data_6DF3 # _model_server_result.job_id oW5Ha62UllZjtFEPczmVdQ _model_server_result.datetime_utc '2025-07-07 06:03:37' _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 6df3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":303}' # _entry.id 6DF3 # _exptl.entry_id 6DF3 _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 90 _cell.angle_gamma 90 _cell.entry_id 6DF3 _cell.length_a 77.702 _cell.length_b 77.702 _cell.length_c 124.785 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 E _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 L 301 NAG 4 n D NAG 2 A 2 NAG L 302 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 105 L CYS 128 1_555 A SG CYS 194 L CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? disulf ? disulf2 B SG CYS 8 C CYS 59 1_555 B SG CYS 55 C CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? disulf ? disulf3 C SG CYS 55 H CYS 89 1_555 C SG CYS 63 H CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 C SG CYS 168 H CYS 202 1_555 C SG CYS 189 H CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? covale ? covale1 A ND2 ASN 57 L ASN 80 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 A ND2 ASN 64 L ASN 87 1_555 E C1 NAG . L NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? # _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 250 n n C1 O1 NAG sing 251 n n C1 O5 NAG sing 252 n n C1 H1 NAG sing 253 n n C2 C3 NAG sing 254 n n C2 N2 NAG sing 255 n n C2 H2 NAG sing 256 n n C3 C4 NAG sing 257 n n C3 O3 NAG sing 258 n n C3 H3 NAG sing 259 n n C4 C5 NAG sing 260 n n C4 O4 NAG sing 261 n n C4 H4 NAG sing 262 n n C5 C6 NAG sing 263 n n C5 O5 NAG sing 264 n n C5 H5 NAG sing 265 n n C6 O6 NAG sing 266 n n C6 H61 NAG sing 267 n n C6 H62 NAG sing 268 n n C7 C8 NAG sing 269 n n C7 N2 NAG sing 270 n n C7 O7 NAG doub 271 n n C8 H81 NAG sing 272 n n C8 H82 NAG sing 273 n n C8 H83 NAG sing 274 n n N2 HN2 NAG sing 275 n n O1 HO1 NAG sing 276 n n O3 HO3 NAG sing 277 n n O4 HO4 NAG sing 278 n n O6 HO6 NAG sing 279 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 6DF3 _atom_sites.fract_transf_matrix[1][1] 0.01287 _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] 0.01287 _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] 0.008014 _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 E 5 NAG L 1 303 303 NAG NAG . F 6 GOL C 1 301 1 GOL GOL . G 6 GOL C 1 302 2 GOL GOL . H 7 HOH L 1 401 60 HOH HOH . H 7 HOH L 2 402 67 HOH HOH . H 7 HOH L 3 403 58 HOH HOH . H 7 HOH L 4 404 24 HOH HOH . H 7 HOH L 5 405 43 HOH HOH . H 7 HOH L 6 406 51 HOH HOH . H 7 HOH L 7 407 30 HOH HOH . H 7 HOH L 8 408 64 HOH HOH . H 7 HOH L 9 409 20 HOH HOH . H 7 HOH L 10 410 59 HOH HOH . H 7 HOH L 11 411 9 HOH HOH . H 7 HOH L 12 412 35 HOH HOH . H 7 HOH L 13 413 19 HOH HOH . H 7 HOH L 14 414 55 HOH HOH . I 7 HOH C 1 401 75 HOH HOH . I 7 HOH C 2 402 16 HOH HOH . I 7 HOH C 3 403 52 HOH HOH . I 7 HOH C 4 404 79 HOH HOH . I 7 HOH C 5 405 14 HOH HOH . I 7 HOH C 6 406 48 HOH HOH . I 7 HOH C 7 407 13 HOH HOH . I 7 HOH C 8 408 42 HOH HOH . I 7 HOH C 9 409 46 HOH HOH . I 7 HOH C 10 410 47 HOH HOH . I 7 HOH C 11 411 62 HOH HOH . I 7 HOH C 12 412 5 HOH HOH . I 7 HOH C 13 413 49 HOH HOH . I 7 HOH C 14 414 10 HOH HOH . I 7 HOH C 15 415 76 HOH HOH . I 7 HOH C 16 416 4 HOH HOH . I 7 HOH C 17 417 31 HOH HOH . I 7 HOH C 18 418 44 HOH HOH . I 7 HOH C 19 419 56 HOH HOH . I 7 HOH C 20 420 45 HOH HOH . I 7 HOH C 21 421 71 HOH HOH . I 7 HOH C 22 422 50 HOH HOH . I 7 HOH C 23 423 33 HOH HOH . I 7 HOH C 24 424 15 HOH HOH . I 7 HOH C 25 425 53 HOH HOH . I 7 HOH C 26 426 39 HOH HOH . I 7 HOH C 27 427 37 HOH HOH . I 7 HOH C 28 428 21 HOH HOH . J 7 HOH H 1 301 77 HOH HOH . J 7 HOH H 2 302 17 HOH HOH . J 7 HOH H 3 303 63 HOH HOH . J 7 HOH H 4 304 36 HOH HOH . J 7 HOH H 5 305 57 HOH HOH . J 7 HOH H 6 306 61 HOH HOH . J 7 HOH H 7 307 80 HOH HOH . J 7 HOH H 8 308 69 HOH HOH . J 7 HOH H 9 309 66 HOH HOH . J 7 HOH H 10 310 2 HOH HOH . J 7 HOH H 11 311 8 HOH HOH . J 7 HOH H 12 312 41 HOH HOH . J 7 HOH H 13 313 32 HOH HOH . J 7 HOH H 14 314 34 HOH HOH . J 7 HOH H 15 315 6 HOH HOH . J 7 HOH H 16 316 72 HOH HOH . J 7 HOH H 17 317 12 HOH HOH . J 7 HOH H 18 318 68 HOH HOH . J 7 HOH H 19 319 28 HOH HOH . J 7 HOH H 20 320 27 HOH HOH . J 7 HOH H 21 321 78 HOH HOH . J 7 HOH H 22 322 26 HOH HOH . J 7 HOH H 23 323 23 HOH HOH . J 7 HOH H 24 324 11 HOH HOH . J 7 HOH H 25 325 7 HOH HOH . J 7 HOH H 26 326 54 HOH HOH . J 7 HOH H 27 327 3 HOH HOH . J 7 HOH H 28 328 40 HOH HOH . J 7 HOH H 29 329 74 HOH HOH . J 7 HOH H 30 330 22 HOH HOH . J 7 HOH H 31 331 18 HOH HOH . J 7 HOH H 32 332 65 HOH HOH . J 7 HOH H 33 333 73 HOH HOH . J 7 HOH H 34 334 1 HOH HOH . J 7 HOH H 35 335 70 HOH HOH . J 7 HOH H 36 336 29 HOH HOH . J 7 HOH H 37 337 38 HOH HOH . J 7 HOH H 38 338 25 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 . . . E 5 12.253 12.755 38.621 1 99.2 ? C1 NAG 303 L 1 HETATM 2 C C2 NAG . . . E 5 12.992 12.944 37.307 1 111.48 ? C2 NAG 303 L 1 HETATM 3 C C3 NAG . . . E 5 12.804 14.415 36.892 1 112.84 ? C3 NAG 303 L 1 HETATM 4 C C4 NAG . . . E 5 11.362 14.567 36.444 1 111.47 ? C4 NAG 303 L 1 HETATM 5 C C5 NAG . . . E 5 10.407 14.168 37.571 1 104.19 ? C5 NAG 303 L 1 HETATM 6 C C6 NAG . . . E 5 9.01 14.092 36.927 1 103.05 ? C6 NAG 303 L 1 HETATM 7 C C7 NAG . . . E 5 14.992 11.923 36.184 1 121.44 ? C7 NAG 303 L 1 HETATM 8 C C8 NAG . . . E 5 14.304 11.812 34.824 1 122.97 ? C8 NAG 303 L 1 HETATM 9 N N2 NAG . . . E 5 14.378 12.428 37.3 1 116.13 ? N2 NAG 303 L 1 HETATM 10 O O3 NAG . . . E 5 13.641 14.758 35.799 1 120.83 ? O3 NAG 303 L 1 HETATM 11 O O4 NAG . . . E 5 11.114 15.897 35.958 1 118.43 ? O4 NAG 303 L 1 HETATM 12 O O5 NAG . . . E 5 10.835 12.955 38.317 1 99.6 ? O5 NAG 303 L 1 HETATM 13 O O6 NAG . . . E 5 8.315 12.881 37.226 1 102.9 ? O6 NAG 303 L 1 HETATM 14 O O7 NAG . . . E 5 16.147 11.533 36.274 1 125.38 ? O7 NAG 303 L 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #