data_6Y0F # _model_server_result.job_id HeFpkesw-8L2rpXjoUJ-lg _model_server_result.datetime_utc '2024-10-20 21:03:05' _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 6y0f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":805}' # _entry.id 6Y0F # _exptl.entry_id 6Y0F _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 89.76 _cell.angle_gamma 90 _cell.entry_id 6Y0F _cell.length_a 67.586 _cell.length_b 253.604 _cell.length_c 115.247 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y0F _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,N,O,P,Q,R,S 1 1 C,D,I,J,K,L,M,T,U,V,W 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 ? 5 N N N ? 5 O N N ? 5 P N N ? 5 R N N ? 5 T N N ? 5 V N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 2 1 FUC NAG C1 O1 . O6 HO6 . 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 2 n E NAG 1 E 1 NAG A 758 NAG 2 n E NAG 2 E 2 NAG A 759 NAG 3 n F NAG 1 F 1 NAG B 758 NAG 3 n F NAG 2 F 2 NAG B 759 NAG 3 n F BMA 3 F 3 BMA B 760 BMA 2 n G NAG 1 G 1 NAG B 762 NAG 2 n G NAG 2 G 2 NAG B 763 NAG 2 n H NAG 1 H 1 NAG B 764 NAG 2 n H NAG 2 H 2 NAG B 765 NAG 2 n I NAG 1 I 1 NAG C 758 NAG 2 n I NAG 2 I 2 NAG C 759 NAG 2 n J NAG 1 J 1 NAG C 760 NAG 2 n J NAG 2 J 2 NAG C 761 NAG 4 n K NAG 1 K 1 NAG D 759 NAG 4 n K FUC 2 K 2 FUC D 760 FUC 4 n L NAG 1 L 1 NAG D 761 NAG 4 n L FUC 2 L 2 FUC D 763 FUC 4 n M NAG 1 M 1 NAG D 764 NAG 4 n M FUC 2 M 2 FUC D 765 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 286 A CYS 321 1_555 A SG CYS 297 A CYS 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 A SG CYS 403 A CYS 438 1_555 A SG CYS 406 A CYS 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 413 A CYS 448 1_555 A SG CYS 431 A CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 608 A CYS 643 1_555 A SG CYS 720 A CYS 755 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 B SG CYS 286 B CYS 321 1_555 B SG CYS 297 B CYS 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf6 B SG CYS 403 B CYS 438 1_555 B SG CYS 406 B CYS 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf7 B SG CYS 413 B CYS 448 1_555 B SG CYS 431 B CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 608 B CYS 643 1_555 B SG CYS 720 B CYS 755 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 C SG CYS 403 C CYS 438 1_555 C SG CYS 406 C CYS 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf10 C SG CYS 413 C CYS 448 1_555 C SG CYS 431 C CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf11 C SG CYS 608 C CYS 643 1_555 C SG CYS 720 C CYS 755 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf12 D SG CYS 403 D CYS 438 1_555 D SG CYS 406 D CYS 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf13 D SG CYS 413 D CYS 448 1_555 D SG CYS 431 D CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 D SG CYS 608 D CYS 643 1_555 D SG CYS 720 D CYS 755 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A ND2 ASN 14 A ASN 49 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 A ND2 ASN 192 A ASN 227 1_555 N C1 NAG . A NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 A ND2 ASN 279 A ASN 314 1_555 O C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 A ND2 ASN 644 A ASN 679 1_555 P C1 NAG . A NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale5 B ND2 ASN 14 B ASN 49 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 B ND2 ASN 57 B ASN 92 1_555 R C1 NAG . B NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 B ND2 ASN 192 B ASN 227 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale8 B ND2 ASN 279 B ASN 314 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale9 C ND2 ASN 14 C ASN 49 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale10 C ND2 ASN 192 C ASN 227 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale11 C ND2 ASN 279 C ASN 314 1_555 T C1 NAG . C NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale12 D ND2 ASN 14 D ASN 49 1_555 V C1 NAG . D NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale13 D ND2 ASN 57 D ASN 92 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale14 D ND2 ASN 192 D ASN 227 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale15 D ND2 ASN 279 D ASN 314 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale16 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale18 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale19 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale20 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale21 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale22 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale23 K O6 NAG . K NAG 1 1_555 K C1 FUC . K FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale24 L O6 NAG . L NAG 1 1_555 L C1 FUC . L FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale25 M O6 NAG . M NAG 1 1_555 M C1 FUC . M FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? # _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 349 n n C1 O1 NAG sing 350 n n C1 O5 NAG sing 351 n n C1 H1 NAG sing 352 n n C2 C3 NAG sing 353 n n C2 N2 NAG sing 354 n n C2 H2 NAG sing 355 n n C3 C4 NAG sing 356 n n C3 O3 NAG sing 357 n n C3 H3 NAG sing 358 n n C4 C5 NAG sing 359 n n C4 O4 NAG sing 360 n n C4 H4 NAG sing 361 n n C5 C6 NAG sing 362 n n C5 O5 NAG sing 363 n n C5 H5 NAG sing 364 n n C6 O6 NAG sing 365 n n C6 H61 NAG sing 366 n n C6 H62 NAG sing 367 n n C7 C8 NAG sing 368 n n C7 N2 NAG sing 369 n n C7 O7 NAG doub 370 n n C8 H81 NAG sing 371 n n C8 H82 NAG sing 372 n n C8 H83 NAG sing 373 n n N2 HN2 NAG sing 374 n n O1 HO1 NAG sing 375 n n O3 HO3 NAG sing 376 n n O4 HO4 NAG sing 377 n n O6 HO6 NAG sing 378 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 6Y0F _atom_sites.fract_transf_matrix[1][1] 0.014796 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000062 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003943 _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] 0.008677 _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 N 5 NAG A 1 803 760 NAG NAG . O 5 NAG A 1 804 762 NAG NAG . P 5 NAG A 1 805 763 NAG NAG . Q 6 356 A 1 806 1 356 LIG . R 5 NAG B 1 804 761 NAG NAG . S 6 356 B 1 809 3 356 LIG . T 5 NAG C 1 805 763 NAG NAG . U 6 356 C 1 806 4 356 LIG . V 5 NAG D 1 801 758 NAG NAG . W 6 356 D 1 808 2 356 LIG . # 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 . . . T 5 -31.053 7.547 109.055 1 65.25 ? C1 NAG 805 C 1 HETATM 2 C C2 NAG . . . T 5 -32.352 7.883 109.792 1 65.85 ? C2 NAG 805 C 1 HETATM 3 C C3 NAG . . . T 5 -33.541 7.263 109.058 1 66.28 ? C3 NAG 805 C 1 HETATM 4 C C4 NAG . . . T 5 -33.564 7.722 107.607 1 66.01 ? C4 NAG 805 C 1 HETATM 5 C C5 NAG . . . T 5 -32.247 7.333 106.942 1 65.94 ? C5 NAG 805 C 1 HETATM 6 C C6 NAG . . . T 5 -32.134 7.822 105.516 1 65.96 ? C6 NAG 805 C 1 HETATM 7 C C7 NAG . . . T 5 -32.344 8.264 112.232 1 66.28 ? C7 NAG 805 C 1 HETATM 8 C C8 NAG . . . T 5 -32.407 7.608 113.581 1 66.12 ? C8 NAG 805 C 1 HETATM 9 N N2 NAG . . . T 5 -32.32 7.433 111.175 1 66.14 ? N2 NAG 805 C 1 HETATM 10 O O3 NAG . . . T 5 -34.764 7.607 109.703 1 66.8 ? O3 NAG 805 C 1 HETATM 11 O O4 NAG . . . T 5 -34.667 7.131 106.92 1 65.81 ? O4 NAG 805 C 1 HETATM 12 O O5 NAG . . . T 5 -31.146 7.909 107.669 1 65.83 ? O5 NAG 805 C 1 HETATM 13 O O6 NAG . . . T 5 -30.881 7.468 104.941 1 66.1 ? O6 NAG 805 C 1 HETATM 14 O O7 NAG . . . T 5 -32.311 9.487 112.103 1 66.34 ? O7 NAG 805 C 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #