data_1LYB # _model_server_result.job_id vbkFofNI2bv9gNCD2ApVIQ _model_server_result.datetime_utc '2024-11-22 01:52:50' _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 1lyb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1}' # _entry.id 1LYB # _exptl.entry_id 1LYB _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 2 _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 1LYB _cell.length_a 125.9 _cell.length_b 125.9 _cell.length_c 104.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1LYB _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # 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 hexameric 6 software_defined_assembly 1 PQS trimeric 3 software_defined_assembly 2 PQS trimeric 3 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,G,I,K,L 1 1 D,E,F,H,J,M,N 1 2 A,B,C,G,I,K,L 2 1 D,E,F,H,J,M,N 3 1 # 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_664 -y+1,x-y+1,z-1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 62.95 109.032598 -34.7 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 I N N ? 5 J N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA 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 4 n G NAG 1 E 1 NAG A 1 NAG 4 n G NAG 2 E 2 NAG A 2 NAG 4 n G BMA 3 E 3 BMA A 3 MAN 4 n G MAN 4 E 4 MAN A 8 MAN 4 n H NAG 1 F 1 NAG C 1 NAG 4 n H NAG 2 F 2 NAG C 2 NAG 4 n H BMA 3 F 3 BMA C 3 MAN 4 n H MAN 4 F 4 MAN C 8 MAN # 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 27 A CYS 27 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 46 A CYS 46 1_555 A SG CYS 53 A CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 117 B CYS 222 1_555 B SG CYS 121 B CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf4 B SG CYS 160 B CYS 265 1_555 B SG CYS 197 B CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 D SG CYS 27 C CYS 27 1_555 D SG CYS 96 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf6 D SG CYS 46 C CYS 46 1_555 D SG CYS 53 C CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? disulf ? disulf7 E SG CYS 117 D CYS 222 1_555 E SG CYS 121 D CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf8 E SG CYS 160 D CYS 265 1_555 E SG CYS 197 D CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale1 A ND2 ASN 70 A ASN 70 1_555 G C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale2 I C1 NAG . B NAG 1 1_555 B ND2 ASN 94 B ASN 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? covale ? covale3 C C IVA 1 I IVA 1 1_555 C N VAL 2 I VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale4 C C VAL 3 I VAL 3 1_555 C N STA 4 I STA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale5 C C STA 4 I STA 4 1_555 C N ALA 5 I ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 C C ALA 5 I ALA 5 1_555 C N STA 6 I STA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 D ND2 ASN 70 C ASN 70 1_555 H C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale8 J C1 NAG . D NAG 1 1_555 E ND2 ASN 94 D ASN 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale9 F C IVA 1 J IVA 1 1_555 F N VAL 2 J VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale10 F C VAL 3 J VAL 3 1_555 F N STA 4 J STA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale11 F C STA 4 J STA 4 1_555 F N ALA 5 J ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale12 F C ALA 5 J ALA 5 1_555 F N STA 6 J STA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale13 G O4 NAG . E NAG 1 1_555 G C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale14 G O4 NAG . E NAG 2 1_555 G C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale15 G O6 BMA . E BMA 3 1_555 G C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale16 H O4 NAG . F NAG 1 1_555 H C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale17 H O4 NAG . F NAG 2 1_555 H C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale18 H O6 BMA . F BMA 3 1_555 H C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? # _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 301 n n C1 O1 NAG sing 302 n n C1 O5 NAG sing 303 n n C1 H1 NAG sing 304 n n C2 C3 NAG sing 305 n n C2 N2 NAG sing 306 n n C2 H2 NAG sing 307 n n C3 C4 NAG sing 308 n n C3 O3 NAG sing 309 n n C3 H3 NAG sing 310 n n C4 C5 NAG sing 311 n n C4 O4 NAG sing 312 n n C4 H4 NAG sing 313 n n C5 C6 NAG sing 314 n n C5 O5 NAG sing 315 n n C5 H5 NAG sing 316 n n C6 O6 NAG sing 317 n n C6 H61 NAG sing 318 n n C6 H62 NAG sing 319 n n C7 C8 NAG sing 320 n n C7 N2 NAG sing 321 n n C7 O7 NAG doub 322 n n C8 H81 NAG sing 323 n n C8 H82 NAG sing 324 n n C8 H83 NAG sing 325 n n N2 HN2 NAG sing 326 n n O1 HO1 NAG sing 327 n n O3 HO3 NAG sing 328 n n O4 HO4 NAG sing 329 n n O6 HO6 NAG sing 330 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 1LYB _atom_sites.fract_transf_matrix[1][1] 0.007943 _atom_sites.fract_transf_matrix[1][2] 0.004586 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009172 _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] 0.009606 _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 5 NAG B 1 1 1 NAG NAG . J 5 NAG D 1 1 1 NAG NAG . K 6 HOH A 1 102 1 HOH HOH . K 6 HOH A 2 103 2 HOH HOH . K 6 HOH A 3 104 3 HOH HOH . K 6 HOH A 4 105 4 HOH HOH . K 6 HOH A 5 106 5 HOH HOH . K 6 HOH A 6 107 6 HOH HOH . K 6 HOH A 7 108 10 HOH HOH . K 6 HOH A 8 109 11 HOH HOH . K 6 HOH A 9 110 28 HOH HOH . L 6 HOH B 1 29 9 HOH HOH . L 6 HOH B 2 32 12 HOH HOH . L 6 HOH B 3 33 13 HOH HOH . L 6 HOH B 4 34 15 HOH HOH . L 6 HOH B 5 35 21 HOH HOH . L 6 HOH B 6 36 22 HOH HOH . L 6 HOH B 7 37 24 HOH HOH . L 6 HOH B 8 38 25 HOH HOH . L 6 HOH B 9 39 26 HOH HOH . L 6 HOH B 10 41 29 HOH HOH . L 6 HOH B 11 42 118 HOH HOH . L 6 HOH B 12 43 120 HOH HOH . L 6 HOH B 13 44 122 HOH HOH . M 6 HOH C 1 102 1 HOH HOH . M 6 HOH C 2 103 2 HOH HOH . M 6 HOH C 3 104 4 HOH HOH . M 6 HOH C 4 105 5 HOH HOH . M 6 HOH C 5 106 6 HOH HOH . M 6 HOH C 6 107 9 HOH HOH . M 6 HOH C 7 108 10 HOH HOH . M 6 HOH C 8 109 11 HOH HOH . M 6 HOH C 9 110 28 HOH HOH . N 6 HOH D 1 3 3 HOH HOH . N 6 HOH D 2 10 12 HOH HOH . N 6 HOH D 3 11 13 HOH HOH . N 6 HOH D 4 12 15 HOH HOH . N 6 HOH D 5 13 21 HOH HOH . N 6 HOH D 6 14 22 HOH HOH . N 6 HOH D 7 15 24 HOH HOH . N 6 HOH D 8 16 25 HOH HOH . N 6 HOH D 9 17 26 HOH HOH . N 6 HOH D 10 19 29 HOH HOH . N 6 HOH D 11 20 118 HOH HOH . N 6 HOH D 12 21 120 HOH HOH . N 6 HOH D 13 22 122 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 . . . I 5 28.911 100.923 34.796 1 69.9 ? C1 NAG 1 B 1 HETATM 2 C C2 NAG . . . I 5 30.317 101.064 35.482 1 74.45 ? C2 NAG 1 B 1 HETATM 3 C C3 NAG . . . I 5 30.145 101.167 37.045 1 77.66 ? C3 NAG 1 B 1 HETATM 4 C C4 NAG . . . I 5 29.181 102.361 37.321 1 77.38 ? C4 NAG 1 B 1 HETATM 5 C C5 NAG . . . I 5 27.804 101.963 36.739 1 75.12 ? C5 NAG 1 B 1 HETATM 6 C C6 NAG . . . I 5 26.656 102.925 37.094 1 73.4 ? C6 NAG 1 B 1 HETATM 7 C C7 NAG . . . I 5 31.882 99.828 34.078 1 74.89 ? C7 NAG 1 B 1 HETATM 8 C C8 NAG . . . I 5 32.592 98.502 33.833 1 75.39 ? C8 NAG 1 B 1 HETATM 9 N N2 NAG . . . I 5 31.101 99.868 35.162 1 75.08 ? N2 NAG 1 B 1 HETATM 10 O O3 NAG . . . I 5 31.39 101.316 37.755 1 77.74 ? O3 NAG 1 B 1 HETATM 11 O O4 NAG . . . I 5 29.128 102.677 38.704 1 77.18 ? O4 NAG 1 B 1 HETATM 12 O O5 NAG . . . I 5 27.937 101.889 35.294 1 73.13 ? O5 NAG 1 B 1 HETATM 13 O O6 NAG . . . I 5 25.511 102.576 36.336 1 70.82 ? O6 NAG 1 B 1 HETATM 14 O O7 NAG . . . I 5 31.987 100.801 33.318 1 73.75 ? O7 NAG 1 B 1 HETATM 15 H H1 NAG . . . I 5 28.457 99.936 34.982 1 15 ? H1 NAG 1 B 1 HETATM 16 H H2 NAG . . . I 5 30.835 101.964 35.121 1 15 ? H2 NAG 1 B 1 HETATM 17 H H3 NAG . . . I 5 29.629 100.253 37.381 1 15 ? H3 NAG 1 B 1 HETATM 18 H H4 NAG . . . I 5 29.559 103.236 36.761 1 15 ? H4 NAG 1 B 1 HETATM 19 H H5 NAG . . . I 5 27.536 100.959 37.11 1 15 ? H5 NAG 1 B 1 HETATM 20 H H61 NAG . . . I 5 26.969 103.963 36.895 1 15 ? H61 NAG 1 B 1 HETATM 21 H H62 NAG . . . I 5 26.452 102.846 38.172 1 15 ? H62 NAG 1 B 1 HETATM 22 H H81 NAG . . . I 5 31.879 97.754 33.448 1 15 ? H81 NAG 1 B 1 HETATM 23 H H82 NAG . . . I 5 33.042 98.117 34.763 1 15 ? H82 NAG 1 B 1 HETATM 24 H H83 NAG . . . I 5 33.39 98.629 33.084 1 15 ? H83 NAG 1 B 1 HETATM 25 H HN2 NAG . . . I 5 31.002 99.055 35.696 1 15 ? HN2 NAG 1 B 1 HETATM 26 H HO3 NAG . . . I 5 31.971 100.58 37.568 1 15 ? HO3 NAG 1 B 1 HETATM 27 H HO4 NAG . . . I 5 30.04 102.616 39.023 1 15 ? HO4 NAG 1 B 1 HETATM 28 H HO6 NAG . . . I 5 25.809 102.066 35.573 1 15 ? HO6 NAG 1 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #