data_8GP5 # _model_server_result.job_id j5Uf_jH3r97pKaUNnbNxQg _model_server_result.datetime_utc '2025-03-05 02:59:18' _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 8gp5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":703}' # _entry.id 8GP5 # _exptl.entry_id 8GP5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _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 8GP5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GP5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _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 _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 ? _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 ? 6 K N N ? 6 L N N ? 6 M N N ? 6 N N N ? 6 O N N ? 6 P N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 5 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . 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 N 1 NAG N 508 NAG 4 n D NAG 2 N 2 NAG N 509 NAG 4 n D BMA 3 N 3 BMA N 510 BMA 4 n D MAN 4 N 4 MAN N 511 MAN 4 n D MAN 5 N 5 MAN N 512 MAN 5 n E NAG 1 A 1 NAG N 514 NAG 5 n E NAG 2 A 2 NAG N 522 NAG 4 n F NAG 1 B 1 NAG N 517 NAG 4 n F NAG 2 B 2 NAG N 518 NAG 4 n F BMA 3 B 3 BMA N 519 BMA 4 n F MAN 4 B 4 MAN N 521 MAN 4 n F MAN 5 B 5 MAN N 520 MAN 5 n G NAG 1 C 1 NAG N 523 NAG 5 n G NAG 2 C 2 NAG N 524 NAG 5 n H NAG 1 D 1 NAG N 525 NAG 5 n H NAG 2 D 2 NAG N 530 NAG 5 n I NAG 1 G 1 NAG N 527 NAG 5 n I NAG 2 G 2 NAG N 528 NAG 5 n J NAG 1 H 1 NAG N 651 NAG 5 n J NAG 2 H 2 NAG N 652 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 22 E CYS 22 1_555 A SG CYS 95 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 23 F CYS 23 1_555 B SG CYS 93 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 C SG CYS 22 X CYS 54 1_555 C SG CYS 42 X CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 C SG CYS 195 X CYS 218 1_555 C SG CYS 224 X CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf5 C SG CYS 205 X CYS 228 1_555 C SG CYS 216 X CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 C SG CYS 273 X CYS 296 1_555 C SG CYS 307 X CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 C SG CYS 352 X CYS 378 1_555 C SG CYS 410 X CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 359 X CYS 385 1_555 C SG CYS 383 X CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 C SG CYS 466 X CYS 501 1_555 C SG CYS 563 X CYS 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 C SG CYS 556 X CYS 598 1_555 C SG CYS 562 X CYS 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 C ND2 ASN 56 X ASN 88 1_555 D C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 C ND2 ASN 211 X ASN 234 1_555 E C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C ND2 ASN 218 X ASN 241 1_555 K C1 NAG . X NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 C ND2 ASN 239 X ASN 262 1_555 F C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 C ND2 ASN 253 X ASN 276 1_555 G C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 C ND2 ASN 266 X ASN 289 1_555 L C1 NAG . X NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 C ND2 ASN 310 X ASN 334 1_555 H C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C ND2 ASN 315 X ASN 339 1_555 N C1 NAG . X NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 C ND2 ASN 360 X ASN 386 1_555 I C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 C ND2 ASN 409 X ASN 444 1_555 O C1 NAG . X NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale11 C ND2 ASN 413 X ASN 448 1_555 M C1 NAG . X NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale12 C ND2 ASN 569 X ASN 611 1_555 P C1 NAG . X NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale13 C ND2 ASN 583 X ASN 625 1_555 J C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale14 D O4 NAG . N NAG 1 1_555 D C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale15 D O4 NAG . N NAG 2 1_555 D C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 D O3 BMA . N BMA 3 1_555 D C1 MAN . N MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale17 D O6 BMA . N BMA 3 1_555 D C1 MAN . N MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale18 E O4 NAG . A NAG 1 1_555 E C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale19 F O4 NAG . B NAG 1 1_555 F C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale20 F O4 NAG . B NAG 2 1_555 F C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale21 F O3 BMA . B BMA 3 1_555 F C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale22 F O6 BMA . B BMA 3 1_555 F C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale23 G O4 NAG . C NAG 1 1_555 G C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale24 H O4 NAG . D NAG 1 1_555 H C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale25 I O4 NAG . G NAG 1 1_555 I C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale26 J O4 NAG . H NAG 1 1_555 J C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 8GP5 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 K 6 NAG X 1 701 513 NAG NAG . L 6 NAG X 1 702 515 NAG NAG . M 6 NAG X 1 703 516 NAG NAG . N 6 NAG X 1 704 526 NAG NAG . O 6 NAG X 1 705 529 NAG NAG . P 6 NAG X 1 706 653 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 6 148.597 108.851 173.035 1 91.73 ? C1 NAG 703 X 1 HETATM 2 C C2 NAG . . . M 6 147.971 109.503 171.807 1 91.73 ? C2 NAG 703 X 1 HETATM 3 C C3 NAG . . . M 6 146.559 109.973 172.132 1 91.73 ? C3 NAG 703 X 1 HETATM 4 C C4 NAG . . . M 6 145.731 108.814 172.67 1 91.73 ? C4 NAG 703 X 1 HETATM 5 C C5 NAG . . . M 6 146.442 108.157 173.851 1 91.73 ? C5 NAG 703 X 1 HETATM 6 C C6 NAG . . . M 6 145.745 106.905 174.331 1 91.73 ? C6 NAG 703 X 1 HETATM 7 C C7 NAG . . . M 6 148.865 110.943 170.033 1 91.73 ? C7 NAG 703 X 1 HETATM 8 C C8 NAG . . . M 6 149.744 112.113 169.712 1 91.73 ? C8 NAG 703 X 1 HETATM 9 N N2 NAG . . . M 6 148.781 110.61 171.325 1 91.73 ? N2 NAG 703 X 1 HETATM 10 O O3 NAG . . . M 6 145.95 110.505 170.962 1 91.73 ? O3 NAG 703 X 1 HETATM 11 O O4 NAG . . . M 6 144.457 109.285 173.093 1 91.73 ? O4 NAG 703 X 1 HETATM 12 O O5 NAG . . . M 6 147.772 107.767 173.476 1 91.73 ? O5 NAG 703 X 1 HETATM 13 O O6 NAG . . . M 6 145.716 105.91 173.317 1 91.73 ? O6 NAG 703 X 1 HETATM 14 O O7 NAG . . . M 6 148.257 110.328 169.163 1 91.73 ? O7 NAG 703 X 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #