data_3K24 # _model_server_result.job_id v-ZS8wi49vKnobKg0AzUGA _model_server_result.datetime_utc '2024-11-15 04:59:45' _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 3k24 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":221}' # _entry.id 3K24 # _exptl.entry_id 3K24 _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 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 3K24 _cell.length_a 62.697 _cell.length_b 62.697 _cell.length_c 205.868 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K24 _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,F,G 1 1 B,C,E,H 2 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 F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NDG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN NDG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 BMA MAN C1 O1 . O6 HO6 . sing 4 ? 3 5 4 NDG BMA C1 O1 . O6 HO6 . sing 5 ? 3 6 3 MAN MAN C1 O1 . O2 HO2 . 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 E NAG 1 E 1 NAG G 10 NAG 3 n E NDG 2 E 2 NDG G 11 NDG 3 n E MAN 3 E 3 MAN G 14 MAN 3 n E BMA 4 E 4 BMA G 13 BMA 3 n E NDG 5 E 5 NDG G 12 NDG 3 n E MAN 6 E 6 MAN G 15 MAN # 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 A CYS 22 1_555 A SG CYS 65 A CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 56 A CYS 56 1_555 A SG CYS 98 A CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 156 A CYS 156 1_555 A SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 22 B CYS 22 1_555 B SG CYS 65 B CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 B SG CYS 56 B CYS 56 1_555 B SG CYS 98 B CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 156 B CYS 156 1_555 B SG CYS 209 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 108 A ASN 108 1_555 F C1 NAG . A NAG 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B ND2 ASN 108 B ASN 108 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 E O4 NAG . E NAG 1 1_555 E C1 NDG . E NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 E O4 NDG . E NDG 2 1_555 E C1 MAN . E MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 E O6 MAN . E MAN 3 1_555 E C1 BMA . E BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 E O2 MAN . E MAN 3 1_555 E C1 MAN . E MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 E O6 BMA . E BMA 4 1_555 E C1 NDG . E NDG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 3K24 _atom_sites.fract_transf_matrix[1][1] 0.01595 _atom_sites.fract_transf_matrix[1][2] 0.009209 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018417 _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] 0.004857 _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 1 221 1 NAG NAG . G 5 HOH A 1 222 1 HOH HOH . G 5 HOH A 2 223 8 HOH HOH . G 5 HOH A 3 224 41 HOH HOH . G 5 HOH A 4 225 44 HOH HOH . G 5 HOH A 5 226 47 HOH HOH . G 5 HOH A 6 227 59 HOH HOH . G 5 HOH A 7 228 65 HOH HOH . G 5 HOH A 8 229 68 HOH HOH . G 5 HOH A 9 230 71 HOH HOH . G 5 HOH A 10 231 102 HOH HOH . G 5 HOH A 11 232 132 HOH HOH . G 5 HOH A 12 233 149 HOH HOH . H 5 HOH B 1 227 2 HOH HOH . H 5 HOH B 2 228 4 HOH HOH . H 5 HOH B 3 229 7 HOH HOH . H 5 HOH B 4 230 10 HOH HOH . H 5 HOH B 5 231 18 HOH HOH . H 5 HOH B 6 232 21 HOH HOH . H 5 HOH B 7 233 24 HOH HOH . H 5 HOH B 8 234 27 HOH HOH . H 5 HOH B 9 235 30 HOH HOH . H 5 HOH B 10 236 33 HOH HOH . H 5 HOH B 11 237 35 HOH HOH . H 5 HOH B 12 238 40 HOH HOH . H 5 HOH B 13 239 70 HOH HOH . H 5 HOH B 14 240 75 HOH HOH . H 5 HOH B 15 241 76 HOH HOH . H 5 HOH B 16 242 78 HOH HOH . H 5 HOH B 17 243 121 HOH HOH . H 5 HOH B 18 244 129 HOH HOH . H 5 HOH B 19 245 134 HOH HOH . H 5 HOH B 20 246 154 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 . . . F 4 9.913 -36.549 -28.458 1 75.29 ? C1 NAG 221 A 1 HETATM 2 C C2 NAG . . . F 4 9.979 -35.772 -29.773 1 79.26 ? C2 NAG 221 A 1 HETATM 3 C C3 NAG . . . F 4 9.656 -36.689 -30.948 1 80.85 ? C3 NAG 221 A 1 HETATM 4 C C4 NAG . . . F 4 10.533 -37.933 -30.901 1 84.84 ? C4 NAG 221 A 1 HETATM 5 C C5 NAG . . . F 4 10.458 -38.588 -29.523 1 85.52 ? C5 NAG 221 A 1 HETATM 6 C C6 NAG . . . F 4 11.394 -39.791 -29.435 1 88.1 ? C6 NAG 221 A 1 HETATM 7 C C7 NAG . . . F 4 9.459 -33.403 -29.474 1 83.99 ? C7 NAG 221 A 1 HETATM 8 C C8 NAG . . . F 4 8.415 -32.33 -29.57 1 82.84 ? C8 NAG 221 A 1 HETATM 9 N N2 NAG . . . F 4 9.063 -34.644 -29.759 1 82.58 ? N2 NAG 221 A 1 HETATM 10 O O3 NAG . . . F 4 9.852 -36.016 -32.172 1 77.29 ? O3 NAG 221 A 1 HETATM 11 O O4 NAG . . . F 4 10.119 -38.845 -31.896 1 85.09 ? O4 NAG 221 A 1 HETATM 12 O O5 NAG . . . F 4 10.797 -37.65 -28.52 1 80.21 ? O5 NAG 221 A 1 HETATM 13 O O6 NAG . . . F 4 12.606 -39.415 -28.815 1 87.34 ? O6 NAG 221 A 1 HETATM 14 O O7 NAG . . . F 4 10.599 -33.124 -29.105 1 84.96 ? O7 NAG 221 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 14 #