data_6VZ8
#
_model_server_result.job_id            hVLo6jZm2elPk0AJXOzMjQ 
_model_server_result.datetime_utc      '2024-11-24 22:30:31' 
_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          6vz8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":703}' 
#
_entry.id    6VZ8 
#
_exptl.entry_id    6VZ8 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    8 
_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            6VZ8 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VZ8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexadecameric 
_pdbx_struct_assembly.oligomeric_count      16 
_pdbx_struct_assembly.details               author_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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA 
_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    ? 
_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
? 5 S N N 
? 5 V N N 
? 5 AA N N 
? 5 DA N N 
? 5 IA N N 
? 5 LA N N 
? 5 QA N N 
? 5 TA 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 O HIS 483 D HIS 567 1_555 Q MG MG . D MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
metalc ? metalc2 Q MG MG . D MG 701 1_555 S O3A TPP . D TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc3 Q MG MG . D MG 701 1_555 S O2B TPP . D TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc4 Q MG MG . D MG 701 1_555 S O3B TPP . D TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? 
metalc ? metalc5 Q MG MG . D MG 701 1_555 S O2A TPP . D TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? 
metalc ? metalc6 Q MG MG . D MG 701 1_555 S O7 TPP . D TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc7 T MG MG . E MG 701 1_555 V O3A TPP . E TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc8 T MG MG . E MG 701 1_555 V O1B TPP . E TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? 
metalc ? metalc9 T MG MG . E MG 701 1_555 V O1A TPP . E TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? 
metalc ? metalc10 E O HIS 483 H HIS 567 1_555 Y MG MG . H MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? 
metalc ? metalc11 Y MG MG . H MG 701 1_555 AA O3A TPP . H TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc12 Y MG MG . H MG 701 1_555 AA O2B TPP . H TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? 
metalc ? metalc13 Y MG MG . H MG 701 1_555 AA O3B TPP . H TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? 
metalc ? metalc14 Y MG MG . H MG 701 1_555 AA O2A TPP . H TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc15 Y MG MG . H MG 701 1_555 AA O7 TPP . H TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc16 BA MG MG . I MG 701 1_555 DA O3A TPP . I TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc17 BA MG MG . I MG 701 1_555 DA O1B TPP . I TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? 
metalc ? metalc18 BA MG MG . I MG 701 1_555 DA O1A TPP . I TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? 
metalc ? metalc19 I O HIS 483 L HIS 567 1_555 GA MG MG . L MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? 
metalc ? metalc20 GA MG MG . L MG 701 1_555 IA O3B TPP . L TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? 
metalc ? metalc21 GA MG MG . L MG 701 1_555 IA O2A TPP . L TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc22 GA MG MG . L MG 701 1_555 IA O3A TPP . L TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? 
metalc ? metalc23 GA MG MG . L MG 701 1_555 IA O2B TPP . L TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? 
metalc ? metalc24 GA MG MG . L MG 701 1_555 IA O7 TPP . L TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc25 JA MG MG . M MG 701 1_555 LA O1A TPP . M TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? 
metalc ? metalc26 JA MG MG . M MG 701 1_555 LA O3A TPP . M TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc27 JA MG MG . M MG 701 1_555 LA O1B TPP . M TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? 
metalc ? metalc28 M O HIS 483 P HIS 567 1_555 OA MG MG . P MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
metalc ? metalc29 OA MG MG . P MG 701 1_555 QA O3B TPP . P TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? 
metalc ? metalc30 OA MG MG . P MG 701 1_555 QA O2A TPP . P TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? 
metalc ? metalc31 OA MG MG . P MG 701 1_555 QA O3A TPP . P TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc32 OA MG MG . P MG 701 1_555 QA O2B TPP . P TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc33 OA MG MG . P MG 701 1_555 QA O7 TPP . P TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc34 RA MG MG . Q MG 701 1_555 TA O3A TPP . Q TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc35 RA MG MG . Q MG 701 1_555 TA O1B TPP . Q TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc36 RA MG MG . Q MG 701 1_555 TA O1A TPP . Q TPP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? 
#
_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 395 n y 
N1' C6' TPP sing 396 n y 
C2' CM2 TPP sing 397 n n 
C2' N3' TPP sing 398 n y 
CM2 HM21 TPP sing 399 n n 
CM2 HM22 TPP sing 400 n n 
CM2 HM23 TPP sing 401 n n 
N3' C4' TPP doub 402 n y 
C4' N4' TPP sing 403 n n 
C4' C5' TPP sing 404 n y 
N4' HN41 TPP sing 405 n n 
N4' HN42 TPP sing 406 n n 
C5' C6' TPP doub 407 n y 
C5' C7' TPP sing 408 n n 
C6' H6' TPP sing 409 n n 
C7' N3 TPP sing 410 n n 
C7' "H7'1" TPP sing 411 n n 
C7' "H7'2" TPP sing 412 n n 
N3 C2 TPP doub 413 n y 
N3 C4 TPP sing 414 n y 
C2 S1 TPP sing 415 n y 
C2 H2 TPP sing 416 n n 
S1 C5 TPP sing 417 n y 
C5 C4 TPP doub 418 n y 
C5 C6 TPP sing 419 n n 
C4 CM4 TPP sing 420 n n 
CM4 HM41 TPP sing 421 n n 
CM4 HM42 TPP sing 422 n n 
CM4 HM43 TPP sing 423 n n 
C6 C7 TPP sing 424 n n 
C6 H61 TPP sing 425 n n 
C6 H62 TPP sing 426 n n 
C7 O7 TPP sing 427 n n 
C7 H71 TPP sing 428 n n 
C7 H72 TPP sing 429 n n 
O7 PA TPP sing 430 n n 
PA O1A TPP doub 431 n n 
PA O2A TPP sing 432 n n 
PA O3A TPP sing 433 n n 
O2A HOA2 TPP sing 434 n n 
O3A PB TPP sing 435 n n 
PB O1B TPP doub 436 n n 
PB O2B TPP sing 437 n n 
PB O3B TPP sing 438 n n 
O2B HOB2 TPP sing 439 n n 
O3B HOB3 TPP sing 440 n n 
#
_atom_sites.entry_id                     6VZ8 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
Q 3 MG D 1 701 32 MG MG . 
R 4 FAD D 1 702 732 FAD FAD . 
S 5 TPP D 1 703 734 TPP TPP . 
T 3 MG E 1 701 31 MG MG . 
U 4 FAD E 1 702 731 FAD FAD . 
V 5 TPP E 1 703 733 TPP TPP . 
W 6 VAL F 1 501 20 VAL VLN . 
X 6 VAL G 1 501 10 VAL VLN . 
Y 3 MG H 1 701 38 MG MG . 
Z 4 FAD H 1 702 738 FAD FAD . 
AA 5 TPP H 1 703 740 TPP TPP . 
BA 3 MG I 1 701 37 MG MG . 
CA 4 FAD I 1 702 737 FAD FAD . 
DA 5 TPP I 1 703 739 TPP TPP . 
EA 6 VAL J 1 501 40 VAL VLN . 
FA 6 VAL K 1 501 30 VAL VLN . 
GA 3 MG L 1 701 36 MG MG . 
HA 4 FAD L 1 702 736 FAD FAD . 
IA 5 TPP L 1 703 738 TPP TPP . 
JA 3 MG M 1 701 35 MG MG . 
KA 4 FAD M 1 702 735 FAD FAD . 
LA 5 TPP M 1 703 737 TPP TPP . 
MA 6 VAL N 1 501 60 VAL VLN . 
NA 6 VAL O 1 501 50 VAL VLN . 
OA 3 MG P 1 701 34 MG MG . 
PA 4 FAD P 1 702 734 FAD FAD . 
QA 5 TPP P 1 703 736 TPP TPP . 
RA 3 MG Q 1 701 33 MG MG . 
SA 4 FAD Q 1 702 733 FAD FAD . 
TA 5 TPP Q 1 703 735 TPP TPP . 
UA 6 VAL R 1 501 80 VAL VLN . 
VA 6 VAL S 1 501 70 VAL VLN . 
#
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 . . . V 5 276.942 176.366 206.282 1 182.5 ? N1' TPP 703 E 1 
HETATM 2 C C2' TPP . . . V 5 276.533 176.788 207.473 1 182.5 ? C2' TPP 703 E 1 
HETATM 3 C CM2 TPP . . . V 5 276.877 178.209 207.838 1 182.5 ? CM2 TPP 703 E 1 
HETATM 4 N N3' TPP . . . V 5 275.899 176.067 208.394 1 182.5 ? N3' TPP 703 E 1 
HETATM 5 C C4' TPP . . . V 5 275.685 174.813 208.074 1 182.5 ? C4' TPP 703 E 1 
HETATM 6 N N4' TPP . . . V 5 275.109 174.114 209.057 1 182.5 ? N4' TPP 703 E 1 
HETATM 7 C C5' TPP . . . V 5 276.092 174.233 206.888 1 182.5 ? C5' TPP 703 E 1 
HETATM 8 C C6' TPP . . . V 5 276.715 175.084 205.988 1 182.5 ? C6' TPP 703 E 1 
HETATM 9 C C7' TPP . . . V 5 275.912 172.759 206.564 1 182.5 ? C7' TPP 703 E 1 
HETATM 10 N N3 TPP . . . V 5 276.932 171.911 207.205 1 182.5 ? N3 TPP 703 E 1 
HETATM 11 C C2 TPP . . . V 5 276.606 171.209 208.334 1 182.5 ? C2 TPP 703 E 1 
HETATM 12 S S1 TPP . . . V 5 278.003 170.357 208.948 1 182.5 ? S1 TPP 703 E 1 
HETATM 13 C C5 TPP . . . V 5 278.948 170.977 207.596 1 182.5 ? C5 TPP 703 E 1 
HETATM 14 C C4 TPP . . . V 5 278.233 171.794 206.735 1 182.5 ? C4 TPP 703 E 1 
HETATM 15 C CM4 TPP . . . V 5 278.823 172.459 205.513 1 182.5 ? CM4 TPP 703 E 1 
HETATM 16 C C6 TPP . . . V 5 280.439 170.704 207.455 1 182.5 ? C6 TPP 703 E 1 
HETATM 17 C C7 TPP . . . V 5 280.899 169.355 208.035 1 182.5 ? C7 TPP 703 E 1 
HETATM 18 O O7 TPP . . . V 5 282.316 169.323 208.068 1 182.5 ? O7 TPP 703 E 1 
HETATM 19 P PA TPP . . . V 5 283.038 169.865 209.405 1 182.5 ? PA TPP 703 E 1 
HETATM 20 O O1A TPP . . . V 5 284.449 170.335 209.137 1 182.5 ? O1A TPP 703 E 1 
HETATM 21 O O2A TPP . . . V 5 282.282 171.02 210.015 1 182.5 ? O2A TPP 703 E 1 
HETATM 22 O O3A TPP . . . V 5 283.069 168.663 210.417 1 182.5 ? O3A TPP 703 E 1 
HETATM 23 P PB TPP . . . V 5 283 167.155 209.976 1 182.5 ? PB TPP 703 E 1 
HETATM 24 O O1B TPP . . . V 5 284.185 166.707 209.133 1 182.5 ? O1B TPP 703 E 1 
HETATM 25 O O2B TPP . . . V 5 283.064 166.393 211.281 1 182.5 ? O2B TPP 703 E 1 
HETATM 26 O O3B TPP . . . V 5 281.692 166.801 209.34 1 182.5 ? O3B TPP 703 E 1 
#
_model_server_stats.io_time_ms              79 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    62 
_model_server_stats.query_time_ms           388 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#