data_5DF0 # _model_server_result.job_id nSX6pCbZziW7rct7J21FxA _model_server_result.datetime_utc '2024-11-24 01:20:21' _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 5df0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":604}' # _entry.id 5DF0 # _exptl.entry_id 5DF0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 237.273 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose _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 5DF0 _cell.length_a 96.712 _cell.length_b 112.766 _cell.length_c 129.591 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DF0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,F,G,H,I,J,K,S 1 1 B,L,M,N,O,P,Q,R,T 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 ? 3 F N N ? 3 O 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 disulf ? disulf1 A SG CYS 106 A CYS 106 1_555 A SG CYS 111 A CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 185 A CYS 185 1_555 A SG CYS 208 A CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 106 B CYS 106 1_555 B SG CYS 111 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 185 B CYS 185 1_555 B SG CYS 208 B CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 F C1 SN5 . A SN5 604 1_555 G O4 58Y . A 58Y 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 B ND2 ASN 444 B ASN 444 1_555 N C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 O C1 SN5 . B SN5 604 1_555 P O4 58Y . B 58Y 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _chem_comp.formula 'C8 H15 N O5 S' _chem_comp.formula_weight 237.273 _chem_comp.id SN5 _chem_comp.mon_nstd_flag n _chem_comp.name 2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-ethanethioyl-beta-D-glucosamine;2-deoxy-2-(ethanethioylamino)-beta-D-glucose;2-deoxy-2-(ethanethioylamino)-D-glucose;2-deoxy-2-(ethanethioylamino)-glucose # 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 S7 C7 SN5 doub 350 n n C7 C8 SN5 sing 351 n n C7 N2 SN5 sing 352 n n N2 C2 SN5 sing 353 n n C2 C1 SN5 sing 354 n n C2 C3 SN5 sing 355 n n C1 O1 SN5 sing 356 n n C1 O5 SN5 sing 357 n n C3 O3 SN5 sing 358 n n C3 C4 SN5 sing 359 n n C4 O4 SN5 sing 360 n n C4 C5 SN5 sing 361 n n C5 O5 SN5 sing 362 n n C5 C6 SN5 sing 363 n n C6 O6 SN5 sing 364 n n C8 H81C SN5 sing 365 n n C8 H82C SN5 sing 366 n n C8 H83C SN5 sing 367 n n N2 HN21 SN5 sing 368 n n C2 H2 SN5 sing 369 n n C1 H1 SN5 sing 370 n n C3 H3 SN5 sing 371 n n O1 HO1 SN5 sing 372 n n O3 HO3 SN5 sing 373 n n C4 H4 SN5 sing 374 n n O4 HO4 SN5 sing 375 n n C5 H5 SN5 sing 376 n n C6 H61 SN5 sing 377 n n C6 H62 SN5 sing 378 n n O6 HO6 SN5 sing 379 n n # _atom_sites.entry_id 5DF0 _atom_sites.fract_transf_matrix[1][1] 0.01034 _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] 0.008868 _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] 0.007717 _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 NAG A 1 601 546 NAG NAG . D 2 NAG A 1 602 547 NAG NAG . E 2 NAG A 1 603 550 NAG NAG . F 3 SN5 A 1 604 561 SN5 SN5 . G 4 58Y A 1 605 560 58Y NGT . H 5 CL A 1 606 554 CL CL . I 6 SO4 A 1 607 766 SO4 SO4 . J 6 SO4 A 1 608 767 SO4 SO4 . K 6 SO4 A 1 609 768 SO4 SO4 . L 2 NAG B 1 601 550 NAG NAG . M 2 NAG B 1 602 552 NAG NAG . N 2 NAG B 1 603 553 NAG NAG . O 3 SN5 B 1 604 561 SN5 SN5 . P 4 58Y B 1 605 560 58Y NGT . Q 6 SO4 B 1 606 901 SO4 SO4 . R 6 SO4 B 1 607 902 SO4 SO4 . S 7 HOH A 1 701 616 HOH HOH . S 7 HOH A 2 702 609 HOH HOH . S 7 HOH A 3 703 717 HOH HOH . S 7 HOH A 4 704 765 HOH HOH . T 7 HOH B 1 701 565 HOH HOH . T 7 HOH B 2 702 577 HOH HOH . T 7 HOH B 3 703 900 HOH HOH . T 7 HOH B 4 704 684 HOH HOH . T 7 HOH B 5 705 774 HOH HOH . T 7 HOH B 6 706 639 HOH HOH . T 7 HOH B 7 707 750 HOH HOH . T 7 HOH B 8 708 877 HOH HOH . T 7 HOH B 9 709 736 HOH HOH . T 7 HOH B 10 710 702 HOH HOH . T 7 HOH B 11 711 641 HOH HOH . T 7 HOH B 12 712 854 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 C C1 SN5 . . . O 3 -58.785 -14.981 278.521 1 34.17 ? C1 SN5 604 B 1 HETATM 2 S S7 SN5 . . . O 3 -59.386 -13.372 282.217 1 29.43 ? S7 SN5 604 B 1 HETATM 3 C C2 SN5 . . . O 3 -59.59 -15.196 279.75 1 35.39 ? C2 SN5 604 B 1 HETATM 4 C C3 SN5 . . . O 3 -60.571 -16.264 279.607 1 32.24 ? C3 SN5 604 B 1 HETATM 5 C C4 SN5 . . . O 3 -61.444 -16.07 278.428 1 37.72 ? C4 SN5 604 B 1 HETATM 6 C C5 SN5 . . . O 3 -60.626 -15.951 277.131 1 36.36 ? C5 SN5 604 B 1 HETATM 7 C C6 SN5 . . . O 3 -61.48 -15.654 276.037 1 30.97 ? C6 SN5 604 B 1 HETATM 8 C C7 SN5 . . . O 3 -58.704 -14.825 282.157 1 40.31 ? C7 SN5 604 B 1 HETATM 9 C C8 SN5 . . . O 3 -58.122 -15.443 283.413 1 41.72 ? C8 SN5 604 B 1 HETATM 10 N N2 SN5 . . . O 3 -58.643 -15.559 280.891 1 41.17 ? N2 SN5 604 B 1 HETATM 11 O O3 SN5 . . . O 3 -61.424 -16.313 280.83 1 35.93 ? O3 SN5 604 B 1 HETATM 12 O O4 SN5 . . . O 3 -62.35 -17.193 278.32 1 72.23 ? O4 SN5 604 B 1 HETATM 13 O O5 SN5 . . . O 3 -59.619 -14.804 277.336 1 37.79 ? O5 SN5 604 B 1 HETATM 14 O O6 SN5 . . . O 3 -60.724 -15.506 274.885 1 31.12 ? O6 SN5 604 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #