data_8VF1 # _model_server_result.job_id KKIV-BZjlSzBI5OygRIulA _model_server_result.datetime_utc '2025-03-26 09:37:32' _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 8vf1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 8VF1 # _exptl.entry_id 8VF1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.483 _cell.angle_gamma 90 _cell.entry_id 8VF1 _cell.length_a 55.822 _cell.length_b 80.155 _cell.length_c 95.136 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VF1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 E N N ? 3 F N N ? 3 G N N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 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 2 n C NAG 1 C 1 NAG A 604 NAG 2 n C NAG 2 C 2 NAG A 605 NAG 2 n C BMA 3 C 3 BMA A 606 BMA 2 n C MAN 4 C 4 MAN A 608 MAN 2 n C MAN 5 C 5 MAN A 607 MAN 2 n D NAG 1 D 1 NAG B 603 NAG 2 n D NAG 2 D 2 NAG B 604 NAG 2 n D BMA 3 D 3 BMA B 605 BMA 2 n D MAN 4 D 4 MAN B 606 MAN 2 n D MAN 5 D 5 MAN B 607 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 38 A CYS 189 1_555 A SG CYS 450 A CYS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 65 A CYS 216 1_555 A SG CYS 89 A CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 131 A CYS 282 1_555 A SG CYS 144 A CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 231 A CYS 382 1_555 A SG CYS 244 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 236 A CYS 387 1_555 A SG CYS 348 A CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 A SG CYS 342 A CYS 493 1_555 A SG CYS 352 A CYS 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 A SG CYS 414 A CYS 565 1_555 A SG CYS 423 A CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 B SG CYS 38 B CYS 189 1_555 B SG CYS 450 B CYS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 65 B CYS 216 1_555 B SG CYS 89 B CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 B SG CYS 131 B CYS 282 1_555 B SG CYS 144 B CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 B SG CYS 231 B CYS 382 1_555 B SG CYS 244 B CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 B SG CYS 236 B CYS 387 1_555 B SG CYS 348 B CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf13 B SG CYS 342 B CYS 493 1_555 B SG CYS 352 B CYS 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf14 B SG CYS 414 B CYS 565 1_555 B SG CYS 423 B CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 266 A ASN 417 1_555 F C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 330 A ASN 481 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale3 A ND2 ASN 378 A ASN 529 1_555 E C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 B ND2 ASN 378 B ASN 529 1_555 G C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.51 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale12 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _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 8VF1 _atom_sites.fract_transf_matrix[1][1] 0.017914 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005301 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012476 _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] 0.010962 _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 NAG A 1 701 609 NAG NAG . F 3 NAG A 1 702 610 NAG NAG . G 3 NAG B 1 701 608 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 . . . E 3 3.977 5.244 11.241 1 58.61 ? C1 NAG 701 A 1 HETATM 2 C C2 NAG . . . E 3 5.312 5.561 11.915 1 51.19 ? C2 NAG 701 A 1 HETATM 3 C C3 NAG . . . E 3 5.416 4.851 13.262 1 49.04 ? C3 NAG 701 A 1 HETATM 4 C C4 NAG . . . E 3 4.22 5.199 14.137 1 44.38 ? C4 NAG 701 A 1 HETATM 5 C C5 NAG . . . E 3 2.927 4.86 13.404 1 41.82 ? C5 NAG 701 A 1 HETATM 6 C C6 NAG . . . E 3 1.691 5.293 14.16 1 58.3 ? C6 NAG 701 A 1 HETATM 7 C C7 NAG . . . E 3 7.194 6.091 10.429 1 71.62 ? C7 NAG 701 A 1 HETATM 8 C C8 NAG . . . E 3 8.291 5.532 9.573 1 66.24 ? C8 NAG 701 A 1 HETATM 9 N N2 NAG . . . E 3 6.426 5.194 11.055 1 61.32 ? N2 NAG 701 A 1 HETATM 10 O O3 NAG . . . E 3 6.62 5.249 13.907 1 35.3 ? O3 NAG 701 A 1 HETATM 11 O O4 NAG . . . E 3 4.283 4.477 15.361 1 66.61 ? O4 NAG 701 A 1 HETATM 12 O O5 NAG . . . E 3 2.891 5.542 12.141 1 54.75 ? O5 NAG 701 A 1 HETATM 13 O O6 NAG . . . E 3 1.353 4.375 15.189 1 68.92 ? O6 NAG 701 A 1 HETATM 14 O O7 NAG . . . E 3 7.013 7.299 10.547 1 61.68 ? O7 NAG 701 A 1 HETATM 15 H H2 NAG . . . E 3 5.348 6.522 12.081 1 62.21 ? H2 NAG 701 A 1 HETATM 16 H H3 NAG . . . E 3 5.435 3.886 13.115 1 59.63 ? H3 NAG 701 A 1 HETATM 17 H H4 NAG . . . E 3 4.235 6.156 14.331 1 54.04 ? H4 NAG 701 A 1 HETATM 18 H H5 NAG . . . E 3 2.888 3.897 13.25 1 50.97 ? H5 NAG 701 A 1 HETATM 19 H H61 NAG . . . E 3 0.944 5.36 13.536 1 70.74 ? H61 NAG 701 A 1 HETATM 20 H H62 NAG . . . E 3 1.852 6.17 14.557 1 70.74 ? H62 NAG 701 A 1 HETATM 21 H H81 NAG . . . E 3 8.789 6.264 9.164 1 80.27 ? H81 NAG 701 A 1 HETATM 22 H H82 NAG . . . E 3 7.904 4.971 8.874 1 80.27 ? H82 NAG 701 A 1 HETATM 23 H H83 NAG . . . E 3 8.893 4.997 10.124 1 80.27 ? H83 NAG 701 A 1 HETATM 24 H HN2 NAG . . . E 3 6.603 4.308 10.929 1 74.37 ? HN2 NAG 701 A 1 HETATM 25 H HO3 NAG . . . E 3 6.52 5.183 14.787 1 43.14 ? HO3 NAG 701 A 1 HETATM 26 H HO4 NAG . . . E 3 3.673 3.832 15.356 1 80.71 ? HO4 NAG 701 A 1 HETATM 27 H HO6 NAG . . . E 3 0.537 4.554 15.489 1 83.49 ? HO6 NAG 701 A 1 # _model_server_stats.io_time_ms 276 _model_server_stats.parse_time_ms 77 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #