data_6FKM # _model_server_result.job_id HZxmrQ4d4mQeqXHP1ImW_Q _model_server_result.datetime_utc '2025-01-18 08:50:06' _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 6fkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1000}' # _entry.id 6FKM # _exptl.entry_id 6FKM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _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 90 _cell.angle_gamma 90 _cell.entry_id 6FKM _cell.length_a 130.94 _cell.length_b 195.09 _cell.length_c 124.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 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 3 n C NAG 1 C 1 NAG B 1000 NAG 3 n C NAG 2 C 2 NAG B 1001 NAG 3 n C BMA 3 C 3 BMA B 1002 BMA 3 n C MAN 4 C 4 MAN B 1003 MAN 3 n C MAN 5 C 5 MAN B 1004 MAN 3 n D NAG 1 D 1 NAG B 1005 NAG 3 n D NAG 2 D 2 NAG B 1006 NAG 3 n D BMA 3 D 3 BMA B 1007 BMA 3 n D MAN 4 D 4 MAN B 1008 MAN 3 n D MAN 5 D 5 MAN B 1009 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 95 A CYS 119 1_555 A SG CYS 100 A CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 128 A CYS 152 1_555 A SG CYS 136 A CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 274 A CYS 298 1_555 A SG CYS 396 A CYS 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 A SG CYS 290 A CYS 314 1_555 A SG CYS 347 A CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf5 A SG CYS 365 A CYS 389 1_555 A SG CYS 383 A CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 A SG CYS 499 A CYS 523 1_555 A SG CYS 516 A CYS 540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf7 A SG CYS 505 A CYS 529 1_555 A SG CYS 549 A CYS 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf8 A SG CYS 508 A CYS 532 1_555 A SG CYS 525 A CYS 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf9 A SG CYS 519 A CYS 543 1_555 A SG CYS 531 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 B SG CYS 72 B CYS 105 1_555 B SG CYS 82 B CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 B SG CYS 100 B CYS 133 1_555 B SG CYS 109 B CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 B SG CYS 233 B CYS 266 1_555 B SG CYS 343 B CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf13 B SG CYS 257 B CYS 290 1_555 B SG CYS 302 B CYS 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf14 B SG CYS 478 B CYS 511 1_555 B SG CYS 495 B CYS 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf15 B SG CYS 484 B CYS 517 1_555 B SG CYS 534 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf16 B SG CYS 487 B CYS 520 1_555 B SG CYS 504 B CYS 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 90 A ASN 114 1_555 H C1 NAG . A NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 143 A ASN 167 1_555 E C1 NAG . A NAG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 161 A ASN 185 1_555 F C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 A ND2 ASN 342 A ASN 366 1_555 G C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 A CB ASP 442 A ASP 466 1_555 G O6 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale6 B ND2 ASN 48 B ASN 81 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 B ND2 ASN 256 B ASN 289 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale10 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale12 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale13 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale14 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale15 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _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 6FKM _atom_sites.fract_transf_matrix[1][1] 0.007637 _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] 0.005126 _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] 0.00801 _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 4 NAG A 1 1000 1000 NAG NAG . F 4 NAG A 1 1001 1001 NAG NAG . G 4 NAG A 1 1002 1002 NAG NAG . H 4 NAG A 1 1003 1003 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 4 12.077 20.11 -23.467 1 102.37 ? C1 NAG 1000 A 1 HETATM 2 C C2 NAG . . . E 4 10.735 20.815 -23.374 1 105.61 ? C2 NAG 1000 A 1 HETATM 3 C C3 NAG . . . E 4 10.165 20.673 -21.962 1 114.12 ? C3 NAG 1000 A 1 HETATM 4 C C4 NAG . . . E 4 10.07 19.2 -21.583 1 103.93 ? C4 NAG 1000 A 1 HETATM 5 C C5 NAG . . . E 4 11.404 18.484 -21.798 1 105.42 ? C5 NAG 1000 A 1 HETATM 6 C C6 NAG . . . E 4 11.282 16.986 -21.648 1 101.87 ? C6 NAG 1000 A 1 HETATM 7 C C7 NAG . . . E 4 11.359 23.201 -23.06 1 97.25 ? C7 NAG 1000 A 1 HETATM 8 C C8 NAG . . . E 4 11.341 24.558 -23.7 1 88.87 ? C8 NAG 1000 A 1 HETATM 9 N N2 NAG . . . E 4 10.821 22.21 -23.785 1 101.65 ? N2 NAG 1000 A 1 HETATM 10 O O3 NAG . . . E 4 8.884 21.29 -21.882 1 124.23 ? O3 NAG 1000 A 1 HETATM 11 O O4 NAG . . . E 4 9.704 19.07 -20.214 1 100.21 ? O4 NAG 1000 A 1 HETATM 12 O O5 NAG . . . E 4 11.914 18.72 -23.122 1 107.03 ? O5 NAG 1000 A 1 HETATM 13 O O6 NAG . . . E 4 10.545 16.422 -22.723 1 98.44 ? O6 NAG 1000 A 1 HETATM 14 O O7 NAG . . . E 4 11.832 23.018 -21.943 1 93.79 ? O7 NAG 1000 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #