data_5VVU # _model_server_result.job_id ySEW9lRNhO2OurvQLi_psQ _model_server_result.datetime_utc '2024-12-22 06:42:17' _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 5vvu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5VVU # _exptl.entry_id 5VVU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-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 114.51 _cell.angle_gamma 90 _cell.entry_id 5VVU _cell.length_a 82.507 _cell.length_b 96.06 _cell.length_c 88.968 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VVU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 # _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 E N N ? 3 F 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 463 A CYS 663 1_555 C SG CYS 463 C CYS 663 2_955 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? covale ? covale1 B OG SER 4 B SER 395 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.369 ? covale ? covale2 C NH1 ARG 25 C ARG 83 1_555 C NZ LYS 29 C LYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.233 ? covale ? covale3 D OG SER 4 D SER 395 1_555 F C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 5VVU _atom_sites.fract_transf_matrix[1][1] 0.01212 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005526 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01041 _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] 0.012353 _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 E 3 NAG B 1 401 401 NAG NAG . F 3 NAG D 1 401 401 NAG NAG . G 4 HOH A 1 801 33 HOH HOH . G 4 HOH A 2 802 17 HOH HOH . G 4 HOH A 3 803 16 HOH HOH . G 4 HOH A 4 804 34 HOH HOH . G 4 HOH A 5 805 26 HOH HOH . G 4 HOH A 6 806 35 HOH HOH . G 4 HOH A 7 807 46 HOH HOH . G 4 HOH A 8 808 13 HOH HOH . G 4 HOH A 9 809 1 HOH HOH . G 4 HOH A 10 810 36 HOH HOH . G 4 HOH A 11 811 19 HOH HOH . G 4 HOH A 12 812 6 HOH HOH . G 4 HOH A 13 813 8 HOH HOH . G 4 HOH A 14 814 27 HOH HOH . G 4 HOH A 15 815 23 HOH HOH . G 4 HOH A 16 816 41 HOH HOH . G 4 HOH A 17 817 45 HOH HOH . G 4 HOH A 18 818 2 HOH HOH . G 4 HOH A 19 819 21 HOH HOH . G 4 HOH A 20 820 37 HOH HOH . G 4 HOH A 21 821 20 HOH HOH . G 4 HOH A 22 822 24 HOH HOH . G 4 HOH A 23 823 18 HOH HOH . G 4 HOH A 24 824 9 HOH HOH . G 4 HOH A 25 825 22 HOH HOH . G 4 HOH A 26 826 39 HOH HOH . G 4 HOH A 27 827 44 HOH HOH . G 4 HOH A 28 828 42 HOH HOH . G 4 HOH A 29 829 4 HOH HOH . H 4 HOH C 1 801 43 HOH HOH . H 4 HOH C 2 802 10 HOH HOH . H 4 HOH C 3 803 5 HOH HOH . H 4 HOH C 4 804 3 HOH HOH . H 4 HOH C 5 805 14 HOH HOH . H 4 HOH C 6 806 38 HOH HOH . H 4 HOH C 7 807 15 HOH HOH . H 4 HOH C 8 808 12 HOH HOH . H 4 HOH C 9 809 29 HOH HOH . H 4 HOH C 10 810 30 HOH HOH . H 4 HOH C 11 811 25 HOH HOH . H 4 HOH C 12 812 7 HOH HOH . H 4 HOH C 13 813 28 HOH HOH . H 4 HOH C 14 814 40 HOH HOH . H 4 HOH C 15 815 47 HOH HOH . H 4 HOH C 16 816 32 HOH HOH . H 4 HOH C 17 817 31 HOH HOH . H 4 HOH C 18 818 49 HOH HOH . H 4 HOH C 19 819 11 HOH HOH . H 4 HOH C 20 820 48 HOH HOH . I 4 HOH D 1 501 50 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 3 163.078 -3.162 26.292 1 57.62 ? C1 NAG 401 B 1 HETATM 2 C C2 NAG . . . E 3 163.5 -2.96 27.89 1 51.72 ? C2 NAG 401 B 1 HETATM 3 C C3 NAG . . . E 3 162.896 -1.561 28.435 1 47.44 ? C3 NAG 401 B 1 HETATM 4 C C4 NAG . . . E 3 162.962 -0.423 27.367 1 50.59 ? C4 NAG 401 B 1 HETATM 5 C C5 NAG . . . E 3 161.934 -0.903 26.287 1 50.64 ? C5 NAG 401 B 1 HETATM 6 C C6 NAG . . . E 3 161.628 0.279 25.249 1 50.18 ? C6 NAG 401 B 1 HETATM 7 C C7 NAG . . . E 3 161.777 -4.672 28.808 1 50.77 ? C7 NAG 401 B 1 HETATM 8 C C8 NAG . . . E 3 161.441 -5.895 29.712 1 49.49 ? C8 NAG 401 B 1 HETATM 9 N N2 NAG . . . E 3 163.055 -4.119 28.697 1 48.52 ? N2 NAG 401 B 1 HETATM 10 O O3 NAG . . . E 3 163.885 -1.199 29.412 1 46.8 ? O3 NAG 401 B 1 HETATM 11 O O4 NAG . . . E 3 162.433 0.768 28.003 1 57.28 ? O4 NAG 401 B 1 HETATM 12 O O5 NAG . . . E 3 162.676 -1.942 25.577 1 55.74 ? O5 NAG 401 B 1 HETATM 13 O O6 NAG . . . E 3 162.751 0.473 24.331 1 47.26 ? O6 NAG 401 B 1 HETATM 14 O O7 NAG . . . E 3 160.843 -4.161 28.186 1 57.29 ? O7 NAG 401 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #