data_4AKM # _model_server_result.job_id TvUr-MCXqPosd9IJBG2kUg _model_server_result.datetime_utc '2024-12-22 04:09:57' _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 4akm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1379}' # _entry.id 4AKM # _exptl.entry_id 4AKM _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 2 _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 4AKM _cell.length_a 52.6 _cell.length_b 52.6 _cell.length_c 141.98 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,I 1 1 B,F,G,H,J 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 ? 3 D N N ? 3 G 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 16 A CYS 237 1_555 A SG CYS 53 A CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 118 A CYS 339 1_555 A SG CYS 155 A CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 B SG CYS 16 B CYS 237 1_555 B SG CYS 53 B CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 B SG CYS 118 B CYS 339 1_555 B SG CYS 155 B CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? covale ? covale1 A ND2 ASN 70 A ASN 291 1_555 D C1 NAG . A NAG 1379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 B ND2 ASN 70 B ASN 291 1_555 G C1 NAG . B NAG 1380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _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 4AKM _atom_sites.fract_transf_matrix[1][1] 0.019011 _atom_sites.fract_transf_matrix[1][2] 0.010976 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021952 _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] 0.007043 _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 2 IR3 A 1 1378 1378 IR3 IR3 . D 3 NAG A 1 1379 1379 NAG NAG . E 2 IR3 A 1 1380 1380 IR3 IR3 . F 2 IR3 B 1 1379 1379 IR3 IR3 . G 3 NAG B 1 1380 1380 NAG NAG . H 2 IR3 B 1 1381 1381 IR3 IR3 . I 4 HOH A 1 2001 2001 HOH HOH . I 4 HOH A 2 2002 2002 HOH HOH . I 4 HOH A 3 2003 2003 HOH HOH . I 4 HOH A 4 2004 2004 HOH HOH . J 4 HOH B 1 2001 2001 HOH HOH . J 4 HOH B 2 2002 2002 HOH HOH . J 4 HOH B 3 2003 2003 HOH HOH . J 4 HOH B 4 2004 2004 HOH HOH . J 4 HOH B 5 2005 2005 HOH HOH . J 4 HOH B 6 2006 2006 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 . . . D 3 29.749 4.478 100.231 1 61.39 ? C1 NAG 1379 A 1 HETATM 2 C C2 NAG . . . D 3 28.942 3.753 101.297 1 63.66 ? C2 NAG 1379 A 1 HETATM 3 C C3 NAG . . . D 3 29.684 3.777 102.63 1 61.38 ? C3 NAG 1379 A 1 HETATM 4 C C4 NAG . . . D 3 31.111 3.269 102.458 1 66.38 ? C4 NAG 1379 A 1 HETATM 5 C C5 NAG . . . D 3 31.806 3.913 101.262 1 67.33 ? C5 NAG 1379 A 1 HETATM 6 C C6 NAG . . . D 3 33.107 3.187 100.959 1 69.81 ? C6 NAG 1379 A 1 HETATM 7 C C7 NAG . . . D 3 26.517 3.685 101.194 1 58.82 ? C7 NAG 1379 A 1 HETATM 8 C C8 NAG . . . D 3 25.253 4.303 101.712 1 49.08 ? C8 NAG 1379 A 1 HETATM 9 N N2 NAG . . . D 3 27.634 4.369 101.421 1 62.71 ? N2 NAG 1379 A 1 HETATM 10 O O3 NAG . . . D 3 29.001 2.96 103.554 1 60.51 ? O3 NAG 1379 A 1 HETATM 11 O O4 NAG . . . D 3 31.867 3.546 103.618 1 66.39 ? O4 NAG 1379 A 1 HETATM 12 O O5 NAG . . . D 3 31.012 3.866 100.095 1 68.1 ? O5 NAG 1379 A 1 HETATM 13 O O6 NAG . . . D 3 33.715 3.807 99.849 1 71.49 ? O6 NAG 1379 A 1 HETATM 14 O O7 NAG . . . D 3 26.493 2.606 100.598 1 62.24 ? O7 NAG 1379 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 43 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 1152 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 14 #