data_3VFK # _model_server_result.job_id JObVHvibNPzdqwKQwgrznA _model_server_result.datetime_utc '2024-12-07 02:35:36' _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 3vfk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":8}' # _entry.id 3VFK # _exptl.entry_id 3VFK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 179.171 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-amino-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.18 _cell.angle_gamma 90 _cell.entry_id 3VFK _cell.length_a 88.01 _cell.length_b 25.18 _cell.length_c 38.71 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VFK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 GLY 75 A GLY 75 1_555 A N CCS 76 A CCS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale2 A C CCS 76 A CCS 76 1_555 A N LYS 77 A LYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C LYS 77 A LYS 77 1_555 A N DAL 78 A DAL 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C DAL 78 A DAL 78 1_555 A N DAL 79 A DAL 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 B C GHP 1 G GHP 1 1_555 B N 3MY 2 G 3MY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 B C5 GHP 1 G GHP 1 1_555 B OD1 3FG 3 G 3FG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale7 B C 3MY 2 G 3MY 2 1_555 B N 3FG 3 G 3FG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 B OBD 3MY 2 G 3MY 2 1_555 B C3 GHP 4 G GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale9 B C 3FG 3 G 3FG 3 1_555 B N GHP 4 G GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 B C GHP 4 G GHP 4 1_555 B N GHP 5 G GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale11 B C5 GHP 4 G GHP 4 1_555 B OH OMX 6 G OMX 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale12 B O4 GHP 4 G GHP 4 1_555 C C1 GCS . G GCS 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale13 B C GHP 5 G GHP 5 1_555 B N OMX 6 G OMX 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 B C3 GHP 5 G GHP 5 1_555 B CG1 3FG 7 G 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale15 B C OMX 6 G OMX 6 1_555 B N 3FG 7 G 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale16 B OC OMX 6 G OMX 6 1_555 E C1 NAG . G NAG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale17 B OD1 3FG 7 G 3FG 7 1_555 F C1 MAN . G MAN 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale18 C N2 GCS . G GCS 8 1_555 D C T55 . G T55 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? # _chem_comp.formula 'C6 H13 N O5' _chem_comp.formula_weight 179.171 _chem_comp.id GCS _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-glucosamine;2-amino-2-deoxy-beta-D-glucose;2-amino-2-deoxy-D-glucose;2-amino-2-deoxy-glucose;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 GCS sing 147 n n C1 O1 GCS sing 148 n n C1 O5 GCS sing 149 n n C1 H1 GCS sing 150 n n C2 C3 GCS sing 151 n n C2 N2 GCS sing 152 n n C2 H2 GCS sing 153 n n C3 C4 GCS sing 154 n n C3 O3 GCS sing 155 n n C3 H3 GCS sing 156 n n C4 C5 GCS sing 157 n n C4 O4 GCS sing 158 n n C4 H4 GCS sing 159 n n C5 C6 GCS sing 160 n n C5 O5 GCS sing 161 n n C5 H5 GCS sing 162 n n C6 O6 GCS sing 163 n n C6 H61 GCS sing 164 n n C6 H62 GCS sing 165 n n N2 HN21 GCS sing 166 n n N2 HN22 GCS sing 167 n n O1 HO1 GCS sing 168 n n O3 HO3 GCS sing 169 n n O4 HO4 GCS sing 170 n n O6 HO6 GCS sing 171 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 GCS DGlcpNb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 GCS b-D-glucopyranosamine 'COMMON NAME' GMML 1 GCS b-D-GlcpN 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 GCS GlcN 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3VFK _atom_sites.fract_transf_matrix[1][1] 0.011362 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003952 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.039714 _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] 0.027351 _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 GCS G 1 8 8 GCS GCS . D 4 T55 G 1 9 9 T55 T55 . E 5 NAG G 1 10 10 NAG NAG . F 6 MAN G 1 11 11 MAN MAN . G 7 HOH A 1 201 1 HOH HOH . G 7 HOH A 2 202 2 HOH HOH . G 7 HOH A 3 203 3 HOH HOH . G 7 HOH A 4 204 4 HOH HOH . G 7 HOH A 5 205 5 HOH HOH . G 7 HOH A 6 206 6 HOH HOH . G 7 HOH A 7 207 7 HOH HOH . G 7 HOH A 8 208 8 HOH HOH . G 7 HOH A 9 209 9 HOH HOH . G 7 HOH A 10 210 10 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 GCS . . . C 3 -5.446 15.149 6.248 1 71.68 ? C1 GCS 8 G 1 HETATM 2 C C2 GCS . . . C 3 -6.666 15.011 5.336 1 67.41 ? C2 GCS 8 G 1 HETATM 3 C C3 GCS . . . C 3 -7.765 14.281 6.092 1 71.55 ? C3 GCS 8 G 1 HETATM 4 C C4 GCS . . . C 3 -7.242 12.908 6.487 1 81.04 ? C4 GCS 8 G 1 HETATM 5 C C5 GCS . . . C 3 -5.987 13.072 7.347 1 77.89 ? C5 GCS 8 G 1 HETATM 6 C C6 GCS . . . C 3 -5.437 11.691 7.722 1 74.42 ? C6 GCS 8 G 1 HETATM 7 N N2 GCS . . . C 3 -7.167 16.337 4.95 1 70.77 ? N2 GCS 8 G 1 HETATM 8 O O3 GCS . . . C 3 -8.912 14.131 5.256 1 71.22 ? O3 GCS 8 G 1 HETATM 9 O O4 GCS . . . C 3 -8.25 12.188 7.203 1 85.32 ? O4 GCS 8 G 1 HETATM 10 O O5 GCS . . . C 3 -4.986 13.832 6.631 1 79.1 ? O5 GCS 8 G 1 HETATM 11 O O6 GCS . . . C 3 -4.263 11.839 8.524 1 74.23 ? O6 GCS 8 G 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 11 #