data_6W4M # _model_server_result.job_id 6pQhh4GDQI6E-a3RmvnWTQ _model_server_result.datetime_utc '2024-10-19 08:22:56' _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 6w4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":509}' # _entry.id 6W4M # _exptl.entry_id 6W4M _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 9 _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 6W4M _cell.length_a 52.687 _cell.length_b 69.522 _cell.length_c 213.468 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6W4M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H N N ? 5 I N N ? 5 J N N ? 5 K N N ? 5 L N N ? 5 M 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 11 G CYS 54 1_555 A SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 A SG CYS 76 G CYS 119 1_555 A SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 102 G CYS 218 1_555 A SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 A SG CYS 112 G CYS 228 1_555 A SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 180 G CYS 296 1_555 A SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 A SG CYS 245 G CYS 378 1_555 A SG CYS 306 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 252 G CYS 385 1_555 A SG CYS 279 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 A SG CYS 262 G CYS 395 1_555 A SG CYS 271 G CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 B SG CYS 23 L CYS 23 1_555 B SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 B SG CYS 135 L CYS 134 1_555 B SG CYS 195 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf11 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 C SG CYS 159 H CYS 140 1_555 C SG CYS 215 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 D SG CYS 6 N CYS 6 1_555 D SG CYS 24 N CYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf14 D SG CYS 10 N CYS 10 1_555 D SG CYS 26 N CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 118 G ASN 234 1_555 E C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 125 G ASN 241 1_555 F C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 146 G ASN 262 1_555 G C1 NAG . G NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 160 G ASN 276 1_555 H C1 NAG . G NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 173 G ASN 289 1_555 I C1 NAG . G NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 A ND2 ASN 179 G ASN 295 1_555 J C1 NAG . G NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 A ND2 ASN 202 G ASN 334 1_555 K C1 NAG . G NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 A ND2 ASN 253 G ASN 386 1_555 L C1 NAG . G NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale9 A ND2 ASN 259 G ASN 392 1_555 M C1 NAG . G NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 C C SER 104 H SER 100 1_555 C N TYS 105 H TYS 100 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.336 ? covale ? covale11 C C TYS 105 H TYS 100 1_555 C N TYS 106 H TYS 100 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 C C TYS 106 H TYS 100 1_555 C N GLU 107 H GLU 100 1_555 B ? ? C ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 D C MPT 1 N MPT 1 1_555 D N ASN 2 N ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale14 D SG MPT 1 N MPT 1 1_555 D SG CYS 19 N CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale15 D C ALA 20 N ALA 20 1_555 D N DPR 21 N DPR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale16 D C DPR 21 N DPR 21 1_555 D N THR 22 N THR 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale17 D C THR 22 N THR 22 1_555 D N U2X 23 N U2X 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale18 D C U2X 23 N U2X 23 1_555 D N CYS 24 N CYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale19 D C VAL 27 N VAL 27 1_555 D N NH2 28 N NH2 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? # _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 263 n n C1 O1 NAG sing 264 n n C1 O5 NAG sing 265 n n C1 H1 NAG sing 266 n n C2 C3 NAG sing 267 n n C2 N2 NAG sing 268 n n C2 H2 NAG sing 269 n n C3 C4 NAG sing 270 n n C3 O3 NAG sing 271 n n C3 H3 NAG sing 272 n n C4 C5 NAG sing 273 n n C4 O4 NAG sing 274 n n C4 H4 NAG sing 275 n n C5 C6 NAG sing 276 n n C5 O5 NAG sing 277 n n C5 H5 NAG sing 278 n n C6 O6 NAG sing 279 n n C6 H61 NAG sing 280 n n C6 H62 NAG sing 281 n n C7 C8 NAG sing 282 n n C7 N2 NAG sing 283 n n C7 O7 NAG doub 284 n n C8 H81 NAG sing 285 n n C8 H82 NAG sing 286 n n C8 H83 NAG sing 287 n n N2 HN2 NAG sing 288 n n O1 HO1 NAG sing 289 n n O3 HO3 NAG sing 290 n n O4 HO4 NAG sing 291 n n O6 HO6 NAG sing 292 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 6W4M _atom_sites.fract_transf_matrix[1][1] 0.01898 _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] 0.014384 _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] 0.004685 _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 5 NAG G 1 501 501 NAG NAG . F 5 NAG G 1 502 502 NAG NAG . G 5 NAG G 1 503 503 NAG NAG . H 5 NAG G 1 504 504 NAG NAG . I 5 NAG G 1 505 505 NAG NAG . J 5 NAG G 1 506 506 NAG NAG . K 5 NAG G 1 507 507 NAG NAG . L 5 NAG G 1 508 508 NAG NAG . M 5 NAG G 1 509 509 NAG NAG . # 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 . . . M 5 11.119 46.428 -34.364 1 78.29 ? C1 NAG 509 G 1 HETATM 2 C C2 NAG . . . M 5 11.4 46.065 -35.845 1 91.24 ? C2 NAG 509 G 1 HETATM 3 C C3 NAG . . . M 5 11.896 47.277 -36.643 1 88.77 ? C3 NAG 509 G 1 HETATM 4 C C4 NAG . . . M 5 11.006 48.49 -36.42 1 86.11 ? C4 NAG 509 G 1 HETATM 5 C C5 NAG . . . M 5 10.932 48.773 -34.93 1 89.7 ? C5 NAG 509 G 1 HETATM 6 C C6 NAG . . . M 5 10.094 49.985 -34.585 1 104.42 ? C6 NAG 509 G 1 HETATM 7 C C7 NAG . . . M 5 12.054 43.691 -35.896 1 86.67 ? C7 NAG 509 G 1 HETATM 8 C C8 NAG . . . M 5 13.203 42.728 -35.976 1 71.63 ? C8 NAG 509 G 1 HETATM 9 N N2 NAG . . . M 5 12.375 44.989 -35.92 1 88.66 ? N2 NAG 509 G 1 HETATM 10 O O3 NAG . . . M 5 11.91 46.945 -38.028 1 93.83 ? O3 NAG 509 G 1 HETATM 11 O O4 NAG . . . M 5 11.546 49.619 -37.095 1 80.81 ? O4 NAG 509 G 1 HETATM 12 O O5 NAG . . . M 5 10.33 47.641 -34.291 1 84.57 ? O5 NAG 509 G 1 HETATM 13 O O6 NAG . . . M 5 8.961 50.112 -35.434 1 113.23 ? O6 NAG 509 G 1 HETATM 14 O O7 NAG . . . M 5 10.891 43.31 -35.813 1 87.04 ? O7 NAG 509 G 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 14 #