data_5J12 # _model_server_result.job_id UCkyrMOz9O53cKlEZR5A3g _model_server_result.datetime_utc '2024-12-23 14:15:20' _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 5j12 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":304}' # _entry.id 5J12 # _exptl.entry_id 5J12 _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 5J12 _cell.length_a 125.442 _cell.length_b 125.442 _cell.length_c 194.573 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5J12 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 H N N ? 4 I N 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 34 A CYS 34 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 69 A CYS 69 1_555 A SG CYS 75 A CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 132 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 26 B CYS 42 1_555 B SG CYS 41 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 58 B CYS 74 1_555 B SG CYS 66 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 92 B CYS 108 1_555 B SG CYS 102 B CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 C SG CYS 71 C CYS 71 1_555 C SG CYS 84 C CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf8 C SG CYS 138 C CYS 138 1_555 C SG CYS 168 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 C SG CYS 180 C CYS 180 1_555 C SG CYS 218 C CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A ND2 ASN 119 A ASN 119 1_555 D C1 NAG . A NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 C ND2 ASN 47 C ASN 47 1_555 I C1 NAG . C NAG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 C ND2 ASN 55 C ASN 55 1_555 H C1 NAG . C NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? # _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 5J12 _atom_sites.fract_transf_matrix[1][1] 0.007972 _atom_sites.fract_transf_matrix[1][2] 0.004603 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009205 _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] 0.005139 _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 D 4 NAG A 1 500 500 NAG NAG . E 5 SO4 C 1 301 250 SO4 SO4 . F 5 SO4 C 1 302 251 SO4 SO4 . G 5 SO4 C 1 303 252 SO4 SO4 . H 4 NAG C 1 304 500 NAG NAG . I 4 NAG C 1 305 501 NAG NAG . J 6 HOH B 1 301 2 HOH HOH . J 6 HOH B 2 302 1 HOH HOH . J 6 HOH B 3 303 5 HOH HOH . K 6 HOH C 1 401 4 HOH HOH . K 6 HOH C 2 402 3 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 . . . H 4 -18.085 -7.827 10.257 1 205.19 ? C1 NAG 304 C 1 HETATM 2 C C2 NAG . . . H 4 -17.849 -6.535 11.036 1 212.4 ? C2 NAG 304 C 1 HETATM 3 C C3 NAG . . . H 4 -19.114 -6.22 11.834 1 216.5 ? C3 NAG 304 C 1 HETATM 4 C C4 NAG . . . H 4 -20.345 -6.172 10.925 1 215.54 ? C4 NAG 304 C 1 HETATM 5 C C5 NAG . . . H 4 -20.422 -7.372 9.979 1 205.53 ? C5 NAG 304 C 1 HETATM 6 C C6 NAG . . . H 4 -21.442 -7.181 8.874 1 203.45 ? C6 NAG 304 C 1 HETATM 7 C C7 NAG . . . H 4 -15.555 -6.107 11.829 1 208.04 ? C7 NAG 304 C 1 HETATM 8 C C8 NAG . . . H 4 -14.361 -6.801 12.416 1 206.8 ? C8 NAG 304 C 1 HETATM 9 N N2 NAG . . . H 4 -16.716 -6.768 11.92 1 209.38 ? N2 NAG 304 C 1 HETATM 10 O O3 NAG . . . H 4 -18.94 -4.951 12.458 1 221.13 ? O3 NAG 304 C 1 HETATM 11 O O4 NAG . . . H 4 -21.522 -6.176 11.725 1 219.81 ? O4 NAG 304 C 1 HETATM 12 O O5 NAG . . . H 4 -19.152 -7.587 9.336 1 204.71 ? O5 NAG 304 C 1 HETATM 13 O O6 NAG . . . H 4 -21.357 -8.178 7.855 1 197.1 ? O6 NAG 304 C 1 HETATM 14 O O7 NAG . . . H 4 -15.465 -5.017 11.27 1 209.51 ? O7 NAG 304 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #