data_6XR0 # _model_server_result.job_id ERtBfsiDp6RosZl7SaXgvQ _model_server_result.datetime_utc '2024-11-26 04:18:50' _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 6xr0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":803}' # _entry.id 6XR0 # _exptl.entry_id 6XR0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 91.46 _cell.angle_gamma 90 _cell.entry_id 6XR0 _cell.length_a 57.829 _cell.length_b 136.91 _cell.length_c 111.135 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XR0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_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,L,M _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 4 n D NAG 1 A 1 NAG M 707 NAG 4 n D NAG 2 A 2 NAG M 708 NAG 4 n E NAG 1 B 1 NAG M 710 NAG 4 n E NAG 2 B 2 NAG M 711 NAG # 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 H CYS 22 1_555 A SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 146 H CYS 146 1_555 A SG CYS 201 H CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 221 H CYS 221 1_555 B SG CYS 214 L CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf4 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf5 B SG CYS 134 L CYS 134 1_555 B SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf6 C SG CYS 26 M CYS 26 1_555 C SG CYS 63 M CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 C SG CYS 36 M CYS 36 1_555 C SG CYS 54 M CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 C SG CYS 130 M CYS 130 1_555 C SG CYS 216 M CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf9 C SG CYS 158 M CYS 158 1_555 C SG CYS 357 M CYS 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf10 C SG CYS 172 M CYS 172 1_555 C SG CYS 189 M CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf11 C SG CYS 186 M CYS 186 1_555 C SG CYS 199 M CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 C SG CYS 257 M CYS 257 1_555 C SG CYS 271 M CYS 271 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf13 C SG CYS 369 M CYS 369 1_555 C SG CYS 406 M CYS 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf14 C SG CYS 379 M CYS 379 1_555 C SG CYS 397 M CYS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf15 C SG CYS 476 M CYS 476 1_555 C SG CYS 562 M CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf16 C SG CYS 518 M CYS 518 1_555 C SG CYS 535 M CYS 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf17 C SG CYS 532 M CYS 532 1_555 C SG CYS 545 M CYS 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf18 C SG CYS 603 M CYS 603 1_555 C SG CYS 617 M CYS 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 C ND2 ASN 38 M ASN 38 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale2 C ND2 ASN 135 M ASN 135 1_555 F C1 NAG . M NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 C ND2 ASN 515 M ASN 515 1_555 E C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale5 E O4 NAG . B NAG 1 1_555 E C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? metalc ? metalc1 A OD1 ASP 220 H ASP 220 1_555 G MG MG . M MG 806 2_656 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc2 A OD2 ASP 220 H ASP 220 1_555 G MG MG . M MG 806 2_656 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 C OD1 ASP 78 M ASP 78 1_555 I FE FE . M FE 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc4 C OH TYR 107 M TYR 107 1_555 I FE FE . M FE 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc5 C OH TYR 210 M TYR 210 1_555 I FE FE . M FE 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc6 C NE2 HIS 279 M HIS 279 1_555 I FE FE . M FE 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc7 C OD1 ASP 505 M ASP 505 1_555 G MG MG . M MG 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc8 C OD2 ASP 505 M ASP 505 1_555 G MG MG . M MG 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc9 C OD1 ASP 652 M ASP 652 1_555 H NA NA . M NA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.14 ? metalc ? metalc10 C OD2 ASP 652 M ASP 652 1_555 H NA NA . M NA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc11 C O PHE 661 M PHE 661 1_555 H NA NA . M NA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc12 C O ASP 675 M ASP 675 1_555 H NA NA . M NA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc13 I FE FE . M FE 808 1_555 J O3 BCT . M BCT 809 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? # _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 241 n n C1 O1 NAG sing 242 n n C1 O5 NAG sing 243 n n C1 H1 NAG sing 244 n n C2 C3 NAG sing 245 n n C2 N2 NAG sing 246 n n C2 H2 NAG sing 247 n n C3 C4 NAG sing 248 n n C3 O3 NAG sing 249 n n C3 H3 NAG sing 250 n n C4 C5 NAG sing 251 n n C4 O4 NAG sing 252 n n C4 H4 NAG sing 253 n n C5 C6 NAG sing 254 n n C5 O5 NAG sing 255 n n C5 H5 NAG sing 256 n n C6 O6 NAG sing 257 n n C6 H61 NAG sing 258 n n C6 H62 NAG sing 259 n n C7 C8 NAG sing 260 n n C7 N2 NAG sing 261 n n C7 O7 NAG doub 262 n n C8 H81 NAG sing 263 n n C8 H82 NAG sing 264 n n C8 H83 NAG sing 265 n n N2 HN2 NAG sing 266 n n O1 HO1 NAG sing 267 n n O3 HO3 NAG sing 268 n n O4 HO4 NAG sing 269 n n O6 HO6 NAG sing 270 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 6XR0 _atom_sites.fract_transf_matrix[1][1] 0.017292 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000441 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007304 _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] 0.009001 _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 5 NAG M 1 803 709 NAG NAG . G 6 MG M 1 806 2 MG MG . H 7 NA M 1 807 1 NA NA . I 8 FE M 1 808 790 FE FE . J 9 BCT M 1 809 792 BCT BCT . K 10 HOH H 1 301 18 HOH HOH . K 10 HOH H 2 302 28 HOH HOH . K 10 HOH H 3 303 34 HOH HOH . K 10 HOH H 4 304 40 HOH HOH . K 10 HOH H 5 305 30 HOH HOH . K 10 HOH H 6 306 44 HOH HOH . K 10 HOH H 7 307 33 HOH HOH . K 10 HOH H 8 308 61 HOH HOH . K 10 HOH H 9 309 9 HOH HOH . L 10 HOH L 1 301 17 HOH HOH . L 10 HOH L 2 302 2 HOH HOH . L 10 HOH L 3 303 21 HOH HOH . L 10 HOH L 4 304 14 HOH HOH . L 10 HOH L 5 305 23 HOH HOH . L 10 HOH L 6 306 13 HOH HOH . L 10 HOH L 7 307 22 HOH HOH . L 10 HOH L 8 308 54 HOH HOH . L 10 HOH L 9 309 31 HOH HOH . L 10 HOH L 10 310 3 HOH HOH . M 10 HOH M 1 901 10 HOH HOH . M 10 HOH M 2 902 52 HOH HOH . M 10 HOH M 3 903 8 HOH HOH . M 10 HOH M 4 904 16 HOH HOH . M 10 HOH M 5 905 50 HOH HOH . M 10 HOH M 6 906 29 HOH HOH . M 10 HOH M 7 907 32 HOH HOH . M 10 HOH M 8 908 25 HOH HOH . M 10 HOH M 9 909 15 HOH HOH . M 10 HOH M 10 910 65 HOH HOH . M 10 HOH M 11 911 6 HOH HOH . M 10 HOH M 12 912 63 HOH HOH . M 10 HOH M 13 913 4 HOH HOH . M 10 HOH M 14 914 64 HOH HOH . M 10 HOH M 15 915 5 HOH HOH . M 10 HOH M 16 916 41 HOH HOH . M 10 HOH M 17 917 24 HOH HOH . M 10 HOH M 18 918 20 HOH HOH . M 10 HOH M 19 919 39 HOH HOH . M 10 HOH M 20 920 1 HOH HOH . M 10 HOH M 21 921 37 HOH HOH . M 10 HOH M 22 922 42 HOH HOH . M 10 HOH M 23 923 27 HOH HOH . M 10 HOH M 24 924 53 HOH HOH . M 10 HOH M 25 925 58 HOH HOH . M 10 HOH M 26 926 60 HOH HOH . M 10 HOH M 27 927 56 HOH HOH . M 10 HOH M 28 928 26 HOH HOH . M 10 HOH M 29 929 57 HOH HOH . M 10 HOH M 30 930 45 HOH HOH . M 10 HOH M 31 931 55 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 5 90.216 22.789 125.975 1 84.42 ? C1 NAG 803 M 1 HETATM 2 C C2 NAG . . . F 5 91.557 23.116 126.64 1 84.9 ? C2 NAG 803 M 1 HETATM 3 C C3 NAG . . . F 5 92.635 22.131 126.188 1 85.49 ? C3 NAG 803 M 1 HETATM 4 C C4 NAG . . . F 5 92.178 20.702 126.438 1 85.79 ? C4 NAG 803 M 1 HETATM 5 C C5 NAG . . . F 5 90.912 20.447 125.626 1 85.51 ? C5 NAG 803 M 1 HETATM 6 C C6 NAG . . . F 5 90.365 19.048 125.806 1 86.13 ? C6 NAG 803 M 1 HETATM 7 C C7 NAG . . . F 5 92.599 25.212 127.355 1 84.84 ? C7 NAG 803 M 1 HETATM 8 C C8 NAG . . . F 5 93.414 26.373 126.867 1 84.42 ? C8 NAG 803 M 1 HETATM 9 N N2 NAG . . . F 5 92.002 24.479 126.413 1 84.87 ? N2 NAG 803 M 1 HETATM 10 O O3 NAG . . . F 5 93.873 22.385 126.849 1 85.6 ? O3 NAG 803 M 1 HETATM 11 O O4 NAG . . . F 5 93.21 19.773 126.103 1 86.08 ? O4 NAG 803 M 1 HETATM 12 O O5 NAG . . . F 5 89.882 21.379 126.024 1 84.68 ? O5 NAG 803 M 1 HETATM 13 O O6 NAG . . . F 5 91.309 18.049 125.393 1 86.47 ? O6 NAG 803 M 1 HETATM 14 O O7 NAG . . . F 5 92.513 24.93 128.547 1 85.11 ? O7 NAG 803 M 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 87 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #