data_7ODU # _model_server_result.job_id '_JN-Y9h-NzVdGteeYnhU2g' _model_server_result.datetime_utc '2024-10-12 13:19:05' _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 7odu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 7ODU # _exptl.entry_id 7ODU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 7ODU _cell.length_a 111.593 _cell.length_b 111.593 _cell.length_c 110.107 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ODU _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,I 1 1 C,E,I 2 1 C,E,I 2 2 A,B,D,F,G,H 3 1 # 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' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 73.404667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N N ? 4 I N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n D NAG 1 D 1 NAG A 301 NAG 3 n D NAG 2 D 2 NAG A 302 NAG 3 n E NAG 1 E 1 NAG C 302 NAG 3 n E NAG 2 E 2 NAG C 303 NAG # 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 7 A CYS 80 1_555 A SG CYS 18 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf2 A SG CYS 35 A CYS 108 1_555 A SG CYS 117 A CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf3 B SG CYS 7 B CYS 80 1_555 B SG CYS 18 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 B SG CYS 35 B CYS 108 1_555 B SG CYS 117 B CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf5 C SG CYS 20 C CYS 94 1_555 C SG CYS 31 C CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf6 C SG CYS 48 C CYS 122 1_555 C SG CYS 136 C CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? disulf ? disulf7 C SG CYS 115 C CYS 189 1_555 C SG CYS 128 C CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? covale ? covale1 A ND2 ASN 27 A ASN 100 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale2 A ND2 ASN 85 A ASN 158 1_555 F C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 B ND2 ASN 27 B ASN 100 1_555 H C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale4 C ND2 ASN 69 C ASN 143 1_555 I C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale5 C ND2 ASN 95 C ASN 169 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? metalc ? metalc1 A OE2 GLU 39 A GLU 112 1_555 G ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc2 A NE2 HIS 125 A HIS 198 1_555 G ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc3 A ND1 HIS 127 A HIS 200 1_555 G ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc4 G ZN ZN . A ZN 302 3_455 B OD2 ASP 62 B ASP 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? # _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 7ODU _atom_sites.fract_transf_matrix[1][1] 0.008961 _atom_sites.fract_transf_matrix[1][2] 0.005174 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010347 _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] 0.009082 _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 F 4 NAG A 1 301 303 NAG NAG . G 5 ZN A 1 302 401 ZN ZN . H 4 NAG B 1 301 301 NAG NAG . I 4 NAG C 1 301 301 NAG NAG . # 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 . . . F 4 -43.37 57.629 24.566 1 215.91 ? C1 NAG 301 A 1 HETATM 2 C C2 NAG . . . F 4 -44.664 57.815 23.755 1 217.24 ? C2 NAG 301 A 1 HETATM 3 C C3 NAG . . . F 4 -45.578 58.76 24.553 1 219.56 ? C3 NAG 301 A 1 HETATM 4 C C4 NAG . . . F 4 -45.832 58.204 25.971 1 219.04 ? C4 NAG 301 A 1 HETATM 5 C C5 NAG . . . F 4 -44.569 57.732 26.714 1 213.41 ? C5 NAG 301 A 1 HETATM 6 C C6 NAG . . . F 4 -44.913 56.796 27.886 1 189.41 ? C6 NAG 301 A 1 HETATM 7 C C7 NAG . . . F 4 -45.133 58.135 21.31 1 182.25 ? C7 NAG 301 A 1 HETATM 8 C C8 NAG . . . F 4 -44.486 58.368 19.961 1 160.16 ? C8 NAG 301 A 1 HETATM 9 N N2 NAG . . . F 4 -44.312 58.191 22.368 1 200.65 ? N2 NAG 301 A 1 HETATM 10 O O3 NAG . . . F 4 -46.836 58.947 23.883 1 215.7 ? O3 NAG 301 A 1 HETATM 11 O O4 NAG . . . F 4 -46.467 59.203 26.783 1 223.51 ? O4 NAG 301 A 1 HETATM 12 O O5 NAG . . . F 4 -43.647 57.038 25.849 1 234.05 ? O5 NAG 301 A 1 HETATM 13 O O6 NAG . . . F 4 -45.149 57.531 29.093 1 164.05 ? O6 NAG 301 A 1 HETATM 14 O O7 NAG . . . F 4 -46.326 57.885 21.431 1 181.74 ? O7 NAG 301 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #