data_6YA2 # _model_server_result.job_id FSU4tYc9lx8WXqXaq-PBOQ _model_server_result.datetime_utc '2025-02-28 15:03:31' _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 6ya2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 6YA2 # _exptl.entry_id 6YA2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.56 _cell.angle_gamma 90 _cell.entry_id 6YA2 _cell.length_a 69.66 _cell.length_b 76.01 _cell.length_c 71.18 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YA2 _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 monomeric 1 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,D,E,F,G,J,K 1 1 C,H,I,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 D NAG 1 D 1 NAG A 297 NAG 2 n D NAG 2 D 2 NAG A 298 NAG 2 n E NAG 1 E 1 NAG B 302 NAG 2 n E NAG 2 E 2 NAG B 303 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 16 A CYS 114 1_555 A SG CYS 47 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf2 A SG CYS 24 A CYS 122 1_555 A SG CYS 58 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 A SG CYS 116 A CYS 214 1_555 B SG CYS 116 B CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf4 A SG CYS 126 A CYS 224 1_555 A SG CYS 187 A CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 B SG CYS 16 B CYS 114 1_555 B SG CYS 47 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 24 B CYS 122 1_555 B SG CYS 58 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 B SG CYS 126 B CYS 224 1_555 B SG CYS 187 B CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 C SG CYS 16 C CYS 114 1_555 C SG CYS 47 C CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? disulf ? disulf9 C SG CYS 24 C CYS 122 1_555 C SG CYS 58 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 C SG CYS 126 C CYS 224 1_555 C SG CYS 187 C CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 18 A ASN 116 1_555 F C1 NAG . A NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 A ND2 ASN 112 A ASN 210 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 B ND2 ASN 18 B ASN 116 1_555 G C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale4 B ND2 ASN 112 B ASN 210 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C ND2 ASN 18 C ASN 116 1_555 I C1 NAG . C NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 C ND2 ASN 112 C ASN 210 1_555 H C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 6YA2 _atom_sites.fract_transf_matrix[1][1] 0.014355 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004269 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013156 _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] 0.014657 _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 F 3 NAG A 1 303 301 NAG NAG . G 3 NAG B 1 301 301 NAG NAG . H 3 NAG C 1 301 296 NAG NAG . I 3 NAG C 1 302 301 NAG NAG . J 4 HOH A 1 401 117 HOH HOH . J 4 HOH A 2 402 116 HOH HOH . J 4 HOH A 3 403 49 HOH HOH . J 4 HOH A 4 404 6 HOH HOH . J 4 HOH A 5 405 14 HOH HOH . J 4 HOH A 6 406 79 HOH HOH . J 4 HOH A 7 407 83 HOH HOH . J 4 HOH A 8 408 35 HOH HOH . J 4 HOH A 9 409 39 HOH HOH . J 4 HOH A 10 410 13 HOH HOH . J 4 HOH A 11 411 11 HOH HOH . J 4 HOH A 12 412 15 HOH HOH . J 4 HOH A 13 413 66 HOH HOH . J 4 HOH A 14 414 45 HOH HOH . J 4 HOH A 15 415 21 HOH HOH . J 4 HOH A 16 416 119 HOH HOH . J 4 HOH A 17 417 54 HOH HOH . J 4 HOH A 18 418 67 HOH HOH . J 4 HOH A 19 419 73 HOH HOH . J 4 HOH A 20 420 106 HOH HOH . J 4 HOH A 21 421 103 HOH HOH . K 4 HOH B 1 401 115 HOH HOH . K 4 HOH B 2 402 109 HOH HOH . K 4 HOH B 3 403 92 HOH HOH . K 4 HOH B 4 404 2 HOH HOH . K 4 HOH B 5 405 107 HOH HOH . K 4 HOH B 6 406 47 HOH HOH . K 4 HOH B 7 407 91 HOH HOH . K 4 HOH B 8 408 10 HOH HOH . K 4 HOH B 9 409 3 HOH HOH . K 4 HOH B 10 410 4 HOH HOH . K 4 HOH B 11 411 88 HOH HOH . K 4 HOH B 12 412 19 HOH HOH . K 4 HOH B 13 413 51 HOH HOH . K 4 HOH B 14 414 33 HOH HOH . K 4 HOH B 15 415 17 HOH HOH . K 4 HOH B 16 416 18 HOH HOH . K 4 HOH B 17 417 41 HOH HOH . K 4 HOH B 18 418 1 HOH HOH . K 4 HOH B 19 419 76 HOH HOH . K 4 HOH B 20 420 60 HOH HOH . K 4 HOH B 21 421 113 HOH HOH . K 4 HOH B 22 422 12 HOH HOH . K 4 HOH B 23 423 43 HOH HOH . K 4 HOH B 24 424 112 HOH HOH . K 4 HOH B 25 425 46 HOH HOH . K 4 HOH B 26 426 36 HOH HOH . K 4 HOH B 27 427 5 HOH HOH . K 4 HOH B 28 428 84 HOH HOH . K 4 HOH B 29 429 26 HOH HOH . K 4 HOH B 30 430 32 HOH HOH . K 4 HOH B 31 431 110 HOH HOH . K 4 HOH B 32 432 122 HOH HOH . K 4 HOH B 33 433 40 HOH HOH . K 4 HOH B 34 434 44 HOH HOH . K 4 HOH B 35 435 58 HOH HOH . K 4 HOH B 36 436 25 HOH HOH . K 4 HOH B 37 437 81 HOH HOH . K 4 HOH B 38 438 108 HOH HOH . K 4 HOH B 39 439 118 HOH HOH . K 4 HOH B 40 440 111 HOH HOH . K 4 HOH B 41 441 28 HOH HOH . K 4 HOH B 42 442 120 HOH HOH . K 4 HOH B 43 443 68 HOH HOH . K 4 HOH B 44 444 105 HOH HOH . K 4 HOH B 45 445 100 HOH HOH . K 4 HOH B 46 446 71 HOH HOH . K 4 HOH B 47 447 121 HOH HOH . L 4 HOH C 1 401 9 HOH HOH . L 4 HOH C 2 402 29 HOH HOH . L 4 HOH C 3 403 94 HOH HOH . L 4 HOH C 4 404 57 HOH HOH . L 4 HOH C 5 405 64 HOH HOH . L 4 HOH C 6 406 75 HOH HOH . L 4 HOH C 7 407 98 HOH HOH . L 4 HOH C 8 408 8 HOH HOH . L 4 HOH C 9 409 101 HOH HOH . L 4 HOH C 10 410 114 HOH HOH . L 4 HOH C 11 411 102 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 . . . G 3 -25.603 -27.268 -17.218 1 148.16 ? C1 NAG 301 B 1 HETATM 2 C C2 NAG . . . G 3 -25.864 -26.929 -18.651 1 147.72 ? C2 NAG 301 B 1 HETATM 3 C C3 NAG . . . G 3 -26.337 -25.491 -18.711 1 148.79 ? C3 NAG 301 B 1 HETATM 4 C C4 NAG . . . G 3 -27.549 -25.301 -17.8 1 151.95 ? C4 NAG 301 B 1 HETATM 5 C C5 NAG . . . G 3 -27.428 -26.016 -16.437 1 153.1 ? C5 NAG 301 B 1 HETATM 6 C C6 NAG . . . G 3 -28.769 -26.206 -15.761 1 154.46 ? C6 NAG 301 B 1 HETATM 7 C C7 NAG . . . G 3 -24.451 -28.26 -20.15 1 146.33 ? C7 NAG 301 B 1 HETATM 8 C C8 NAG . . . G 3 -23.173 -28.317 -20.938 1 144.53 ? C8 NAG 301 B 1 HETATM 9 N N2 NAG . . . G 3 -24.677 -27.127 -19.469 1 147.23 ? N2 NAG 301 B 1 HETATM 10 O O3 NAG . . . G 3 -26.641 -25.108 -20.047 1 148.91 ? O3 NAG 301 B 1 HETATM 11 O O4 NAG . . . G 3 -27.72 -23.914 -17.533 1 150.42 ? O4 NAG 301 B 1 HETATM 12 O O5 NAG . . . G 3 -26.828 -27.323 -16.527 1 151.16 ? O5 NAG 301 B 1 HETATM 13 O O6 NAG . . . G 3 -28.65 -26.385 -14.356 1 154.21 ? O6 NAG 301 B 1 HETATM 14 O O7 NAG . . . G 3 -25.249 -29.201 -20.136 1 146.48 ? O7 NAG 301 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #