data_5SVT # _model_server_result.job_id u8Lyx8J4WNwLEdHyVVXf6g _model_server_result.datetime_utc '2024-11-05 21:14:41' _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 5svt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5SVT # _exptl.entry_id 5SVT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 5SVT _cell.length_a 119.95 _cell.length_b 119.95 _cell.length_c 236.41 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVT _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 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 disulf ? disulf1 A SG CYS 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 B C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 C C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 D C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5SVT _atom_sites.fract_transf_matrix[1][1] 0.008337 _atom_sites.fract_transf_matrix[1][2] 0.004813 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009627 _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] 0.00423 _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 B 2 NAG A 1 401 500 NAG NAG . C 2 NAG A 1 402 501 NAG NAG . D 2 NAG A 1 403 502 NAG NAG . E 3 MG A 1 404 1 MG MG . F 4 NA A 1 405 1 NA NA . # 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 NAG . . . B 2 -13.825 -25.887 -34.119 1 217.26 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . B 2 -13.081 -26.81 -33.146 1 217.93 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . B 2 -13.698 -28.21 -33.158 1 218.72 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . B 2 -15.196 -28.135 -32.889 1 224.84 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . B 2 -15.848 -27.2 -33.902 1 225.95 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . B 2 -17.323 -26.975 -33.651 1 230.13 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . B 2 -10.681 -26.745 -32.597 1 217.45 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . B 2 -9.285 -26.862 -33.136 1 213.73 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . B 2 -11.667 -26.884 -33.491 1 217.35 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . B 2 -13.071 -29.01 -32.161 1 218.65 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . B 2 -15.769 -29.435 -32.989 1 233.49 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . B 2 -15.226 -25.909 -33.828 1 220.58 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . B 2 -17.915 -26.217 -34.698 1 233.55 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . B 2 -10.904 -26.533 -31.409 1 218.72 ? O7 NAG 401 A 1 HETATM 15 H H1 NAG . . . B 2 -13.681 -26.198 -35.032 1 260.71 ? H1 NAG 401 A 1 HETATM 16 H H2 NAG . . . B 2 -13.167 -26.446 -32.244 1 261.52 ? H2 NAG 401 A 1 HETATM 17 H H3 NAG . . . B 2 -13.551 -28.616 -34.033 1 262.47 ? H3 NAG 401 A 1 HETATM 18 H H4 NAG . . . B 2 -15.343 -27.787 -31.989 1 269.8 ? H4 NAG 401 A 1 HETATM 19 H H5 NAG . . . B 2 -15.726 -27.564 -34.8 1 271.14 ? H5 NAG 401 A 1 HETATM 20 H H61 NAG . . . B 2 -17.434 -26.497 -32.808 1 276.15 ? H61 NAG 401 A 1 HETATM 21 H H62 NAG . . . B 2 -17.772 -27.84 -33.59 1 276.15 ? H62 NAG 401 A 1 HETATM 22 H H81 NAG . . . B 2 -9.139 -26.173 -33.812 1 256.48 ? H81 NAG 401 A 1 HETATM 23 H H82 NAG . . . B 2 -8.645 -26.746 -32.409 1 256.48 ? H82 NAG 401 A 1 HETATM 24 H H83 NAG . . . B 2 -9.165 -27.743 -33.539 1 256.48 ? H83 NAG 401 A 1 HETATM 25 H HN2 NAG . . . B 2 -11.443 -27.044 -34.36 1 260.82 ? HN2 NAG 401 A 1 HETATM 26 H HO3 NAG . . . B 2 -13.288 -28.704 -31.356 1 262.38 ? HO3 NAG 401 A 1 HETATM 27 H HO4 NAG . . . B 2 -16.451 -29.415 -33.557 1 280.19 ? HO4 NAG 401 A 1 HETATM 28 H HO6 NAG . . . B 2 -18.675 -25.858 -34.41 1 280.26 ? HO6 NAG 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #