data_5VVT # _model_server_result.job_id VIK_3HbCgelO-algjONsOw _model_server_result.datetime_utc '2024-12-22 07:26:03' _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 5vvt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5VVT # _exptl.entry_id 5VVT _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 5VVT _cell.length_a 82.363 _cell.length_b 95.793 _cell.length_c 89.323 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VVT _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 _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 covale ? covale1 B OG1 THR 4 B THR 381 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 D OG1 THR 4 D THR 381 1_555 F C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? # _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 5VVT _atom_sites.fract_transf_matrix[1][1] 0.012141 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005536 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010439 _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] 0.012304 _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 3 HOH HOH . G 4 HOH A 2 802 30 HOH HOH . G 4 HOH A 3 803 23 HOH HOH . G 4 HOH A 4 804 25 HOH HOH . G 4 HOH A 5 805 37 HOH HOH . G 4 HOH A 6 806 32 HOH HOH . G 4 HOH A 7 807 12 HOH HOH . G 4 HOH A 8 808 2 HOH HOH . G 4 HOH A 9 809 13 HOH HOH . G 4 HOH A 10 810 4 HOH HOH . G 4 HOH A 11 811 5 HOH HOH . G 4 HOH A 12 812 7 HOH HOH . G 4 HOH A 13 813 33 HOH HOH . G 4 HOH A 14 814 1 HOH HOH . G 4 HOH A 15 815 9 HOH HOH . G 4 HOH A 16 816 24 HOH HOH . G 4 HOH A 17 817 35 HOH HOH . G 4 HOH A 18 818 26 HOH HOH . G 4 HOH A 19 819 40 HOH HOH . G 4 HOH A 20 820 18 HOH HOH . G 4 HOH A 21 821 16 HOH HOH . G 4 HOH A 22 822 48 HOH HOH . G 4 HOH A 23 823 22 HOH HOH . G 4 HOH A 24 824 21 HOH HOH . G 4 HOH A 25 825 44 HOH HOH . G 4 HOH A 26 826 28 HOH HOH . G 4 HOH A 27 827 39 HOH HOH . G 4 HOH A 28 828 46 HOH HOH . H 4 HOH C 1 801 19 HOH HOH . H 4 HOH C 2 802 14 HOH HOH . H 4 HOH C 3 803 43 HOH HOH . H 4 HOH C 4 804 31 HOH HOH . H 4 HOH C 5 805 27 HOH HOH . H 4 HOH C 6 806 36 HOH HOH . H 4 HOH C 7 807 15 HOH HOH . H 4 HOH C 8 808 6 HOH HOH . H 4 HOH C 9 809 41 HOH HOH . H 4 HOH C 10 810 34 HOH HOH . H 4 HOH C 11 811 45 HOH HOH . H 4 HOH C 12 812 38 HOH HOH . H 4 HOH C 13 813 29 HOH HOH . H 4 HOH C 14 814 10 HOH HOH . H 4 HOH C 15 815 47 HOH HOH . H 4 HOH C 16 816 17 HOH HOH . H 4 HOH C 17 817 20 HOH HOH . H 4 HOH C 18 818 11 HOH HOH . H 4 HOH C 19 819 8 HOH HOH . H 4 HOH C 20 820 49 HOH HOH . H 4 HOH C 21 821 42 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 3 245.176 -1.575 26.405 1 56.23 ? C1 NAG 401 B 1 HETATM 2 C C2 NAG . . . E 3 245.544 -1.196 28.008 1 52.88 ? C2 NAG 401 B 1 HETATM 3 C C3 NAG . . . E 3 244.768 0.152 28.447 1 47.09 ? C3 NAG 401 B 1 HETATM 4 C C4 NAG . . . E 3 244.887 1.167 27.366 1 47.64 ? C4 NAG 401 B 1 HETATM 5 C C5 NAG . . . E 3 243.837 0.657 26.378 1 47.34 ? C5 NAG 401 B 1 HETATM 6 C C6 NAG . . . E 3 243.565 1.843 25.327 1 45.51 ? C6 NAG 401 B 1 HETATM 7 C C7 NAG . . . E 3 243.866 -2.771 29.021 1 48.94 ? C7 NAG 401 B 1 HETATM 8 C C8 NAG . . . E 3 243.421 -3.899 30.055 1 42.28 ? C8 NAG 401 B 1 HETATM 9 N N2 NAG . . . E 3 245.15 -2.238 28.918 1 50.75 ? N2 NAG 401 B 1 HETATM 10 O O3 NAG . . . E 3 245.636 0.63 29.477 1 45.08 ? O3 NAG 401 B 1 HETATM 11 O O4 NAG . . . E 3 244.412 2.396 27.925 1 49.93 ? O4 NAG 401 B 1 HETATM 12 O O5 NAG . . . E 3 244.559 -0.428 25.675 1 55.03 ? O5 NAG 401 B 1 HETATM 13 O O6 NAG . . . E 3 244.772 2.135 24.528 1 41.14 ? O6 NAG 401 B 1 HETATM 14 O O7 NAG . . . E 3 243.012 -2.331 28.274 1 48.1 ? O7 NAG 401 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #