data_5C0R # _model_server_result.job_id qLqjkLvZHPDLR7qJ6KN9EQ _model_server_result.datetime_utc '2025-03-06 01:31:52' _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 5c0r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5C0R # _exptl.entry_id 5C0R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _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 120 _cell.entry_id 5C0R _cell.length_a 112.038 _cell.length_b 112.038 _cell.length_c 205.125 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C0R _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 1,2,3 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 B 1 NAG A 736 NAG 4 n D NAG 2 B 2 NAG A 737 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 4 A CYS 4 1_555 A SG CYS 222 A CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 229 A CYS 226 1_555 A SG CYS 233 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 134 L CYS 134 1_555 B SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 C SG CYS 22 H CYS 22 1_555 C SG CYS 98 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 149 H CYS 140 1_555 C SG CYS 204 H CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 122 A ASN 119 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 239 A ASN 236 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 5C0R _atom_sites.fract_transf_matrix[1][1] 0.008926 _atom_sites.fract_transf_matrix[1][2] 0.005153 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010306 _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] 0.004875 _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 5 NAG A 1 401 619 NAG NAG . F 6 HOH A 1 501 3 HOH HOH . F 6 HOH A 2 502 1 HOH HOH . F 6 HOH A 3 503 8 HOH HOH . F 6 HOH A 4 504 4 HOH HOH . F 6 HOH A 5 505 2 HOH HOH . F 6 HOH A 6 506 5 HOH HOH . G 6 HOH L 1 301 6 HOH HOH . H 6 HOH H 1 301 7 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 5 16.333 6.255 -64.095 1 143.73 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . E 5 17.741 6.46 -63.543 1 145.34 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . E 5 18.783 6.118 -64.605 1 144.19 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . E 5 18.538 4.722 -65.16 1 154.76 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . E 5 17.101 4.609 -65.659 1 143.94 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . E 5 16.747 3.221 -66.141 1 142.62 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . E 5 18.497 8.136 -61.911 1 150.53 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . E 5 18.593 9.599 -61.595 1 141.55 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . E 5 17.919 7.826 -63.076 1 157.06 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . E 5 20.083 6.19 -64.029 1 150.82 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . E 5 19.436 4.458 -66.232 1 150.93 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . E 5 16.198 4.921 -64.588 1 152.88 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . E 5 16.159 2.445 -65.106 1 155.15 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . E 5 18.924 7.277 -61.146 1 149.41 ? O7 NAG 401 A 1 HETATM 15 H H1 NAG . . . E 5 16.178 6.885 -64.825 1 51.28 ? H1 NAG 401 A 1 HETATM 16 H H2 NAG . . . E 5 17.867 5.853 -62.789 1 57.59 ? H2 NAG 401 A 1 HETATM 17 H H3 NAG . . . E 5 18.721 6.766 -65.332 1 58.93 ? H3 NAG 401 A 1 HETATM 18 H H4 NAG . . . E 5 18.683 4.066 -64.452 1 63.62 ? H4 NAG 401 A 1 HETATM 19 H H5 NAG . . . E 5 16.965 5.245 -66.387 1 51.5 ? H5 NAG 401 A 1 HETATM 20 H H61 NAG . . . E 5 17.558 2.776 -66.452 1 63.21 ? H61 NAG 401 A 1 HETATM 21 H H62 NAG . . . E 5 16.117 3.293 -66.883 1 60.36 ? H62 NAG 401 A 1 HETATM 22 H H81 NAG . . . E 5 17.7 9.993 -61.605 1 53.01 ? H81 NAG 401 A 1 HETATM 23 H H82 NAG . . . E 5 19.151 10.04 -62.264 1 61.51 ? H82 NAG 401 A 1 HETATM 24 H H83 NAG . . . E 5 18.99 9.715 -60.711 1 53.12 ? H83 NAG 401 A 1 HETATM 25 H HN2 NAG . . . E 5 17.62 8.506 -63.605 1 57.13 ? HN2 NAG 401 A 1 HETATM 26 H HO3 NAG . . . E 5 20.528 6.871 -64.386 1 62.93 ? HO3 NAG 401 A 1 HETATM 27 H HO6 NAG . . . E 5 16.72 1.8 -64.865 1 57.36 ? HO6 NAG 401 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 143 _model_server_stats.query_time_ms 380 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #