data_5K5T # _model_server_result.job_id qTJlY353SmWoEvP0PkgGYw _model_server_result.datetime_utc '2025-08-31 04:04:41' _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 5k5t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":710}' # _entry.id 5K5T # _exptl.entry_id 5K5T _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 7 _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 5K5T _cell.length_a 126.33 _cell.length_b 150.15 _cell.length_c 214.58 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K5T _symmetry.cell_setting ? _symmetry.Int_Tables_number 22 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'F 2 2 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M 1 1,5 A,B,C,D,E,F,G,H,I,J,K,L,M 2 1,2 A,B,C,D,E,F,G,H,I,J,K,L,M 3 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 11_554 -x+1/2,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 63.165 0 -107.29 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L 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 60 A CYS 60 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 129 A CYS 129 1_555 A SG CYS 129 A CYS 129 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf3 A SG CYS 236 A CYS 236 1_555 A SG CYS 561 A CYS 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 358 A CYS 358 1_555 A SG CYS 395 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 437 A CYS 437 1_555 A SG CYS 449 A CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 A SG CYS 542 A CYS 542 1_555 A SG CYS 562 A CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 A SG CYS 546 A CYS 546 1_555 A SG CYS 565 A CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 A SG CYS 568 A CYS 568 1_555 A SG CYS 582 A CYS 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 A SG CYS 585 A CYS 585 1_555 A SG CYS 598 A CYS 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 261 A ASN 261 1_555 F C1 NAG . A NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 287 A ASN 287 1_555 G C1 NAG . A NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 A ND2 ASN 446 A ASN 446 1_555 H C1 NAG . A NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 A ND2 ASN 468 A ASN 468 1_555 I C1 NAG . A NAG 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 488 A ASN 488 1_555 J C1 NAG . A NAG 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 A ND2 ASN 541 A ASN 541 1_555 K C1 NAG . A NAG 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 A ND2 ASN 594 A ASN 594 1_555 L C1 NAG . A NAG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A OG1 THR 100 A THR 100 1_555 B CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.81 ? metalc ? metalc2 A OG1 THR 145 A THR 145 1_555 B CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.156 ? # _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 5K5T _atom_sites.fract_transf_matrix[1][1] 0.007916 _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] 0.00666 _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] 0.00466 _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 B 2 CA A 1 701 1 CA CA . C 3 SO4 A 1 702 1 SO4 SO4 . D 3 SO4 A 1 703 1 SO4 SO4 . E 3 SO4 A 1 704 1 SO4 SO4 . F 4 NAG A 1 705 501 NAG NAG . G 4 NAG A 1 706 502 NAG NAG . H 4 NAG A 1 707 503 NAG NAG . I 4 NAG A 1 708 504 NAG NAG . J 4 NAG A 1 709 505 NAG NAG . K 4 NAG A 1 710 506 NAG NAG . L 4 NAG A 1 711 507 NAG NAG . M 5 HOH A 1 801 36 HOH HOH . M 5 HOH A 2 802 30 HOH HOH . M 5 HOH A 3 803 26 HOH HOH . M 5 HOH A 4 804 42 HOH HOH . M 5 HOH A 5 805 41 HOH HOH . M 5 HOH A 6 806 40 HOH HOH . M 5 HOH A 7 807 3 HOH HOH . M 5 HOH A 8 808 28 HOH HOH . M 5 HOH A 9 809 21 HOH HOH . M 5 HOH A 10 810 34 HOH HOH . M 5 HOH A 11 811 23 HOH HOH . M 5 HOH A 12 812 31 HOH HOH . M 5 HOH A 13 813 16 HOH HOH . M 5 HOH A 14 814 19 HOH HOH . M 5 HOH A 15 815 38 HOH HOH . M 5 HOH A 16 816 11 HOH HOH . M 5 HOH A 17 817 32 HOH HOH . M 5 HOH A 18 818 37 HOH HOH . M 5 HOH A 19 819 12 HOH HOH . M 5 HOH A 20 820 39 HOH HOH . M 5 HOH A 21 821 18 HOH HOH . M 5 HOH A 22 822 27 HOH HOH . M 5 HOH A 23 823 6 HOH HOH . M 5 HOH A 24 824 2 HOH HOH . M 5 HOH A 25 825 4 HOH HOH . M 5 HOH A 26 826 1 HOH HOH . M 5 HOH A 27 827 33 HOH HOH . M 5 HOH A 28 828 15 HOH HOH . M 5 HOH A 29 829 24 HOH HOH . M 5 HOH A 30 830 14 HOH HOH . M 5 HOH A 31 831 43 HOH HOH . M 5 HOH A 32 832 9 HOH HOH . M 5 HOH A 33 833 35 HOH HOH . M 5 HOH A 34 834 5 HOH HOH . M 5 HOH A 35 835 7 HOH HOH . M 5 HOH A 36 836 29 HOH HOH . M 5 HOH A 37 837 22 HOH HOH . M 5 HOH A 38 838 13 HOH HOH . M 5 HOH A 39 839 17 HOH HOH . M 5 HOH A 40 840 10 HOH HOH . M 5 HOH A 41 841 8 HOH HOH . M 5 HOH A 42 842 25 HOH HOH . M 5 HOH A 43 843 20 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 . . . K 4 -4.948 -26.601 -14.818 1 126.18 ? C1 NAG 710 A 1 HETATM 2 C C2 NAG . . . K 4 -5.014 -28.003 -14.212 1 127.01 ? C2 NAG 710 A 1 HETATM 3 C C3 NAG . . . K 4 -5.756 -28.857 -15.238 1 126.71 ? C3 NAG 710 A 1 HETATM 4 C C4 NAG . . . K 4 -7.166 -28.314 -15.459 1 125.92 ? C4 NAG 710 A 1 HETATM 5 C C5 NAG . . . K 4 -7.116 -26.838 -15.854 1 125.56 ? C5 NAG 710 A 1 HETATM 6 C C6 NAG . . . K 4 -8.477 -26.176 -15.842 1 124.87 ? C6 NAG 710 A 1 HETATM 7 C C7 NAG . . . K 4 -3.451 -29.285 -12.8 1 131.04 ? C7 NAG 710 A 1 HETATM 8 C C8 NAG . . . K 4 -2.064 -29.842 -12.69 1 131.47 ? C8 NAG 710 A 1 HETATM 9 N N2 NAG . . . K 4 -3.711 -28.574 -13.912 1 128.72 ? N2 NAG 710 A 1 HETATM 10 O O3 NAG . . . K 4 -5.814 -30.211 -14.803 1 127.25 ? O3 NAG 710 A 1 HETATM 11 O O4 NAG . . . K 4 -7.821 -29.06 -16.478 1 125.43 ? O4 NAG 710 A 1 HETATM 12 O O5 NAG . . . K 4 -6.289 -26.107 -14.927 1 126.06 ? O5 NAG 710 A 1 HETATM 13 O O6 NAG . . . K 4 -9.25 -26.545 -16.975 1 124.4 ? O6 NAG 710 A 1 HETATM 14 O O7 NAG . . . K 4 -4.299 -29.479 -11.933 1 132.23 ? O7 NAG 710 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #