data_6FYT # _model_server_result.job_id f-oybYJS4dRpmnTtvD9qaA _model_server_result.datetime_utc '2024-11-23 14:40:16' _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 6fyt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 6FYT # _exptl.entry_id 6FYT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 6FYT _cell.length_a 107.54 _cell.length_b 107.54 _cell.length_c 198.33 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FYT _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 53.77 93.132372 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -53.77 93.132372 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 I N N ? 7 J N N ? 7 K N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 FUC NAG C1 O1 . O3 HO3 . sing 2 ? 4 3 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 1 FUC NAG C1 O1 . O6 HO6 . sing 4 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . 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 C 1 NAG A 502 NAG 4 n D FUC 2 C 2 FUC A 504 FUC 4 n D NAG 3 C 3 NAG A 505 NAG 4 n D FUC 4 C 4 FUC A 503 FUC 5 n E NAG 1 D 1 NAG A 506 NAG 5 n E NAG 2 D 2 NAG A 507 NAG 6 n F NAG 1 E 1 NAG A 508 NAG 6 n F NAG 2 E 2 NAG A 509 NAG 6 n F BMA 3 E 3 BMA A 510 BMA 5 n G NAG 1 F 1 NAG A 512 NAG 5 n G NAG 2 F 2 NAG A 513 NAG 4 n H NAG 1 G 1 NAG B 501 NAG 4 n H FUC 2 G 2 FUC B 503 FUC 4 n H NAG 3 G 3 NAG B 504 NAG 4 n H FUC 4 G 4 FUC B 502 FUC # 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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 278 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 59 A CYS 64 1_555 A SG CYS 71 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 94 A CYS 97 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf5 A SG CYS 282 A CYS 281 1_555 A SG CYS 306 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 C SG CYS 22 I CYS 22 1_555 C SG CYS 95 I CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 15 A ASN 21 1_555 I C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 A ND2 ASN 27 A ASN 33 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 58 A ASN 63 1_555 E C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 A ND2 ASN 91 A ASN 95 1_555 F C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale5 A ND2 ASN 129 A ASN 129 1_555 J C1 NAG . A NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 A ND2 ASN 163 A ASN 163 1_555 G C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 A ND2 ASN 290 A ASN 289 1_555 K C1 NAG . A NAG 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 B ND2 ASN 154 B ASN 154 1_555 H C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 D O3 NAG . C NAG 1 1_555 D C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 D O6 NAG . C NAG 1 1_555 D C1 FUC . C FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 E O4 NAG . D NAG 1 1_555 E C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale13 F O4 NAG . E NAG 1 1_555 F C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale14 F O4 NAG . E NAG 2 1_555 F C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale15 G O4 NAG . F NAG 1 1_555 G C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale16 H O3 NAG . G NAG 1 1_555 H C1 FUC . G FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale17 H O4 NAG . G NAG 1 1_555 H C1 NAG . G NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale18 H O6 NAG . G NAG 1 1_555 H C1 FUC . G FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _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 282 n n C1 O1 NAG sing 283 n n C1 O5 NAG sing 284 n n C1 H1 NAG sing 285 n n C2 C3 NAG sing 286 n n C2 N2 NAG sing 287 n n C2 H2 NAG sing 288 n n C3 C4 NAG sing 289 n n C3 O3 NAG sing 290 n n C3 H3 NAG sing 291 n n C4 C5 NAG sing 292 n n C4 O4 NAG sing 293 n n C4 H4 NAG sing 294 n n C5 C6 NAG sing 295 n n C5 O5 NAG sing 296 n n C5 H5 NAG sing 297 n n C6 O6 NAG sing 298 n n C6 H61 NAG sing 299 n n C6 H62 NAG sing 300 n n C7 C8 NAG sing 301 n n C7 N2 NAG sing 302 n n C7 O7 NAG doub 303 n n C8 H81 NAG sing 304 n n C8 H82 NAG sing 305 n n C8 H83 NAG sing 306 n n N2 HN2 NAG sing 307 n n O1 HO1 NAG sing 308 n n O3 HO3 NAG sing 309 n n O4 HO4 NAG sing 310 n n O6 HO6 NAG sing 311 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 6FYT _atom_sites.fract_transf_matrix[1][1] 0.009299 _atom_sites.fract_transf_matrix[1][2] 0.005369 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010737 _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] 0.005042 _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 I 7 NAG A 1 501 501 NAG NAG . J 7 NAG A 1 511 511 NAG NAG . K 7 NAG A 1 514 514 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 NAG . . . I 7 29.437 74.336 -39.177 1 99.11 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . I 7 30.642 74.822 -38.36 1 112.76 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . I 7 30.492 76.303 -38.007 1 116.71 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . I 7 30.202 77.132 -39.251 1 122.31 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . I 7 29.009 76.555 -40.004 1 117.06 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . I 7 28.741 77.257 -41.316 1 110.33 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . I 7 31.835 73.198 -36.959 1 131.56 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . I 7 31.851 72.469 -35.65 1 129.55 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . I 7 30.808 74.031 -37.152 1 124.41 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . I 7 31.69 76.766 -37.395 1 116.07 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . I 7 29.916 78.475 -38.875 1 127.3 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . I 7 29.256 75.177 -40.318 1 110.57 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . I 7 29.446 76.652 -42.392 1 103.37 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . I 7 32.708 73.038 -37.804 1 135.64 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #