data_3VKF # _model_server_result.job_id oqqMJtg8llE1s6tZoNt3ag _model_server_result.datetime_utc '2025-03-04 08:44:12' _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 3vkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":2001}' # _entry.id 3VKF # _exptl.entry_id 3VKF _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.62 _cell.angle_gamma 90 _cell.entry_id 3VKF _cell.length_a 81.261 _cell.length_b 95.186 _cell.length_c 120.396 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 PISA monomeric 1 software_defined_assembly 4 PISA monomeric 1 software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1 A,E,F 2 1 B,G 3 1 C,H 4 1 D,I 5 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 F N N ? 4 G 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 # 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 E NAG 1 E 1 NAG A 2002 NAG 3 n E NAG 2 E 2 NAG A 2003 NAG 3 n E BMA 3 E 3 BMA A 2004 BMA # 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 73 A CYS 117 1_555 A SG CYS 109 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf2 A SG CYS 128 A CYS 172 1_555 A SG CYS 137 A CYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 289 A CYS 342 1_555 A SG CYS 300 A CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 459 A CYS 512 1_555 A SG CYS 493 A CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 B SG CYS 73 B CYS 117 1_555 B SG CYS 109 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 B SG CYS 289 B CYS 342 1_555 B SG CYS 300 B CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 B SG CYS 459 B CYS 512 1_555 B SG CYS 493 B CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 290 A ASN 343 1_555 F C1 NAG . A NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 494 A ASN 547 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 B ND2 ASN 290 B ASN 343 1_555 G C1 NAG . B NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? metalc ? metalc1 C OD2 ASP 56 C ASP 136 1_555 H CA CA . C CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc2 C O VAL 73 C VAL 153 1_555 H CA CA . C CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc3 C O ILE 125 C ILE 235 1_555 H CA CA . C CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc4 C OD1 ASN 127 C ASN 237 1_555 H CA CA . C CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc5 D OD2 ASP 56 D ASP 136 1_555 I CA CA . D CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc6 D O VAL 73 D VAL 153 1_555 I CA CA . D CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc7 D O ILE 125 D ILE 235 1_555 I CA CA . D CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc8 D OD1 ASN 127 D ASN 237 1_555 I CA CA . D CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 3VKF _atom_sites.fract_transf_matrix[1][1] 0.012306 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004146 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010506 _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] 0.008765 _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 4 NAG A 1 2001 2001 NAG NAG . G 4 NAG B 1 2001 2001 NAG NAG . H 5 CA C 1 2001 2001 CA CA . I 5 CA D 1 2001 2001 CA CA . # 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 . . . G 4 -22.293 -29.883 -19.718 1 107.46 ? C1 NAG 2001 B 1 HETATM 2 C C2 NAG . . . G 4 -22.309 -30.037 -18.19 1 106.87 ? C2 NAG 2001 B 1 HETATM 3 C C3 NAG . . . G 4 -21.13 -30.838 -17.614 1 108.04 ? C3 NAG 2001 B 1 HETATM 4 C C4 NAG . . . G 4 -20.545 -31.905 -18.547 1 111.67 ? C4 NAG 2001 B 1 HETATM 5 C C5 NAG . . . G 4 -20.546 -31.419 -19.999 1 111.21 ? C5 NAG 2001 B 1 HETATM 6 C C6 NAG . . . G 4 -19.968 -32.432 -20.981 1 114.88 ? C6 NAG 2001 B 1 HETATM 7 C C7 NAG . . . G 4 -23.419 -28.109 -17.154 1 101.22 ? C7 NAG 2001 B 1 HETATM 8 C C8 NAG . . . G 4 -23.354 -27.48 -15.792 1 98.53 ? C8 NAG 2001 B 1 HETATM 9 N N2 NAG . . . G 4 -22.313 -28.718 -17.581 1 102.45 ? N2 NAG 2001 B 1 HETATM 10 O O3 NAG . . . G 4 -21.55 -31.461 -16.422 1 109.63 ? O3 NAG 2001 B 1 HETATM 11 O O4 NAG . . . G 4 -19.233 -32.212 -18.124 1 111.39 ? O4 NAG 2001 B 1 HETATM 12 O O5 NAG . . . G 4 -21.871 -31.074 -20.362 1 111.33 ? O5 NAG 2001 B 1 HETATM 13 O O6 NAG . . . G 4 -20.889 -33.476 -21.196 1 119.29 ? O6 NAG 2001 B 1 HETATM 14 O O7 NAG . . . G 4 -24.452 -28.04 -17.82 1 102.3 ? O7 NAG 2001 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #