1 47.3 ? C4' TPP 902 D 1 
HETATM 6 N N4' TPP . . . Q 2 -0.651 11.057 63.658 1 48.57 ? N4' TPP 902 D 1 
HETATM 7 C C5' TPP . . . Q 2 -1.819 11.385 61.485 1 49.44 ? C5' TPP 902 D 1 
HETATM 8 C C6' TPP . . . Q 2 -2.063 12.493 60.436 1 47.1 ? C6' TPP 902 D 1 
HETATM 9 C C7' TPP . . . Q 2 -3.126 10.753 62.069 1 52.7 ? C7' TPP 902 D 1 
HETATM 10 N N3 TPP . . . Q 2 -2.818 9.542 62.892 1 49.55 ? N3 TPP 902 D 1 
HETATM 11 C C2 TPP . . . Q 2 -1.693 8.734 62.387 1 50.81 ? C2 TPP 902 D 1 
HETATM 12 S S1 TPP . . . Q 2 -2.333 7.113 61.875 1 55.43 ? S1 TPP 902 D 1 
HETATM 13 C C5 TPP . . . Q 2 -4.049 7.415 62.444 1 60.75 ? C5 TPP 902 D 1 
HETATM 14 C C4 TPP . . . Q 2 -3.974 8.68 63.345 1 49.23 ? C4 TPP 902 D 1 
HETATM 15 C CM4 TPP . . . Q 2 -5.271 9.47 63.468 1 47.67 ? CM4 TPP 902 D 1 
HETATM 16 C C6 TPP . . . Q 2 -4.761 6.187 63.024 1 64.22 ? C6 TPP 902 D 1 
HETATM 17 C C7 TPP . . . Q 2 -5.599 5.41 61.989 1 76.4 ? C7 TPP 902 D 1 
HETATM 18 O O7 TPP . . . Q 2 -5.535 4.017 62.277 1 100.12 ? O7 TPP 902 D 1 
HETATM 19 P PA TPP . . . Q 2 -6.465 2.891 61.633 1 185.29 ? PA TPP 902 D 1 
HETATM 20 O O1A TPP . . . Q 2 -7.094 3.798 60.508 1 118.7 ? O1A TPP 902 D 1 
HETATM 21 O O2A TPP . . . Q 2 -7.274 2.004 62.478 1 184.36 ? O2A TPP 902 D 1 
HETATM 22 O O3A TPP . . . Q 2 -5.814 1.721 60.774 1 103.24 ? O3A TPP 902 D 1 
HETATM 23 P PB TPP . . . Q 2 -6.346 0.812 59.594 1 129.96 ? PB TPP 902 D 1 
HETATM 24 O O1B TPP . . . Q 2 -5.105 0.099 58.957 1 74.14 ? O1B TPP 902 D 1 
HETATM 25 O O2B TPP . . . Q 2 -6.939 -0.451 60.338 1 93.18 ? O2B TPP 902 D 1 
HETATM 26 O O3B TPP . . . Q 2 -7.43 1.347 58.751 1 129.49 ? O3B TPP 902 D 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          16 
_model_server_stats.element_count           26 
#