data_8EDF # _model_server_result.job_id Ym2nWDZZWkEfbdKE5gPQFw _model_server_result.datetime_utc '2024-11-16 08:18:01' _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 8edf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 8EDF # _exptl.entry_id 8EDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-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 90 _cell.angle_gamma 90 _cell.entry_id 8EDF _cell.length_a 162.841 _cell.length_b 162.841 _cell.length_c 125.171 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 4 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 22 L CYS 23 1_555 A SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 138 L CYS 134 1_555 A SG CYS 197 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 95 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 B SG CYS 108 H CYS 105 1_555 B SG CYS 131 H CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 122 H CYS 119 1_555 B SG CYS 129 H CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 B SG CYS 136 H CYS 133 1_555 B SG CYS 141 H CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf7 B SG CYS 196 H CYS 194 1_555 B SG CYS 252 H CYS 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 C SG CYS 3 A CYS 336 1_555 C SG CYS 28 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 C SG CYS 46 A CYS 379 1_555 C SG CYS 99 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 58 A CYS 391 1_555 C SG CYS 192 A CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 C SG CYS 147 A CYS 480 1_555 C SG CYS 155 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 C ND2 ASN 10 A ASN 343 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _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 216 n n C1 O1 NAG sing 217 n n C1 O5 NAG sing 218 n n C1 H1 NAG sing 219 n n C2 C3 NAG sing 220 n n C2 N2 NAG sing 221 n n C2 H2 NAG sing 222 n n C3 C4 NAG sing 223 n n C3 O3 NAG sing 224 n n C3 H3 NAG sing 225 n n C4 C5 NAG sing 226 n n C4 O4 NAG sing 227 n n C4 H4 NAG sing 228 n n C5 C6 NAG sing 229 n n C5 O5 NAG sing 230 n n C5 H5 NAG sing 231 n n C6 O6 NAG sing 232 n n C6 H61 NAG sing 233 n n C6 H62 NAG sing 234 n n C7 C8 NAG sing 235 n n C7 N2 NAG sing 236 n n C7 O7 NAG doub 237 n n C8 H81 NAG sing 238 n n C8 H82 NAG sing 239 n n C8 H83 NAG sing 240 n n N2 HN2 NAG sing 241 n n O1 HO1 NAG sing 242 n n O3 HO3 NAG sing 243 n n O4 HO4 NAG sing 244 n n O6 HO6 NAG sing 245 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 8EDF _atom_sites.fract_transf_matrix[1][1] 0.006141 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006141 _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] 0.007989 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id D _pdbx_nonpoly_scheme.entity_id 4 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 601 _pdbx_nonpoly_scheme.auth_seq_num 534 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . D 4 81.781 -3.125 -33.602 1 68.69 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . D 4 82.757 -3.862 -34.532 1 55.88 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . D 4 83.887 -2.934 -34.97 1 63.19 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . D 4 83.352 -1.595 -35.466 1 41.49 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . D 4 82.311 -1.011 -34.51 1 45.66 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . D 4 81.62 0.21 -35.067 1 54.03 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . D 4 82.639 -6.204 -33.781 1 53.78 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . D 4 83.381 -7.319 -33.106 1 50.89 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . D 4 83.306 -5.052 -33.902 1 61.7 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . D 4 84.616 -3.567 -36.017 1 53.07 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . D 4 84.435 -0.689 -35.637 1 49.11 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . D 4 81.287 -1.981 -34.248 1 44.62 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . D 4 80.335 -0.118 -35.579 1 53.42 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . D 4 81.492 -6.34 -34.194 1 57.91 ? O7 NAG 601 A 1 HETATM 15 H H2 NAG . . . D 4 82.255 -4.131 -35.325 1 68.71 ? H2 NAG 601 A 1 HETATM 16 H H3 NAG . . . D 4 84.468 -2.768 -34.204 1 77.48 ? H3 NAG 601 A 1 HETATM 17 H H4 NAG . . . D 4 82.905 -1.731 -36.323 1 51.44 ? H4 NAG 601 A 1 HETATM 18 H H5 NAG . . . D 4 82.748 -0.777 -33.669 1 56.45 ? H5 NAG 601 A 1 HETATM 19 H H61 NAG . . . D 4 82.163 0.586 -35.785 1 66.49 ? H61 NAG 601 A 1 HETATM 20 H H62 NAG . . . D 4 81.522 0.874 -34.359 1 66.49 ? H62 NAG 601 A 1 HETATM 21 H H81 NAG . . . D 4 82.775 -7.797 -32.509 1 62.72 ? H81 NAG 601 A 1 HETATM 22 H H82 NAG . . . D 4 84.122 -6.95 -32.589 1 62.72 ? H82 NAG 601 A 1 HETATM 23 H H83 NAG . . . D 4 83.727 -7.934 -33.779 1 62.72 ? H83 NAG 601 A 1 HETATM 24 H HN2 NAG . . . D 4 84.155 -5.01 -33.571 1 75.69 ? HN2 NAG 601 A 1 HETATM 25 H HO3 NAG . . . D 4 85.076 -2.964 -36.479 1 65.33 ? HO3 NAG 601 A 1 HETATM 26 H HO4 NAG . . . D 4 84.281 0.046 -35.165 1 60.59 ? HO4 NAG 601 A 1 HETATM 27 H HO6 NAG . . . D 4 80.191 -0.99 -35.488 1 65.75 ? HO6 NAG 601 A 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 380 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #