data_8S5U # _model_server_result.job_id jeUsnjw5cSwY9jcrViSfcg _model_server_result.datetime_utc '2025-04-08 01:43:12' _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 8s5u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 8S5U # _exptl.entry_id 8S5U _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 265.355 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM _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 90 _cell.entry_id 8S5U _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8S5U _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 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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 22 B CYS 22 1_555 A SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 B ND2 ASN 45 A ASN 45 1_555 C C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? # _chem_comp.formula 'C12 H17 N4 O S 1' _chem_comp.formula_weight 265.355 _chem_comp.id VIB _chem_comp.mon_nstd_flag . _chem_comp.name 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'THIAMIN;VITAMIN B1' # 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 CM2 C2A VIB sing 404 n n CM2 HM21 VIB sing 405 n n CM2 HM22 VIB sing 406 n n CM2 HM23 VIB sing 407 n n N4A C4A VIB sing 408 n n N4A H4A1 VIB sing 409 n n N4A H4A2 VIB sing 410 n n CM4 C4 VIB sing 411 n n CM4 HM41 VIB sing 412 n n CM4 HM42 VIB sing 413 n n CM4 HM43 VIB sing 414 n n O1 C7 VIB sing 415 n n O1 HO1 VIB sing 416 n n C7 C6 VIB sing 417 n n C7 HC71 VIB sing 418 n n C7 HC72 VIB sing 419 n n C6 C5 VIB sing 420 n n C6 HC61 VIB sing 421 n n C6 HC62 VIB sing 422 n n C2 S1 VIB sing 423 n y C2 N3 VIB doub 424 n y C2 HC2 VIB sing 425 n n S1 C5 VIB sing 426 n y C5 C4 VIB doub 427 n y C4 N3 VIB sing 428 n y N3 C7A VIB sing 429 n n C7A C5A VIB sing 430 n n C7A H7A1 VIB sing 431 n n C7A H7A2 VIB sing 432 n n C4A N3A VIB sing 433 n y C4A C5A VIB doub 434 n y N3A C2A VIB doub 435 n y C2A N1A VIB sing 436 n y N1A C6A VIB doub 437 n y C6A C5A VIB sing 438 n y C6A H6AC VIB sing 439 n n # _atom_sites.entry_id 8S5U _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 C 3 NAG A 1 601 502 NAG NAG . D 4 VIB A 1 602 503 VIB VIB . # 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 CM2 VIB . . . D 4 165.607 156.229 155.044 1 40 ? CM2 VIB 602 A 1 HETATM 2 N N4A VIB . . . D 4 166.774 161.167 155.656 1 40 ? N4A VIB 602 A 1 HETATM 3 C CM4 VIB . . . D 4 168.959 159.019 159.524 1 40 ? CM4 VIB 602 A 1 HETATM 4 O O1 VIB . . . D 4 172.218 158.877 160.492 1 40 ? O1 VIB 602 A 1 HETATM 5 C C7 VIB . . . D 4 171.797 160.212 160.491 1 40 ? C7 VIB 602 A 1 HETATM 6 C C6 VIB . . . D 4 171.656 160.709 159.055 1 40 ? C6 VIB 602 A 1 HETATM 7 C C2 VIB . . . D 4 168.322 162.587 158.103 1 40 ? C2 VIB 602 A 1 HETATM 8 S S1 VIB . . . D 4 169.855 162.542 158.229 1 40 ? S1 VIB 602 A 1 HETATM 9 C C5 VIB . . . D 4 170.236 161.19 158.778 1 40 ? C5 VIB 602 A 1 HETATM 10 C C4 VIB . . . D 4 169.028 160.441 158.979 1 40 ? C4 VIB 602 A 1 HETATM 11 N N3 VIB . . . D 4 167.812 161.341 158.55 1 40 1 N3 VIB 602 A 1 HETATM 12 C C7A VIB . . . D 4 166.412 160.973 158.59 1 40 ? C7A VIB 602 A 1 HETATM 13 C C4A VIB . . . D 4 166.393 159.889 156.22 1 40 ? C4A VIB 602 A 1 HETATM 14 N N3A VIB . . . D 4 166.197 158.74 155.366 1 40 ? N3A VIB 602 A 1 HETATM 15 C C2A VIB . . . D 4 165.813 157.437 155.949 1 40 ? C2A VIB 602 A 1 HETATM 16 N N1A VIB . . . D 4 165.625 157.304 157.412 1 40 ? N1A VIB 602 A 1 HETATM 17 C C6A VIB . . . D 4 165.811 158.45 158.28 1 40 ? C6A VIB 602 A 1 HETATM 18 C C5A VIB . . . D 4 166.202 159.762 157.691 1 40 ? C5A VIB 602 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 18 #