data_5WVG # _model_server_result.job_id -zQKxpVVp2DuWxM-x1RWUQ _model_server_result.datetime_utc '2024-11-26 17:33:47' _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 5wvg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1006}' # _entry.id 5WVG # _exptl.entry_id 5WVG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 90 _cell.entry_id 5WVG _cell.length_a 71.362 _cell.length_b 71.362 _cell.length_c 175.023 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WVG _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 2 5 4 NAG NAG C1 O1 . O4 HO4 . 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 2 n B NAG 1 B 1 NAG L 1502 NAG 2 n B NAG 2 B 2 NAG L 1501 NAG 2 n B NAG 3 B 3 NAG L 1500 NAG 2 n B NAG 4 B 4 NAG L 1499 NAG 2 n B NAG 5 B 5 NAG L 1498 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 6 A CYS 533 1_555 A SG CYS 31 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 251 A ASN 778 1_555 C C1 NAG . A NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 B O4 NAG . B NAG 2 1_555 B C1 NAG . B NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale4 B O4 NAG . B NAG 3 1_555 B C1 NAG . B NAG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale5 B O4 NAG . B NAG 4 1_555 B C1 NAG . B NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 5WVG _atom_sites.fract_transf_matrix[1][1] 0.014013 _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] 0.014013 _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] 0.005714 _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 NAG A 1 1006 1600 NAG NAG . D 4 HOH A 1 1101 28 HOH HOH . D 4 HOH A 2 1102 27 HOH HOH . D 4 HOH A 3 1103 46 HOH HOH . D 4 HOH A 4 1104 43 HOH HOH . D 4 HOH A 5 1105 14 HOH HOH . D 4 HOH A 6 1106 15 HOH HOH . D 4 HOH A 7 1107 13 HOH HOH . D 4 HOH A 8 1108 41 HOH HOH . D 4 HOH A 9 1109 1 HOH HOH . D 4 HOH A 10 1110 3 HOH HOH . D 4 HOH A 11 1111 35 HOH HOH . D 4 HOH A 12 1112 32 HOH HOH . D 4 HOH A 13 1113 30 HOH HOH . D 4 HOH A 14 1114 2 HOH HOH . D 4 HOH A 15 1115 12 HOH HOH . D 4 HOH A 16 1116 33 HOH HOH . D 4 HOH A 17 1117 8 HOH HOH . D 4 HOH A 18 1118 48 HOH HOH . D 4 HOH A 19 1119 45 HOH HOH . D 4 HOH A 20 1120 22 HOH HOH . D 4 HOH A 21 1121 40 HOH HOH . D 4 HOH A 22 1122 47 HOH HOH . D 4 HOH A 23 1123 9 HOH HOH . D 4 HOH A 24 1124 44 HOH HOH . D 4 HOH A 25 1125 38 HOH HOH . D 4 HOH A 26 1126 19 HOH HOH . D 4 HOH A 27 1127 49 HOH HOH . D 4 HOH A 28 1128 16 HOH HOH . D 4 HOH A 29 1129 29 HOH HOH . D 4 HOH A 30 1130 21 HOH HOH . D 4 HOH A 31 1131 36 HOH HOH . D 4 HOH A 32 1132 20 HOH HOH . D 4 HOH A 33 1133 24 HOH HOH . D 4 HOH A 34 1134 23 HOH HOH . D 4 HOH A 35 1135 37 HOH HOH . D 4 HOH A 36 1136 17 HOH HOH . D 4 HOH A 37 1137 50 HOH HOH . D 4 HOH A 38 1138 18 HOH HOH . D 4 HOH A 39 1139 11 HOH HOH . D 4 HOH A 40 1140 39 HOH HOH . D 4 HOH A 41 1141 31 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 . . . C 3 -39.722 2.656 4.336 1 67.61 ? C1 NAG 1006 A 1 HETATM 2 C C2 NAG . . . C 3 -40.646 1.451 4.562 1 70.66 ? C2 NAG 1006 A 1 HETATM 3 C C3 NAG . . . C 3 -41.988 1.625 3.853 1 60.2 ? C3 NAG 1006 A 1 HETATM 4 C C4 NAG . . . C 3 -42.603 2.988 4.142 1 72.79 ? C4 NAG 1006 A 1 HETATM 5 C C5 NAG . . . C 3 -41.599 4.06 3.75 1 71.5 ? C5 NAG 1006 A 1 HETATM 6 C C6 NAG . . . C 3 -42.087 5.466 4.017 1 71.46 ? C6 NAG 1006 A 1 HETATM 7 C C7 NAG . . . C 3 -39.612 -0.76 4.934 1 71.6 ? C7 NAG 1006 A 1 HETATM 8 C C8 NAG . . . C 3 -39.887 -0.54 6.392 1 70.29 ? C8 NAG 1006 A 1 HETATM 9 N N2 NAG . . . C 3 -39.99 0.227 4.115 1 73.06 ? N2 NAG 1006 A 1 HETATM 10 O O3 NAG . . . C 3 -42.897 0.601 4.242 1 74.96 ? O3 NAG 1006 A 1 HETATM 11 O O4 NAG . . . C 3 -43.809 3.164 3.405 1 77.37 ? O4 NAG 1006 A 1 HETATM 12 O O5 NAG . . . C 3 -40.434 3.871 4.553 1 68.25 ? O5 NAG 1006 A 1 HETATM 13 O O6 NAG . . . C 3 -41.156 6.424 3.525 1 69.08 ? O6 NAG 1006 A 1 HETATM 14 O O7 NAG . . . C 3 -39.069 -1.785 4.511 1 71.65 ? O7 NAG 1006 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #