data_3KJ4 # _model_server_result.job_id 8Fk26YnCGVvRFpMw1pl-Fw _model_server_result.datetime_utc '2024-11-24 21:49:03' _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 3kj4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":314}' # _entry.id 3KJ4 # _exptl.entry_id 3KJ4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-alpha-D-glucopyranose _entity.pdbx_number_of_molecules 4 _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 3KJ4 _cell.length_a 188.664 _cell.length_b 125.488 _cell.length_c 90.575 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KJ4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,J,K 1 1 D,E,F,L,M,N,O 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 I N N ? 6 J N N ? 6 M N N ? 6 N 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 23 L CYS 23 1_555 A SG CYS 94 L CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? disulf ? disulf2 A SG CYS 139 L CYS 139 1_555 A SG CYS 199 L CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 95 H CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf4 B SG CYS 147 H CYS 147 1_555 B SG CYS 202 H CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? disulf ? disulf5 C SG CYS 1 A CYS 27 1_555 C SG CYS 7 A CYS 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf6 C SG CYS 5 A CYS 31 1_555 C SG CYS 17 A CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf7 C SG CYS 238 A CYS 264 1_555 C SG CYS 261 A CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 D SG CYS 23 B CYS 23 1_555 D SG CYS 94 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? disulf ? disulf9 D SG CYS 139 B CYS 139 1_555 D SG CYS 199 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf10 E SG CYS 22 C CYS 22 1_555 E SG CYS 95 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? disulf ? disulf11 E SG CYS 147 C CYS 147 1_555 E SG CYS 202 C CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? disulf ? disulf12 F SG CYS 1 D CYS 27 1_555 F SG CYS 7 D CYS 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf13 F SG CYS 5 D CYS 31 1_555 F SG CYS 17 D CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf14 F SG CYS 238 D CYS 264 1_555 F SG CYS 261 D CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NDG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-glucopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-glucosamine;2-acetamido-2-deoxy-alpha-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE # 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 NDG sing 289 n n C1 O5 NDG sing 290 n n C1 O1 NDG sing 291 n n C1 H1 NDG sing 292 n n C2 C3 NDG sing 293 n n C2 N2 NDG sing 294 n n C2 H2 NDG sing 295 n n C3 C4 NDG sing 296 n n C3 O3 NDG sing 297 n n C3 H3 NDG sing 298 n n C4 C5 NDG sing 299 n n C4 O4 NDG sing 300 n n C4 H4 NDG sing 301 n n C5 C6 NDG sing 302 n n C5 O5 NDG sing 303 n n C5 H5 NDG sing 304 n n C6 O6 NDG sing 305 n n C6 H61 NDG sing 306 n n C6 H62 NDG sing 307 n n C7 C8 NDG sing 308 n n C7 O7 NDG doub 309 n n C7 N2 NDG sing 310 n n C8 H81 NDG sing 311 n n C8 H82 NDG sing 312 n n C8 H83 NDG sing 313 n n O3 HO3 NDG sing 314 n n O4 HO4 NDG sing 315 n n O6 HO6 NDG sing 316 n n N2 HN2 NDG sing 317 n n O1 HO1 NDG sing 318 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 NDG DGlcpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NDG N-acetyl-a-D-glucopyranosamine 'COMMON NAME' GMML 1 NDG a-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NDG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3KJ4 _atom_sites.fract_transf_matrix[1][1] 0.0053 _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] 0.007969 _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] 0.011041 _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 G 4 MAN H 1 303 303 MAN MAN . H 5 ZN H 1 221 1 ZN ZN . I 6 NDG A 1 313 301 NDG NDG . J 6 NDG A 1 314 302 NDG NDG . K 7 NAG A 1 315 305 NAG NAG . L 5 ZN C 1 221 3 ZN ZN . M 6 NDG D 1 401 401 NDG NDG . N 6 NDG D 1 402 402 NDG NDG . O 7 NAG D 1 405 405 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 NDG . . . J 6 99.691 50.472 24.275 1 82.44 ? C1 NDG 314 A 1 HETATM 2 C C2 NDG . . . J 6 100.632 51.279 25.216 1 84.38 ? C2 NDG 314 A 1 HETATM 3 C C3 NDG . . . J 6 100.497 52.798 24.963 1 84.8 ? C3 NDG 314 A 1 HETATM 4 C C4 NDG . . . J 6 100.611 53.202 23.475 1 82.99 ? C4 NDG 314 A 1 HETATM 5 C C5 NDG . . . J 6 99.895 52.231 22.533 1 82.28 ? C5 NDG 314 A 1 HETATM 6 C C6 NDG . . . J 6 100.985 51.716 21.61 1 79.48 ? C6 NDG 314 A 1 HETATM 7 C C7 NDG . . . J 6 101.362 50.191 27.487 1 81.91 ? C7 NDG 314 A 1 HETATM 8 C C8 NDG . . . J 6 100.771 48.824 27.738 1 80.19 ? C8 NDG 314 A 1 HETATM 9 O O5 NDG . . . J 6 99.072 51.199 23.175 1 80.53 ? O5 NDG 314 A 1 HETATM 10 O O3 NDG . . . J 6 101.528 53.455 25.715 1 84.79 ? O3 NDG 314 A 1 HETATM 11 O O4 NDG . . . J 6 100.069 54.523 23.208 1 82.63 ? O4 NDG 314 A 1 HETATM 12 O O6 NDG . . . J 6 100.392 50.76 20.739 1 80.8 ? O6 NDG 314 A 1 HETATM 13 O O7 NDG . . . J 6 102.433 50.528 28.013 1 74.31 ? O7 NDG 314 A 1 HETATM 14 N N2 NDG . . . J 6 100.499 50.952 26.661 1 83.22 ? N2 NDG 314 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #