data_6F83 # _model_server_result.job_id 1cq2v3a49Ls6jHxMSEJXDQ _model_server_result.datetime_utc '2025-02-05 06:00:24' _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 6f83 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 6F83 # _exptl.entry_id 6F83 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 624.71 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-deoxy-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-1-thio-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranoside' _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 6F83 _cell.length_a 44.447 _cell.length_b 58.689 _cell.length_c 112.353 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6F83 _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 ? 2 C N N ? 2 D 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 15 A GLU 15 1_555 A N CME 16 A CME 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C CME 16 A CME 16 1_555 A N LEU 17 A LEU 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale3 A C LEU 41 A LEU 41 1_555 A N CME 42 A CME 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 A C CME 42 A CME 42 1_555 A N LEU 43 A LEU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C VAL 59 A VAL 59 1_555 A N CME 60 A CME 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 A C CME 60 A CME 60 1_555 A N ASN 61 A ASN 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale7 A C VAL 87 A VAL 87 1_555 A N CME 88 A CME 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C CME 88 A CME 88 1_555 A N ILE 89 A ILE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale9 A C LYS 129 A LYS 129 1_555 A N CME 130 A CME 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 A C CME 130 A CME 130 1_555 A N VAL 131 A VAL 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale11 B C GLU 15 B GLU 15 1_555 B N CME 16 B CME 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale12 B C CME 16 B CME 16 1_555 B N LEU 17 B LEU 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale13 B C LEU 41 B LEU 41 1_555 B N CME 42 B CME 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale14 B C CME 42 B CME 42 1_555 B N LEU 43 B LEU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale15 B C VAL 59 B VAL 59 1_555 B N CME 60 B CME 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale16 B C CME 60 B CME 60 1_555 B N ASN 61 B ASN 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale17 B C VAL 87 B VAL 87 1_555 B N CME 88 B CME 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale18 B C CME 88 B CME 88 1_555 B N ILE 89 B ILE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 B C LYS 129 B LYS 129 1_555 B N CME 130 B CME 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale20 B C CME 130 B CME 130 1_555 B N VAL 131 B VAL 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C24 H28 N6 O8 S3' _chem_comp.formula_weight 624.71 _chem_comp.id 5KT _chem_comp.mon_nstd_flag . _chem_comp.name '3-deoxy-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-1-thio-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranoside' _chem_comp.type d-saccharide _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 O6' C6' 5KT sing 1 n n C6' C5' 5KT sing 2 n n C5' O5' 5KT sing 3 n n C5' C4' 5KT sing 4 n n N2 N3 5KT doub 5 n y N2 N1 5KT sing 6 n y O5' C1' 5KT sing 7 n n O2 C2 5KT sing 8 n n N3 CB 5KT sing 9 n y C3 N1 5KT sing 10 n n C3 C2 5KT sing 11 n n C3 C4 5KT sing 12 n n C4' O4' 5KT sing 13 n n C4' C3' 5KT sing 14 n n C1 C2 5KT sing 15 n n C1 S1 5KT sing 16 n n C1 O5 5KT sing 17 n n N1 CA 5KT sing 18 n y C1' S1 5KT sing 19 n n C1' C2' 5KT sing 20 n n C5 C4 5KT sing 21 n n C5 O5 5KT sing 22 n n C5 C6 5KT sing 23 n n C4 O4 5KT sing 24 n n CB CA 5KT doub 25 n y CB CD 5KT sing 26 n n O6 C6 5KT sing 27 n n CF CD 5KT sing 28 n y CF CG 5KT doub 29 n y C3' C2' 5KT sing 30 n n C3' N1' 5KT sing 31 n n CD CE 5KT doub 32 n y C2' O2' 5KT sing 33 n n CG S2 5KT sing 34 n y N1' CA' 5KT sing 35 n y N1' N2' 5KT sing 36 n y CE S2 5KT sing 37 n y CA' CB' 5KT doub 38 n y N2' N3' 5KT doub 39 n y CB' N3' 5KT sing 40 n y CB' CD' 5KT sing 41 n n CD' CF' 5KT sing 42 n y CD' CE' 5KT doub 43 n y CF' CG' 5KT doub 44 n y CE' S2' 5KT sing 45 n y CG' S2' 5KT sing 46 n y C6 H1 5KT sing 47 n n C6 H2 5KT sing 48 n n C5 H3 5KT sing 49 n n C2 H4 5KT sing 50 n n C4 H5 5KT sing 51 n n C5' H6 5KT sing 52 n n C4' H7 5KT sing 53 n n C2' H8 5KT sing 54 n n C6' H9 5KT sing 55 n n C6' H10 5KT sing 56 n n O6 H11 5KT sing 57 n n O4 H12 5KT sing 58 n n C3 H13 5KT sing 59 n n CF H14 5KT sing 60 n n CE H15 5KT sing 61 n n CG H16 5KT sing 62 n n CA H17 5KT sing 63 n n O2 H18 5KT sing 64 n n C1 H19 5KT sing 65 n n C1' H20 5KT sing 66 n n O6' H21 5KT sing 67 n n O2' H22 5KT sing 68 n n C3' H23 5KT sing 69 n n O4' H24 5KT sing 70 n n CA' H25 5KT sing 71 n n CF' H26 5KT sing 72 n n CE' H27 5KT sing 73 n n CG' H28 5KT sing 74 n n # _atom_sites.entry_id 6F83 _atom_sites.fract_transf_matrix[1][1] 0.022499 _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] 0.017039 _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] 0.008901 _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 5KT A 1 201 1 5KT TDM . D 2 5KT B 1 201 1 5KT TDM . E 3 HOH A 1 301 59 HOH HOH . E 3 HOH A 2 302 56 HOH HOH . E 3 HOH A 3 303 18 HOH HOH . E 3 HOH A 4 304 80 HOH HOH . E 3 HOH A 5 305 24 HOH HOH . E 3 HOH A 6 306 28 HOH HOH . E 3 HOH A 7 307 77 HOH HOH . E 3 HOH A 8 308 11 HOH HOH . E 3 HOH A 9 309 31 HOH HOH . E 3 HOH A 10 310 42 HOH HOH . E 3 HOH A 11 311 82 HOH HOH . E 3 HOH A 12 312 67 HOH HOH . E 3 HOH A 13 313 66 HOH HOH . E 3 HOH A 14 314 19 HOH HOH . E 3 HOH A 15 315 20 HOH HOH . E 3 HOH A 16 316 58 HOH HOH . E 3 HOH A 17 317 10 HOH HOH . E 3 HOH A 18 318 75 HOH HOH . E 3 HOH A 19 319 15 HOH HOH . E 3 HOH A 20 320 49 HOH HOH . E 3 HOH A 21 321 52 HOH HOH . E 3 HOH A 22 322 78 HOH HOH . E 3 HOH A 23 323 46 HOH HOH . E 3 HOH A 24 324 70 HOH HOH . E 3 HOH A 25 325 62 HOH HOH . E 3 HOH A 26 326 57 HOH HOH . E 3 HOH A 27 327 27 HOH HOH . E 3 HOH A 28 328 4 HOH HOH . E 3 HOH A 29 329 30 HOH HOH . E 3 HOH A 30 330 61 HOH HOH . E 3 HOH A 31 331 47 HOH HOH . E 3 HOH A 32 332 29 HOH HOH . E 3 HOH A 33 333 9 HOH HOH . E 3 HOH A 34 334 7 HOH HOH . E 3 HOH A 35 335 81 HOH HOH . E 3 HOH A 36 336 39 HOH HOH . E 3 HOH A 37 337 45 HOH HOH . E 3 HOH A 38 338 84 HOH HOH . F 3 HOH B 1 301 72 HOH HOH . F 3 HOH B 2 302 2 HOH HOH . F 3 HOH B 3 303 23 HOH HOH . F 3 HOH B 4 304 8 HOH HOH . F 3 HOH B 5 305 73 HOH HOH . F 3 HOH B 6 306 14 HOH HOH . F 3 HOH B 7 307 69 HOH HOH . F 3 HOH B 8 308 43 HOH HOH . F 3 HOH B 9 309 22 HOH HOH . F 3 HOH B 10 310 3 HOH HOH . F 3 HOH B 11 311 85 HOH HOH . F 3 HOH B 12 312 12 HOH HOH . F 3 HOH B 13 313 50 HOH HOH . F 3 HOH B 14 314 16 HOH HOH . F 3 HOH B 15 315 74 HOH HOH . F 3 HOH B 16 316 64 HOH HOH . F 3 HOH B 17 317 34 HOH HOH . F 3 HOH B 18 318 36 HOH HOH . F 3 HOH B 19 319 33 HOH HOH . F 3 HOH B 20 320 6 HOH HOH . F 3 HOH B 21 321 55 HOH HOH . F 3 HOH B 22 322 13 HOH HOH . F 3 HOH B 23 323 35 HOH HOH . F 3 HOH B 24 324 40 HOH HOH . F 3 HOH B 25 325 51 HOH HOH . F 3 HOH B 26 326 1 HOH HOH . F 3 HOH B 27 327 76 HOH HOH . F 3 HOH B 28 328 48 HOH HOH . F 3 HOH B 29 329 5 HOH HOH . F 3 HOH B 30 330 21 HOH HOH . F 3 HOH B 31 331 38 HOH HOH . F 3 HOH B 32 332 41 HOH HOH . F 3 HOH B 33 333 32 HOH HOH . F 3 HOH B 34 334 53 HOH HOH . F 3 HOH B 35 335 44 HOH HOH . F 3 HOH B 36 336 25 HOH HOH . F 3 HOH B 37 337 68 HOH HOH . F 3 HOH B 38 338 79 HOH HOH . F 3 HOH B 39 339 83 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 C6 5KT . . . D 2 11.777 44.397 20.471 1 40.75 ? C6 5KT 201 B 1 HETATM 2 C C5 5KT . . . D 2 11.153 43.991 21.808 1 45.83 ? C5 5KT 201 B 1 HETATM 3 S S1 5KT . . . D 2 8.283 45.758 23.913 1 51.99 ? S1 5KT 201 B 1 HETATM 4 C C2 5KT . . . D 2 9 43.271 23.623 1 44.33 ? C2 5KT 201 B 1 HETATM 5 N N3 5KT . . . D 2 9.068 38.708 23.306 1 43.98 ? N3 5KT 201 B 1 HETATM 6 C C4 5KT . . . D 2 10.427 42.648 21.683 1 41.8 ? C4 5KT 201 B 1 HETATM 7 C C5' 5KT . . . D 2 9.958 48.972 25.542 1 76.52 ? C5' 5KT 201 B 1 HETATM 8 C C4' 5KT . . . D 2 9.079 50.064 24.944 1 78.33 ? C4' 5KT 201 B 1 HETATM 9 N N3' 5KT . . . D 2 7.857 52.905 22.084 1 77.72 ? N3' 5KT 201 B 1 HETATM 10 C C2' 5KT . . . D 2 8.277 48.352 23.285 1 61.59 ? C2' 5KT 201 B 1 HETATM 11 N N1' 5KT . . . D 2 8.088 50.769 22.728 1 58.86 ? N1' 5KT 201 B 1 HETATM 12 C C6' 5KT . . . D 2 10.237 49.221 27.016 1 71.35 ? C6' 5KT 201 B 1 HETATM 13 O O6 5KT . . . D 2 12.232 45.75 20.535 1 31.69 ? O6 5KT 201 B 1 HETATM 14 O O5 5KT . . . D 2 10.245 44.991 22.31 1 49.42 ? O5 5KT 201 B 1 HETATM 15 O O4 5KT . . . D 2 9.337 42.727 20.745 1 33.89 ? O4 5KT 201 B 1 HETATM 16 C C3 5KT . . . D 2 9.928 42.215 23.06 1 43.53 ? C3 5KT 201 B 1 HETATM 17 N N1 5KT . . . D 2 9.186 40.931 22.99 1 37.38 ? N1 5KT 201 B 1 HETATM 18 N N2 5KT . . . D 2 9.917 39.817 23.442 1 39.85 ? N2 5KT 201 B 1 HETATM 19 C CB 5KT . . . D 2 7.925 39.234 22.812 1 44.55 ? CB 5KT 201 B 1 HETATM 20 C CD 5KT . . . D 2 6.763 38.36 22.499 1 36.3 ? CD 5KT 201 B 1 HETATM 21 C CF 5KT . . . D 2 5.708 38.767 21.694 1 38.57 ? CF 5KT 201 B 1 HETATM 22 C CE 5KT . . . D 2 6.744 37.057 22.958 1 47.46 ? CE 5KT 201 B 1 HETATM 23 S S2 5KT . . . D 2 5.305 36.236 22.424 1 53.56 ? S2 5KT 201 B 1 HETATM 24 C CG 5KT . . . D 2 4.827 37.697 21.578 1 36.39 ? CG 5KT 201 B 1 HETATM 25 C CA 5KT . . . D 2 7.951 40.601 22.592 1 36.51 ? CA 5KT 201 B 1 HETATM 26 O O2 5KT . . . D 2 8.661 42.92 24.965 1 39.26 ? O2 5KT 201 B 1 HETATM 27 C C1 5KT . . . D 2 9.626 44.665 23.581 1 51.29 ? C1 5KT 201 B 1 HETATM 28 C C1' 5KT . . . D 2 9.119 47.318 24.023 1 67.01 ? C1' 5KT 201 B 1 HETATM 29 O O5' 5KT . . . D 2 9.319 47.701 25.389 1 75.79 ? O5' 5KT 201 B 1 HETATM 30 O O6' 5KT . . . D 2 11.152 48.214 27.443 1 54.13 ? O6' 5KT 201 B 1 HETATM 31 O O2' 5KT . . . D 2 8.268 47.998 21.902 1 43.52 ? O2' 5KT 201 B 1 HETATM 32 C C3' 5KT . . . D 2 8.879 49.737 23.458 1 68.94 ? C3' 5KT 201 B 1 HETATM 33 O O4' 5KT . . . D 2 7.85 50.148 25.688 1 74.38 ? O4' 5KT 201 B 1 HETATM 34 N N2' 5KT . . . D 2 8.68 52.04 22.816 1 76.82 ? N2' 5KT 201 B 1 HETATM 35 C CB' 5KT . . . D 2 6.861 52.124 21.63 1 61.39 ? CB' 5KT 201 B 1 HETATM 36 C CA' 5KT . . . D 2 6.96 50.792 21.982 1 52 ? CA' 5KT 201 B 1 HETATM 37 C CD' 5KT . . . D 2 5.821 52.736 20.757 1 62.8 ? CD' 5KT 201 B 1 HETATM 38 C CF' 5KT . . . D 2 4.454 52.621 20.946 1 60.99 ? CF' 5KT 201 B 1 HETATM 39 C CE' 5KT . . . D 2 6.304 53.46 19.676 1 67.49 ? CE' 5KT 201 B 1 HETATM 40 S S2' 5KT . . . D 2 4.949 54.087 18.785 1 91.05 ? S2' 5KT 201 B 1 HETATM 41 C CG' 5KT . . . D 2 3.828 53.327 19.924 1 78.91 ? CG' 5KT 201 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 41 #