data_5VJL # _model_server_result.job_id J8jshy19Ic-ecxbN71Z5Xw _model_server_result.datetime_utc '2024-10-17 21:46:22' _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 5vjl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":3003}' # _entry.id 5VJL # _exptl.entry_id 5VJL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 5VJL _cell.length_a 116.375 _cell.length_b 116.375 _cell.length_c 296.008 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VJL _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I _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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -58.1875 100.783706 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -116.375 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G 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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 272 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 133 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf5 A SG CYS 276 A CYS 281 1_555 A SG CYS 300 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? covale ? covale1 A ND2 ASN 32 A ASN 38 1_555 F C1 NAG . A NAG 3004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale2 A ND2 ASN 235 A ASN 240 1_555 E C1 NAG . A NAG 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C C2 SIA . A SIA 3001 1_555 D O MOH . A MOH 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 B ND2 ASN 82 B ASN 82 1_555 G C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.536 ? # _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 242 n n C1 O1 NAG sing 243 n n C1 O5 NAG sing 244 n n C1 H1 NAG sing 245 n n C2 C3 NAG sing 246 n n C2 N2 NAG sing 247 n n C2 H2 NAG sing 248 n n C3 C4 NAG sing 249 n n C3 O3 NAG sing 250 n n C3 H3 NAG sing 251 n n C4 C5 NAG sing 252 n n C4 O4 NAG sing 253 n n C4 H4 NAG sing 254 n n C5 C6 NAG sing 255 n n C5 O5 NAG sing 256 n n C5 H5 NAG sing 257 n n C6 O6 NAG sing 258 n n C6 H61 NAG sing 259 n n C6 H62 NAG sing 260 n n C7 C8 NAG sing 261 n n C7 N2 NAG sing 262 n n C7 O7 NAG doub 263 n n C8 H81 NAG sing 264 n n C8 H82 NAG sing 265 n n C8 H83 NAG sing 266 n n N2 HN2 NAG sing 267 n n O1 HO1 NAG sing 268 n n O3 HO3 NAG sing 269 n n O4 HO4 NAG sing 270 n n O6 HO6 NAG sing 271 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 5VJL _atom_sites.fract_transf_matrix[1][1] 0.008593 _atom_sites.fract_transf_matrix[1][2] 0.004961 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009922 _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] 0.003378 _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 SIA A 1 3001 3001 SIA SIA . D 4 MOH A 1 3002 3002 MOH GAL . E 5 NAG A 1 3003 501 NAG NAG . F 5 NAG A 1 3004 502 NAG NAG . G 5 NAG B 1 201 502 NAG NAG . H 6 HOH A 1 3101 2 HOH HOH . H 6 HOH A 2 3102 16 HOH HOH . H 6 HOH A 3 3103 15 HOH HOH . H 6 HOH A 4 3104 8 HOH HOH . H 6 HOH A 5 3105 9 HOH HOH . H 6 HOH A 6 3106 3 HOH HOH . H 6 HOH A 7 3107 20 HOH HOH . H 6 HOH A 8 3108 21 HOH HOH . H 6 HOH A 9 3109 31 HOH HOH . H 6 HOH A 10 3110 17 HOH HOH . H 6 HOH A 11 3111 11 HOH HOH . H 6 HOH A 12 3112 30 HOH HOH . H 6 HOH A 13 3113 19 HOH HOH . H 6 HOH A 14 3114 18 HOH HOH . I 6 HOH B 1 301 4 HOH HOH . I 6 HOH B 2 302 10 HOH HOH . I 6 HOH B 3 303 1 HOH HOH . I 6 HOH B 4 304 14 HOH HOH . I 6 HOH B 5 305 6 HOH HOH . I 6 HOH B 6 306 5 HOH HOH . I 6 HOH B 7 307 23 HOH HOH . I 6 HOH B 8 308 12 HOH HOH . I 6 HOH B 9 309 7 HOH HOH . I 6 HOH B 10 310 22 HOH HOH . I 6 HOH B 11 311 26 HOH HOH . I 6 HOH B 12 312 13 HOH HOH . I 6 HOH B 13 313 27 HOH HOH . I 6 HOH B 14 314 24 HOH HOH . I 6 HOH B 15 315 28 HOH HOH . I 6 HOH B 16 316 25 HOH HOH . I 6 HOH B 17 317 29 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 NAG . . . E 5 -83.267 12.802 -17.873 1 115.3 ? C1 NAG 3003 A 1 HETATM 2 C C2 NAG . . . E 5 -83.769 12.978 -16.438 1 129.33 ? C2 NAG 3003 A 1 HETATM 3 C C3 NAG . . . E 5 -84.442 11.69 -15.948 1 131.59 ? C3 NAG 3003 A 1 HETATM 4 C C4 NAG . . . E 5 -85.495 11.214 -16.945 1 129.55 ? C4 NAG 3003 A 1 HETATM 5 C C5 NAG . . . E 5 -84.92 11.152 -18.362 1 124.56 ? C5 NAG 3003 A 1 HETATM 6 C C6 NAG . . . E 5 -85.959 10.828 -19.415 1 124.95 ? C6 NAG 3003 A 1 HETATM 7 C C7 NAG . . . E 5 -82.46 14.624 -15.151 1 132.3 ? C7 NAG 3003 A 1 HETATM 8 C C8 NAG . . . E 5 -81.282 14.834 -14.252 1 128.11 ? C8 NAG 3003 A 1 HETATM 9 N N2 NAG . . . E 5 -82.678 13.363 -15.551 1 135.34 ? N2 NAG 3003 A 1 HETATM 10 O O3 NAG . . . E 5 -85.042 11.914 -14.674 1 130.39 ? O3 NAG 3003 A 1 HETATM 11 O O4 NAG . . . E 5 -85.974 9.926 -16.568 1 128.66 ? O4 NAG 3003 A 1 HETATM 12 O O5 NAG . . . E 5 -84.349 12.422 -18.715 1 117.66 ? O5 NAG 3003 A 1 HETATM 13 O O6 NAG . . . E 5 -85.378 10.322 -20.613 1 122.8 ? O6 NAG 3003 A 1 HETATM 14 O O7 NAG . . . E 5 -83.18 15.55 -15.499 1 133.02 ? O7 NAG 3003 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #