data_6CYM # _model_server_result.job_id J0PkAINdENa2w91GiEM9UQ _model_server_result.datetime_utc '2024-11-29 20:56:04' _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 6cym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 6CYM # _exptl.entry_id 6CYM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 _cell.angle_gamma 90 _cell.entry_id 6CYM _cell.length_a 91.67 _cell.length_b 99.73 _cell.length_c 146.01 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6CYM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # 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,J 1 1 C,D,H,I,K,L 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 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 28 A CYS 42 1_555 A SG CYS 44 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 119 A CYS 133 1_555 B SG CYS 3 B CYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf3 A SG CYS 173 A CYS 187 1_555 A SG CYS 187 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 A SG CYS 201 A CYS 215 1_555 A SG CYS 231 A CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf5 C SG CYS 28 C CYS 42 1_555 C SG CYS 44 C CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 C SG CYS 119 C CYS 133 1_555 D SG CYS 3 D CYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf7 C SG CYS 173 C CYS 187 1_555 C SG CYS 187 C CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf8 C SG CYS 201 C CYS 215 1_555 C SG CYS 231 C CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 A ND2 ASN 53 A ASN 67 1_555 F C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A OG SER 205 A SER 219 1_555 E C8 71F . A 71F 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.521 ? covale ? covale3 C OG SER 205 C SER 219 1_555 H C8 71F . C 71F 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.559 sing metalc ? metalc1 A O ARG 233 A ARG 247 1_555 G NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc2 A O LYS 236 A LYS 250 1_555 G NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc3 G NA NA . A NA 302 1_555 J O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.159 ? metalc ? metalc4 G NA NA . A NA 302 1_555 J O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc5 G NA NA . A NA 302 1_555 J O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc6 C O ARG 233 C ARG 247 1_555 I NA NA . C NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc7 C O LYS 236 C LYS 250 1_555 I NA NA . C NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? # _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 256 n n C1 O1 NAG sing 257 n n C1 O5 NAG sing 258 n n C1 H1 NAG sing 259 n n C2 C3 NAG sing 260 n n C2 N2 NAG sing 261 n n C2 H2 NAG sing 262 n n C3 C4 NAG sing 263 n n C3 O3 NAG sing 264 n n C3 H3 NAG sing 265 n n C4 C5 NAG sing 266 n n C4 O4 NAG sing 267 n n C4 H4 NAG sing 268 n n C5 C6 NAG sing 269 n n C5 O5 NAG sing 270 n n C5 H5 NAG sing 271 n n C6 O6 NAG sing 272 n n C6 H61 NAG sing 273 n n C6 H62 NAG sing 274 n n C7 C8 NAG sing 275 n n C7 N2 NAG sing 276 n n C7 O7 NAG doub 277 n n C8 H81 NAG sing 278 n n C8 H82 NAG sing 279 n n C8 H83 NAG sing 280 n n N2 HN2 NAG sing 281 n n O1 HO1 NAG sing 282 n n O3 HO3 NAG sing 283 n n O4 HO4 NAG sing 284 n n O6 HO6 NAG sing 285 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 6CYM _atom_sites.fract_transf_matrix[1][1] 0.010909 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010027 _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] 0.006849 _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 E 3 71F A 1 300 300 71F MBA . F 4 NAG A 1 301 301 NAG NAG . G 5 NA A 1 302 302 NA NA . H 3 71F C 1 301 300 71F MBA . I 5 NA C 1 302 302 NA NA . J 6 HOH A 1 401 21 HOH HOH . J 6 HOH A 2 402 22 HOH HOH . J 6 HOH A 3 403 8 HOH HOH . J 6 HOH A 4 404 1 HOH HOH . J 6 HOH A 5 405 25 HOH HOH . J 6 HOH A 6 406 20 HOH HOH . J 6 HOH A 7 407 7 HOH HOH . J 6 HOH A 8 408 16 HOH HOH . J 6 HOH A 9 409 9 HOH HOH . J 6 HOH A 10 410 24 HOH HOH . J 6 HOH A 11 411 19 HOH HOH . J 6 HOH A 12 412 26 HOH HOH . J 6 HOH A 13 413 23 HOH HOH . J 6 HOH A 14 414 11 HOH HOH . J 6 HOH A 15 415 2 HOH HOH . K 6 HOH C 1 401 17 HOH HOH . K 6 HOH C 2 402 18 HOH HOH . K 6 HOH C 3 403 28 HOH HOH . K 6 HOH C 4 404 14 HOH HOH . K 6 HOH C 5 405 10 HOH HOH . K 6 HOH C 6 406 27 HOH HOH . L 6 HOH D 1 101 12 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 . . . F 4 -1.597 12.563 -12.655 1 82.96 ? C1 NAG 301 A 1 HETATM 2 C C2 NAG . . . F 4 -2.637 11.501 -12.289 1 82.95 ? C2 NAG 301 A 1 HETATM 3 C C3 NAG . . . F 4 -1.827 10.285 -11.831 1 82.4 ? C3 NAG 301 A 1 HETATM 4 C C4 NAG . . . F 4 -0.926 9.78 -12.959 1 83.78 ? C4 NAG 301 A 1 HETATM 5 C C5 NAG . . . F 4 -0.051 10.912 -13.508 1 85.12 ? C5 NAG 301 A 1 HETATM 6 C C6 NAG . . . F 4 0.648 10.555 -14.803 1 85.16 ? C6 NAG 301 A 1 HETATM 7 C C7 NAG . . . F 4 -4.716 12.585 -11.487 1 84.74 ? C7 NAG 301 A 1 HETATM 8 C C8 NAG . . . F 4 -5.626 12.755 -10.307 1 85.7 ? C8 NAG 301 A 1 HETATM 9 N N2 NAG . . . F 4 -3.573 11.911 -11.252 1 83.52 ? N2 NAG 301 A 1 HETATM 10 O O3 NAG . . . F 4 -2.697 9.251 -11.383 1 80.61 ? O3 NAG 301 A 1 HETATM 11 O O4 NAG . . . F 4 -0.121 8.689 -12.512 1 81.85 ? O4 NAG 301 A 1 HETATM 12 O O5 NAG . . . F 4 -0.847 12.088 -13.779 1 84.38 ? O5 NAG 301 A 1 HETATM 13 O O6 NAG . . . F 4 1.083 11.72 -15.494 1 84.72 ? O6 NAG 301 A 1 HETATM 14 O O7 NAG . . . F 4 -4.997 13.04 -12.595 1 84.31 ? O7 NAG 301 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #