data_6P8M # _model_server_result.job_id QS5K7bCGN9IdDMTBLG01Rw _model_server_result.datetime_utc '2025-04-10 22:17:08' _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 6p8m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":1422}' # _entry.id 6P8M # _exptl.entry_id 6P8M _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 6P8M _cell.length_a 146.796 _cell.length_b 176.755 _cell.length_c 108.573 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6P8M _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T N N ? 5 U N N ? 5 V N N ? 5 W N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type 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 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 5 3 MAN BMA C1 O1 . O6 HO6 . 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 D NAG 1 A 1 NAG C 606 NAG 4 n D NAG 2 A 2 NAG C 607 NAG 4 n D BMA 3 A 3 BMA C 608 BMA 4 n D MAN 4 A 4 MAN C 609 MAN 4 n D MAN 5 A 5 MAN C 610 MAN # 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 C CYS 54 1_555 A SG CYS 31 C CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 22 C CYS 65 1_555 A SG CYS 72 C CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 76 C CYS 119 1_555 A SG CYS 89 C CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 A SG CYS 102 C CYS 218 1_555 A SG CYS 131 C CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 112 C CYS 228 1_555 A SG CYS 123 C CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 180 C CYS 296 1_555 A SG CYS 199 C CYS 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 A SG CYS 245 C CYS 378 1_555 A SG CYS 298 C CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 A SG CYS 252 C CYS 385 1_555 A SG CYS 271 C CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 A SG CYS 312 C CYS 459 1_555 B SG CYS 61 H CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 B SG CYS 148 H CYS 140 1_555 B SG CYS 204 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf12 C SG CYS 23 L CYS 23 1_555 C SG CYS 94 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 C SG CYS 136 L CYS 134 1_555 C SG CYS 196 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 81 C ASN 124 1_555 P C1 NAG . C NAG 1417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 114 C ASN 230 1_555 Q C1 NAG . C NAG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 A ND2 ASN 125 C ASN 241 1_555 R C1 NAG . C NAG 1419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 A ND2 ASN 146 C ASN 262 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 A ND2 ASN 173 C ASN 289 1_555 S C1 NAG . C NAG 1420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 A ND2 ASN 205 C ASN 338 1_555 T C1 NAG . C NAG 1421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 A ND2 ASN 225 C ASN 358 1_555 U C1 NAG . C NAG 1422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 A ND2 ASN 253 C ASN 386 1_555 V C1 NAG . C NAG 1423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale9 A ND2 ASN 259 C ASN 392 1_555 W C1 NAG . C NAG 1424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale10 A ND2 ASN 264 C ASN 397 1_555 E C1 NAG . C NAG 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale11 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale12 D O4 NAG . A NAG 2 1_555 D C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale13 D O3 BMA . A BMA 3 1_555 D C1 MAN . A MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 D O6 BMA . A BMA 3 1_555 D C1 MAN . A MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 294 n n C1 O1 NAG sing 295 n n C1 O5 NAG sing 296 n n C1 H1 NAG sing 297 n n C2 C3 NAG sing 298 n n C2 N2 NAG sing 299 n n C2 H2 NAG sing 300 n n C3 C4 NAG sing 301 n n C3 O3 NAG sing 302 n n C3 H3 NAG sing 303 n n C4 C5 NAG sing 304 n n C4 O4 NAG sing 305 n n C4 H4 NAG sing 306 n n C5 C6 NAG sing 307 n n C5 O5 NAG sing 308 n n C5 H5 NAG sing 309 n n C6 O6 NAG sing 310 n n C6 H61 NAG sing 311 n n C6 H62 NAG sing 312 n n C7 C8 NAG sing 313 n n C7 N2 NAG sing 314 n n C7 O7 NAG doub 315 n n C8 H81 NAG sing 316 n n C8 H82 NAG sing 317 n n C8 H83 NAG sing 318 n n N2 HN2 NAG sing 319 n n O1 HO1 NAG sing 320 n n O3 HO3 NAG sing 321 n n O4 HO4 NAG sing 322 n n O6 HO6 NAG sing 323 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 6P8M _atom_sites.fract_transf_matrix[1][1] 0.006812 _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] 0.005658 _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] 0.00921 _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 C 1 1401 1397 NAG NAG . F 6 NH4 C 1 1402 4 NH4 NH4 . G 6 NH4 C 1 1403 6 NH4 NH4 . H 6 NH4 C 1 1404 7 NH4 NH4 . I 7 EDO C 1 1405 1 EDO EDO . J 7 EDO C 1 1406 2 EDO EDO . K 8 PEG C 1 1407 2 PEG PEG . L 9 NA C 1 1408 1 NA NA . M 9 NA C 1 1409 3 NA NA . N 9 NA C 1 1410 4 NA NA . O 10 CL C 1 1411 1 CL CL . P 5 NAG C 1 1417 1124 NAG NAG . Q 5 NAG C 1 1418 1230 NAG NAG . R 5 NAG C 1 1419 1241 NAG NAG . S 5 NAG C 1 1420 1289 NAG NAG . T 5 NAG C 1 1421 1338 NAG NAG . U 5 NAG C 1 1422 1358 NAG NAG . V 5 NAG C 1 1423 1386 NAG NAG . W 5 NAG C 1 1424 1392 NAG NAG . X 8 PEG H 1 301 1 PEG PEG . Y 9 NA H 1 302 2 NA NA . Z 6 NH4 L 1 301 1 NH4 NH4 . AA 11 HOH C 1 1501 13 HOH HOH . AA 11 HOH C 2 1502 15 HOH HOH . AA 11 HOH C 3 1503 11 HOH HOH . AA 11 HOH C 4 1504 12 HOH HOH . AA 11 HOH C 5 1505 9 HOH HOH . AA 11 HOH C 6 1506 14 HOH HOH . AA 11 HOH C 7 1507 10 HOH HOH . BA 11 HOH L 1 401 6 HOH HOH . BA 11 HOH L 2 402 2 HOH HOH . BA 11 HOH L 3 403 1 HOH HOH . BA 11 HOH L 4 404 8 HOH HOH . BA 11 HOH L 5 405 16 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 . . . U 5 25.01 19.742 24.919 1 122.24 ? C1 NAG 1422 C 1 HETATM 2 C C2 NAG . . . U 5 24.078 18.538 24.884 1 140.21 ? C2 NAG 1422 C 1 HETATM 3 C C3 NAG . . . U 5 22.851 18.758 25.685 1 154.93 ? C3 NAG 1422 C 1 HETATM 4 C C4 NAG . . . U 5 23.185 19.127 27.094 1 160.45 ? C4 NAG 1422 C 1 HETATM 5 C C5 NAG . . . U 5 24.026 20.404 27.132 1 152.6 ? C5 NAG 1422 C 1 HETATM 6 C C6 NAG . . . U 5 24.45 20.673 28.566 1 143.24 ? C6 NAG 1422 C 1 HETATM 7 C C7 NAG . . . U 5 24.39 17.236 22.682 1 130.88 ? C7 NAG 1422 C 1 HETATM 8 C C8 NAG . . . U 5 23.998 16.971 21.232 1 132.33 ? C8 NAG 1422 C 1 HETATM 9 N N2 NAG . . . U 5 23.691 18.273 23.456 1 128.85 ? N2 NAG 1422 C 1 HETATM 10 O O3 NAG . . . U 5 22.059 17.551 25.694 1 150.91 ? O3 NAG 1422 C 1 HETATM 11 O O4 NAG . . . U 5 21.986 19.337 27.832 1 175.14 ? O4 NAG 1422 C 1 HETATM 12 O O5 NAG . . . U 5 25.228 20.301 26.3 1 122.53 ? O5 NAG 1422 C 1 HETATM 13 O O6 NAG . . . U 5 25.495 21.641 28.575 1 126.2 ? O6 NAG 1422 C 1 HETATM 14 O O7 NAG . . . U 5 25.263 16.609 23.183 1 142.59 ? O7 NAG 1422 C 1 HETATM 15 H H2 NAG . . . U 5 24.545 17.767 25.241 1 168.46 ? H2 NAG 1422 C 1 HETATM 16 H H3 NAG . . . U 5 22.329 19.466 25.277 1 186.13 ? H3 NAG 1422 C 1 HETATM 17 H H4 NAG . . . U 5 23.67 18.398 27.51 1 192.76 ? H4 NAG 1422 C 1 HETATM 18 H H5 NAG . . . U 5 23.483 21.141 26.811 1 183.33 ? H5 NAG 1422 C 1 HETATM 19 H H61 NAG . . . U 5 24.767 19.85 28.97 1 172.1 ? H61 NAG 1422 C 1 HETATM 20 H H62 NAG . . . U 5 23.692 21.009 29.07 1 172.1 ? H62 NAG 1422 C 1 HETATM 21 H H81 NAG . . . U 5 23.922 17.815 20.759 1 159.01 ? H81 NAG 1422 C 1 HETATM 22 H H82 NAG . . . U 5 23.146 16.508 21.206 1 159.01 ? H82 NAG 1422 C 1 HETATM 23 H H83 NAG . . . U 5 24.677 16.423 20.808 1 159.01 ? H83 NAG 1422 C 1 HETATM 24 H HN2 NAG . . . U 5 23.059 18.729 23.091 1 154.83 ? HN2 NAG 1422 C 1 HETATM 25 H HO3 NAG . . . U 5 21.383 17.663 26.198 1 181.3 ? HO3 NAG 1422 C 1 HETATM 26 H HO4 NAG . . . U 5 22.177 19.434 28.656 1 210.38 ? HO4 NAG 1422 C 1 HETATM 27 H HO6 NAG . . . U 5 26.184 21.307 28.945 1 151.66 ? HO6 NAG 1422 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #