data_5XF1 # _model_server_result.job_id JCHI1DLKXGXn5kC2I7PVgQ _model_server_result.datetime_utc '2024-11-22 00:06:16' _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 5xf1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1206}' # _entry.id 5XF1 # _exptl.entry_id 5XF1 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.16 _cell.angle_gamma 90 _cell.entry_id 5XF1 _cell.length_a 71.46 _cell.length_b 248.79 _cell.length_c 93.33 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XF1 _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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,C,D,G,H,I,M,P 1 1 B,E,F,J,K,L,N,O 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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id N _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 NAG 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 G NAG 1 E 1 NAG A 2059 NAG 4 n G NAG 2 E 2 NAG A 2060 NAG 4 n H NAG 1 F 1 NAG A 2074 NAG 4 n H NAG 2 F 2 NAG A 2075 NAG 4 n I NAG 1 G 1 NAG A 2078 NAG 4 n I NAG 2 G 2 NAG A 2079 NAG 4 n J NAG 1 I 1 NAG B 2046 NAG 4 n J NAG 2 I 2 NAG B 2047 NAG 5 n K NAG 1 J 1 NAG B 2059 NAG 5 n K NAG 2 J 2 NAG B 2060 NAG 5 n K NAG 3 J 3 NAG B 2061 NAG 4 n L NAG 1 K 1 NAG B 2078 NAG 4 n L NAG 2 K 2 NAG B 2079 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 20 A CYS 43 1_555 A SG CYS 44 A CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf2 A SG CYS 35 A CYS 58 1_555 A SG CYS 77 A CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 58 A CYS 81 1_555 A SG CYS 98 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 201 A CYS 224 1_555 A SG CYS 428 A CYS 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 B SG CYS 20 B CYS 43 1_555 B SG CYS 44 B CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf6 B SG CYS 35 B CYS 58 1_555 B SG CYS 77 B CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf7 B SG CYS 58 B CYS 81 1_555 B SG CYS 98 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 201 B CYS 224 1_555 B SG CYS 428 B CYS 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf9 C SG CYS 22 C CYS 236 1_555 C SG CYS 96 C CYS 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf10 C SG CYS 155 C CYS 369 1_555 C SG CYS 211 C CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf11 C SG CYS 231 C CYS 445 1_555 D SG CYS 214 D CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf12 D SG CYS 23 D CYS 23 1_555 D SG CYS 88 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? disulf ? disulf13 D SG CYS 134 D CYS 134 1_555 D SG CYS 194 D CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf14 E SG CYS 22 H CYS 236 1_555 E SG CYS 96 H CYS 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf15 E SG CYS 155 H CYS 369 1_555 E SG CYS 211 H CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf16 E SG CYS 231 H CYS 445 1_555 F SG CYS 214 L CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 F SG CYS 23 L CYS 23 1_555 F SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? disulf ? disulf18 F SG CYS 134 L CYS 134 1_555 F SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 36 A ASN 59 1_555 G C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale2 A ND2 ASN 51 A ASN 74 1_555 H C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 A ND2 ASN 55 A ASN 78 1_555 I C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 B ND2 ASN 23 B ASN 46 1_555 J C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 B ND2 ASN 36 B ASN 59 1_555 K C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale6 B ND2 ASN 51 B ASN 74 1_555 N C1 NAG . B NAG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 B ND2 ASN 55 B ASN 78 1_555 L C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 G O4 NAG . E NAG 1 1_555 G C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale9 H O4 NAG . F NAG 1 1_555 H C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale10 I O4 NAG . G NAG 1 1_555 I C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale11 J O4 NAG . I NAG 1 1_555 J C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale12 K O4 NAG . J NAG 1 1_555 K C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 K O4 NAG . J NAG 2 1_555 K C1 NAG . J NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.527 ? covale ? covale14 L O4 NAG . K NAG 1 1_555 L C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.484 ? # _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 313 n n C1 O1 NAG sing 314 n n C1 O5 NAG sing 315 n n C1 H1 NAG sing 316 n n C2 C3 NAG sing 317 n n C2 N2 NAG sing 318 n n C2 H2 NAG sing 319 n n C3 C4 NAG sing 320 n n C3 O3 NAG sing 321 n n C3 H3 NAG sing 322 n n C4 C5 NAG sing 323 n n C4 O4 NAG sing 324 n n C4 H4 NAG sing 325 n n C5 C6 NAG sing 326 n n C5 O5 NAG sing 327 n n C5 H5 NAG sing 328 n n C6 O6 NAG sing 329 n n C6 H61 NAG sing 330 n n C6 H62 NAG sing 331 n n C7 C8 NAG sing 332 n n C7 N2 NAG sing 333 n n C7 O7 NAG doub 334 n n C8 H81 NAG sing 335 n n C8 H82 NAG sing 336 n n C8 H83 NAG sing 337 n n N2 HN2 NAG sing 338 n n O1 HO1 NAG sing 339 n n O3 HO3 NAG sing 340 n n O4 HO4 NAG sing 341 n n O6 HO6 NAG sing 342 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 5XF1 _atom_sites.fract_transf_matrix[1][1] 0.013994 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00004 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004019 _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] 0.010715 _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 M 6 97V A 1 1207 3001 97V 97V . N 7 NAG B 1 1206 2074 NAG NAG . O 6 97V B 1 1209 3001 97V 97V . P 8 HOH A 1 1301 801 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 . . . N 7 179.529 60.145 18.164 1 132.15 ? C1 NAG 1206 B 1 HETATM 2 C C2 NAG . . . N 7 179.601 58.621 18.213 1 130.79 ? C2 NAG 1206 B 1 HETATM 3 C C3 NAG . . . N 7 179.845 58.194 19.661 1 135.85 ? C3 NAG 1206 B 1 HETATM 4 C C4 NAG . . . N 7 181.093 58.85 20.236 1 131.8 ? C4 NAG 1206 B 1 HETATM 5 C C5 NAG . . . N 7 181.182 60.339 19.912 1 133.75 ? C5 NAG 1206 B 1 HETATM 6 C C6 NAG . . . N 7 182.6 60.856 20.158 1 134.2 ? C6 NAG 1206 B 1 HETATM 7 C C7 NAG . . . N 7 178.415 56.878 16.929 1 123.17 ? C7 NAG 1206 B 1 HETATM 8 C C8 NAG . . . N 7 177.085 56.29 16.56 1 124.39 ? C8 NAG 1206 B 1 HETATM 9 N N2 NAG . . . N 7 178.397 57.952 17.729 1 127.41 ? N2 NAG 1206 B 1 HETATM 10 O O3 NAG . . . N 7 179.983 56.765 19.738 1 149.46 ? O3 NAG 1206 B 1 HETATM 11 O O4 NAG . . . N 7 181.08 58.686 21.655 1 128.88 ? O4 NAG 1206 B 1 HETATM 12 O O5 NAG . . . N 7 180.837 60.587 18.544 1 136.09 ? O5 NAG 1206 B 1 HETATM 13 O O6 NAG . . . N 7 182.569 62.208 20.618 1 137.71 ? O6 NAG 1206 B 1 HETATM 14 O O7 NAG . . . N 7 179.44 56.377 16.509 1 126.16 ? O7 NAG 1206 B 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #