data_5L7D # _model_server_result.job_id G8gZfcmaGPvuUPMkUl6hMQ _model_server_result.datetime_utc '2024-10-28 02:22:34' _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 5l7d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1202}' # _entry.id 5L7D # _exptl.entry_id 5L7D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _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 96.64 _cell.angle_gamma 90 _cell.entry_id 5L7D _cell.length_a 122.9 _cell.length_b 63.02 _cell.length_c 208.59 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L7D _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,E,F,G 1 1 B 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 ? 2 C N N ? 2 D N N # 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 33 A CYS 64 1_555 A SG CYS 147 A CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 39 A CYS 70 1_555 A SG CYS 103 A CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 47 A CYS 78 1_555 A SG CYS 96 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 87 A CYS 118 1_555 A SG CYS 123 A CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 116 A CYS 147 1_555 A SG CYS 138 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 A SG CYS 162 A CYS 193 1_555 A SG CYS 182 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 A SG CYS 186 A CYS 217 1_555 A SG CYS 264 A CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 A SG CYS 283 A CYS 314 1_555 A SG CYS 359 A CYS 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 A SG CYS 563 A CYS 490 1_555 A SG CYS 580 A CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 B SG CYS 33 B CYS 64 1_555 B SG CYS 147 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 B SG CYS 39 B CYS 70 1_555 B SG CYS 103 B CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 B SG CYS 47 B CYS 78 1_555 B SG CYS 96 B CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf13 B SG CYS 87 B CYS 118 1_555 B SG CYS 123 B CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf14 B SG CYS 116 B CYS 147 1_555 B SG CYS 138 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf15 B SG CYS 162 B CYS 193 1_555 B SG CYS 182 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf16 B SG CYS 186 B CYS 217 1_555 B SG CYS 264 B CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf17 B SG CYS 283 B CYS 314 1_555 B SG CYS 359 B CYS 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf18 B SG CYS 563 B CYS 490 1_555 B SG CYS 580 B CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 157 A ASN 188 1_555 C C1 NAG . A NAG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 A ND2 ASN 566 A ASN 493 1_555 D C1 NAG . A NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? metalc ? metalc1 A O THR 59 A THR 90 1_555 F NA NA . A NA 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc2 A O ALA 62 A ALA 93 1_555 F NA NA . A NA 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc3 A O SER 65 A SER 96 1_555 F NA NA . A NA 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc4 A O PRO 275 A PRO 306 1_555 G NA NA . A NA 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? # _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 312 n n C1 O1 NAG sing 313 n n C1 O5 NAG sing 314 n n C1 H1 NAG sing 315 n n C2 C3 NAG sing 316 n n C2 N2 NAG sing 317 n n C2 H2 NAG sing 318 n n C3 C4 NAG sing 319 n n C3 O3 NAG sing 320 n n C3 H3 NAG sing 321 n n C4 C5 NAG sing 322 n n C4 O4 NAG sing 323 n n C4 H4 NAG sing 324 n n C5 C6 NAG sing 325 n n C5 O5 NAG sing 326 n n C5 H5 NAG sing 327 n n C6 O6 NAG sing 328 n n C6 H61 NAG sing 329 n n C6 H62 NAG sing 330 n n C7 C8 NAG sing 331 n n C7 N2 NAG sing 332 n n C7 O7 NAG doub 333 n n C8 H81 NAG sing 334 n n C8 H82 NAG sing 335 n n C8 H83 NAG sing 336 n n N2 HN2 NAG sing 337 n n O1 HO1 NAG sing 338 n n O3 HO3 NAG sing 339 n n O4 HO4 NAG sing 340 n n O6 HO6 NAG sing 341 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 5L7D _atom_sites.fract_transf_matrix[1][1] 0.008137 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000947 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015868 _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] 0.004826 _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 C 2 NAG A 1 1201 1 NAG NAG . D 2 NAG A 1 1202 2 NAG NAG . E 3 CLR A 1 1203 1 CLR CLR . F 4 NA A 1 1204 1 NA NA . G 4 NA A 1 1205 2 NA NA . # 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 . . . D 2 -28.291 -0.69 95.413 1 171 ? C1 NAG 1202 A 1 HETATM 2 C C2 NAG . . . D 2 -27.383 -1.172 94.279 1 172.45 ? C2 NAG 1202 A 1 HETATM 3 C C3 NAG . . . D 2 -28.137 -2.16 93.391 1 173.36 ? C3 NAG 1202 A 1 HETATM 4 C C4 NAG . . . D 2 -28.706 -3.301 94.228 1 174.16 ? C4 NAG 1202 A 1 HETATM 5 C C5 NAG . . . D 2 -29.618 -2.738 95.319 1 172.92 ? C5 NAG 1202 A 1 HETATM 6 C C6 NAG . . . D 2 -30.126 -3.788 96.281 1 172.71 ? C6 NAG 1202 A 1 HETATM 7 C C7 NAG . . . D 2 -25.573 0.037 93.119 1 173.53 ? C7 NAG 1202 A 1 HETATM 8 C C8 NAG . . . D 2 -25.256 1.136 92.15 1 173.51 ? C8 NAG 1202 A 1 HETATM 9 N N2 NAG . . . D 2 -26.86 -0.07 93.486 1 172.9 ? N2 NAG 1202 A 1 HETATM 10 O O3 NAG . . . D 2 -27.264 -2.669 92.387 1 173.13 ? O3 NAG 1202 A 1 HETATM 11 O O4 NAG . . . D 2 -29.426 -4.2 93.392 1 175.59 ? O4 NAG 1202 A 1 HETATM 12 O O5 NAG . . . D 2 -28.89 -1.786 96.115 1 171.86 ? O5 NAG 1202 A 1 HETATM 13 O O6 NAG . . . D 2 -31.217 -4.512 95.737 1 172.54 ? O6 NAG 1202 A 1 HETATM 14 O O7 NAG . . . D 2 -24.706 -0.724 93.543 1 173.91 ? O7 NAG 1202 A 1 # _model_server_stats.io_time_ms 87 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #