data_5KVM # _model_server_result.job_id 6oX12aOj-DZ-cznLdgcuLw _model_server_result.datetime_utc '2025-01-09 02:04:47' _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 5kvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":900}' # _entry.id 5KVM # _exptl.entry_id 5KVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 5KVM _cell.length_a 120.336 _cell.length_b 120.336 _cell.length_c 72.85 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 BMA BMA C1 O1 . O6 HO6 . sing 4 ? 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 D 1 NAG A 901 NAG 4 n D NAG 2 D 2 NAG A 902 NAG 4 n D BMA 3 D 3 BMA A 903 BMA 4 n D BMA 4 D 4 BMA A 904 BMA 5 n E NAG 1 E 1 NAG A 905 NAG 5 n E NAG 2 E 2 NAG A 906 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 8 A CYS 35 1_555 A SG CYS 64 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 94 A CYS 121 1_555 A SG CYS 150 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 319 A CYS 346 1_555 A SG CYS 350 A CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 A SG CYS 339 A CYS 366 1_555 A SG CYS 352 A CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 12 A ASN 39 1_555 F C1 NAG . A NAG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 121 A ASN 148 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 207 A ASN 234 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 D O6 BMA . D BMA 3 1_555 D C1 BMA . D BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 274 n n C1 O1 NAG sing 275 n n C1 O5 NAG sing 276 n n C1 H1 NAG sing 277 n n C2 C3 NAG sing 278 n n C2 N2 NAG sing 279 n n C2 H2 NAG sing 280 n n C3 C4 NAG sing 281 n n C3 O3 NAG sing 282 n n C3 H3 NAG sing 283 n n C4 C5 NAG sing 284 n n C4 O4 NAG sing 285 n n C4 H4 NAG sing 286 n n C5 C6 NAG sing 287 n n C5 O5 NAG sing 288 n n C5 H5 NAG sing 289 n n C6 O6 NAG sing 290 n n C6 H61 NAG sing 291 n n C6 H62 NAG sing 292 n n C7 C8 NAG sing 293 n n C7 N2 NAG sing 294 n n C7 O7 NAG doub 295 n n C8 H81 NAG sing 296 n n C8 H82 NAG sing 297 n n C8 H83 NAG sing 298 n n N2 HN2 NAG sing 299 n n O1 HO1 NAG sing 300 n n O3 HO3 NAG sing 301 n n O4 HO4 NAG sing 302 n n O6 HO6 NAG sing 303 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 5KVM _atom_sites.fract_transf_matrix[1][1] 0.00831 _atom_sites.fract_transf_matrix[1][2] 0.004798 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009596 _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] 0.013727 _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 F 6 NAG A 1 900 900 NAG NAG . G 7 GOL A 1 907 907 GOL GOL . H 8 HOH A 1 1001 10 HOH HOH . H 8 HOH A 2 1002 6 HOH HOH . H 8 HOH A 3 1003 13 HOH HOH . H 8 HOH A 4 1004 16 HOH HOH . H 8 HOH A 5 1005 18 HOH HOH . H 8 HOH A 6 1006 11 HOH HOH . H 8 HOH A 7 1007 2 HOH HOH . H 8 HOH A 8 1008 20 HOH HOH . H 8 HOH A 9 1009 5 HOH HOH . H 8 HOH A 10 1010 23 HOH HOH . H 8 HOH A 11 1011 12 HOH HOH . H 8 HOH A 12 1012 8 HOH HOH . I 8 HOH B 1 401 17 HOH HOH . J 8 HOH C 1 101 14 HOH HOH . J 8 HOH C 2 102 3 HOH HOH . J 8 HOH C 3 103 7 HOH HOH . J 8 HOH C 4 104 19 HOH HOH . J 8 HOH C 5 105 4 HOH HOH . J 8 HOH C 6 106 1 HOH HOH . J 8 HOH C 7 107 22 HOH HOH . J 8 HOH C 8 108 9 HOH HOH . J 8 HOH C 9 109 24 HOH HOH . J 8 HOH C 10 110 15 HOH HOH . J 8 HOH C 11 111 21 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 . . . F 6 25.912 14.668 38.46 1 89.71 ? C1 NAG 900 A 1 HETATM 2 C C2 NAG . . . F 6 26.692 13.503 39.089 1 108.28 ? C2 NAG 900 A 1 HETATM 3 C C3 NAG . . . F 6 26.146 13.177 40.477 1 112.28 ? C3 NAG 900 A 1 HETATM 4 C C4 NAG . . . F 6 26.14 14.422 41.351 1 111.24 ? C4 NAG 900 A 1 HETATM 5 C C5 NAG . . . F 6 25.35 15.531 40.663 1 110.48 ? C5 NAG 900 A 1 HETATM 6 C C6 NAG . . . F 6 25.385 16.837 41.423 1 107.4 ? C6 NAG 900 A 1 HETATM 7 C C7 NAG . . . F 6 25.589 11.607 37.938 1 112.59 ? C7 NAG 900 A 1 HETATM 8 C C8 NAG . . . F 6 25.806 10.422 37.048 1 107.62 ? C8 NAG 900 A 1 HETATM 9 N N2 NAG . . . F 6 26.684 12.321 38.238 1 110.41 ? N2 NAG 900 A 1 HETATM 10 O O3 NAG . . . F 6 26.942 12.16 41.074 1 111.14 ? O3 NAG 900 A 1 HETATM 11 O O4 NAG . . . F 6 25.543 14.131 42.609 1 105.65 ? O4 NAG 900 A 1 HETATM 12 O O5 NAG . . . F 6 25.905 15.793 39.364 1 101.79 ? O5 NAG 900 A 1 HETATM 13 O O6 NAG . . . F 6 25.45 17.956 40.549 1 108.13 ? O6 NAG 900 A 1 HETATM 14 O O7 NAG . . . F 6 24.475 11.903 38.363 1 114.85 ? O7 NAG 900 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #