data_1TKB
#
_model_server_result.job_id            fGD-FbzvAavZBAEXC06npQ 
_model_server_result.datetime_utc      '2024-11-22 10:13:07' 
_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          1tkb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":681}' 
#
_entry.id    1TKB 
#
_exptl.entry_id    1TKB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              423.318 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "1'-DEAZO-THIAMIN 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          90 
_cell.angle_gamma         90 
_cell.entry_id            1TKB 
_cell.length_a            76.3 
_cell.length_b            113.3 
_cell.length_c            160.9 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1TKB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
#
_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
? 3 D N N 
? 3 F 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 155 A ASP 157 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc2 A ND2 ASN 185 A ASN 187 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.254 ? 
metalc ? metalc3 A OD1 ASN 185 A ASN 187 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? 
metalc ? metalc4 A O ILE 187 A ILE 189 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc5 D O1B N1T . A N1T 681 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.669 ? 
metalc ? metalc6 D O2A N1T . A N1T 681 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
metalc ? metalc7 B OD2 ASP 155 B ASP 157 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc8 B OD1 ASN 185 B ASN 187 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? 
metalc ? metalc9 B ND2 ASN 185 B ASN 187 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.159 ? 
metalc ? metalc10 B O ILE 187 B ILE 189 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? 
metalc ? metalc11 F O2B N1T . B N1T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? 
metalc ? metalc12 F O3B N1T . B N1T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.173 ? 
metalc ? metalc13 F O3A N1T . B N1T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.33 ? 
metalc ? metalc14 F O2A N1T . B N1T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
#
_chem_comp.formula           'C13 H19 N3 O7 P2 S' 
_chem_comp.formula_weight    423.318 
_chem_comp.id                N1T 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "1'-DEAZO-THIAMIN 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
C1' C2' N1T sing 235 n y 
C1' C6' N1T doub 236 n y 
C1' H1' N1T sing 237 n n 
C2' CM2 N1T sing 238 n n 
C2' N3' N1T doub 239 n y 
CM2 HM21 N1T sing 240 n n 
CM2 HM22 N1T sing 241 n n 
CM2 HM23 N1T sing 242 n n 
N3' C4' N1T sing 243 n y 
C4' N4' N1T sing 244 n n 
C4' C5' N1T doub 245 n y 
N4' HN41 N1T sing 246 n n 
N4' HN42 N1T sing 247 n n 
C5' C6' N1T sing 248 n y 
C5' C7' N1T sing 249 n n 
C6' H6' N1T sing 250 n n 
C7' N3 N1T sing 251 n n 
C7' "H7'1" N1T sing 252 n n 
C7' "H7'2" N1T sing 253 n n 
N3 C2 N1T doub 254 n y 
N3 C4 N1T sing 255 n y 
C2 S1 N1T sing 256 n y 
C2 H2 N1T sing 257 n n 
S1 C5 N1T sing 258 n y 
C5 C4 N1T doub 259 n y 
C5 C6 N1T sing 260 n n 
C4 CM4 N1T sing 261 n n 
CM4 HM41 N1T sing 262 n n 
CM4 HM42 N1T sing 263 n n 
CM4 HM43 N1T sing 264 n n 
C6 C7 N1T sing 265 n n 
C6 H61 N1T sing 266 n n 
C6 H62 N1T sing 267 n n 
C7 O7 N1T sing 268 n n 
C7 H71 N1T sing 269 n n 
C7 H72 N1T sing 270 n n 
O7 PA N1T sing 271 n n 
PA O1A N1T doub 272 n n 
PA O2A N1T sing 273 n n 
PA O3A N1T sing 274 n n 
O2A HOA2 N1T sing 275 n n 
O3A PB N1T sing 276 n n 
PB O1B N1T doub 277 n n 
PB O2B N1T sing 278 n n 
PB O3B N1T sing 279 n n 
O3B HOB3 N1T sing 280 n n 
#
_atom_sites.entry_id                     1TKB 
_atom_sites.fract_transf_matrix[1][1]    0.013106 
_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]    0.008826 
_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]    0.006215 
_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
C 2 CA A 1 682 682 CA CA . 
D 3 N1T A 1 681 681 N1T N1T . 
E 2 CA B 1 682 682 CA CA . 
F 3 N1T B 1 681 681 N1T N1T . 
#
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 C C1' N1T . . . F 3 15.151 71.652 26.562 1 5.66 ? C1' N1T 681 B 1 
HETATM 2 C C2' N1T . . . F 3 14.181 72.603 26.086 1 7.3 ? C2' N1T 681 B 1 
HETATM 3 C CM2 N1T . . . F 3 12.832 72.133 25.759 1 5.37 ? CM2 N1T 681 B 1 
HETATM 4 N N3' N1T . . . F 3 14.452 73.907 26.167 1 9.72 ? N3' N1T 681 B 1 
HETATM 5 C C4' N1T . . . F 3 15.729 74.334 26.368 1 9.39 ? C4' N1T 681 B 1 
HETATM 6 N N4' N1T . . . F 3 15.854 75.614 26.424 1 4.51 ? N4' N1T 681 B 1 
HETATM 7 C C5' N1T . . . F 3 16.808 73.446 26.679 1 9.51 ? C5' N1T 681 B 1 
HETATM 8 C C6' N1T . . . F 3 16.49 72.143 26.857 1 8.08 ? C6' N1T 681 B 1 
HETATM 9 C C7' N1T . . . F 3 18.173 73.933 27.146 1 10.98 ? C7' N1T 681 B 1 
HETATM 10 N N3 N1T . . . F 3 19.073 74.519 26.085 1 16.12 ? N3 N1T 681 B 1 
HETATM 11 C C2 N1T . . . F 3 18.949 75.774 25.656 1 14.37 ? C2 N1T 681 B 1 
HETATM 12 S S1 N1T . . . F 3 19.764 76.041 24.224 1 14.54 ? S1 N1T 681 B 1 
HETATM 13 C C5 N1T . . . F 3 20.226 74.402 24.163 1 16.59 ? C5 N1T 681 B 1 
HETATM 14 C C4 N1T . . . F 3 19.889 73.76 25.334 1 15.48 ? C4 N1T 681 B 1 
HETATM 15 C CM4 N1T . . . F 3 19.91 72.268 25.541 1 12.36 ? CM4 N1T 681 B 1 
HETATM 16 C C6 N1T . . . F 3 20.594 73.77 22.844 1 13.74 ? C6 N1T 681 B 1 
HETATM 17 C C7 N1T . . . F 3 21.626 74.486 22.024 1 14.07 ? C7 N1T 681 B 1 
HETATM 18 O O7 N1T . . . F 3 20.81 75.484 21.438 1 13.41 ? O7 N1T 681 B 1 
HETATM 19 P PA N1T . . . F 3 20.948 76.243 20.066 1 13.79 ? PA N1T 681 B 1 
HETATM 20 O O1A N1T . . . F 3 19.53 76.603 19.735 1 13.8 ? O1A N1T 681 B 1 
HETATM 21 O O2A N1T . . . F 3 21.744 75.568 18.989 1 14.53 ? O2A N1T 681 B 1 
HETATM 22 O O3A N1T . . . F 3 21.721 77.604 20.309 1 16.31 ? O3A N1T 681 B 1 
HETATM 23 P PB N1T . . . F 3 23.112 78.223 19.944 1 19.98 ? PB N1T 681 B 1 
HETATM 24 O O1B N1T . . . F 3 22.875 79.492 20.629 1 20.92 ? O1B N1T 681 B 1 
HETATM 25 O O2B N1T . . . F 3 23.12 78.037 18.462 1 26.91 ? O2B N1T 681 B 1 
HETATM 26 O O3B N1T . . . F 3 24.111 77.358 20.572 1 25.49 ? O3B N1T 681 B 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#