data_3GKH # _model_server_result.job_id qSWswr_ddc-2sXz9JUxCug _model_server_result.datetime_utc '2024-11-16 09:50:21' _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 3gkh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":3}' # _entry.id 3GKH # _exptl.entry_id 3GKH _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 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 3GKH _cell.length_a 66.181 _cell.length_b 66.181 _cell.length_c 82.644 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GKH _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 B NAG 1 B 1 NAG B 1 NAG 2 n B NAG 2 B 2 NAG B 2 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 5 A CYS 25 1_555 A SG CYS 54 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 11 A CYS 31 1_555 A SG CYS 22 A CYS 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 43 A CYS 63 1_555 A SG CYS 89 A CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 A SG CYS 55 A CYS 75 1_555 A SG CYS 93 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf5 A SG CYS 77 A CYS 97 1_555 A SG CYS 218 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 A SG CYS 80 A CYS 100 1_555 A SG CYS 140 A CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf7 A SG CYS 157 A CYS 177 1_555 A SG CYS 164 A CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf8 A SG CYS 207 A CYS 227 1_555 A SG CYS 223 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf9 A SG CYS 220 A CYS 240 1_555 A SG CYS 227 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 C C1 NAG . A NAG 3 1_555 A ND2 ASN 138 A ASN 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 202 A ASN 222 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? # _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 250 n n C1 O1 NAG sing 251 n n C1 O5 NAG sing 252 n n C1 H1 NAG sing 253 n n C2 C3 NAG sing 254 n n C2 N2 NAG sing 255 n n C2 H2 NAG sing 256 n n C3 C4 NAG sing 257 n n C3 O3 NAG sing 258 n n C3 H3 NAG sing 259 n n C4 C5 NAG sing 260 n n C4 O4 NAG sing 261 n n C4 H4 NAG sing 262 n n C5 C6 NAG sing 263 n n C5 O5 NAG sing 264 n n C5 H5 NAG sing 265 n n C6 O6 NAG sing 266 n n C6 H61 NAG sing 267 n n C6 H62 NAG sing 268 n n C7 C8 NAG sing 269 n n C7 N2 NAG sing 270 n n C7 O7 NAG doub 271 n n C8 H81 NAG sing 272 n n C8 H82 NAG sing 273 n n C8 H83 NAG sing 274 n n N2 HN2 NAG sing 275 n n O1 HO1 NAG sing 276 n n O3 HO3 NAG sing 277 n n O4 HO4 NAG sing 278 n n O6 HO6 NAG sing 279 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 3GKH _atom_sites.fract_transf_matrix[1][1] 0.01511 _atom_sites.fract_transf_matrix[1][2] 0.008724 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017448 _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] 0.0121 _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 C 3 NAG A 1 3 3 NAG NAG . D 4 GOL A 1 253 1 GOL GOL . E 4 GOL A 1 254 2 GOL GOL . F 5 HOH A 1 4 4 HOH HOH . F 5 HOH A 2 5 5 HOH HOH . F 5 HOH A 3 6 6 HOH HOH . F 5 HOH A 4 7 7 HOH HOH . F 5 HOH A 5 8 8 HOH HOH . F 5 HOH A 6 9 9 HOH HOH . F 5 HOH A 7 10 10 HOH HOH . F 5 HOH A 8 11 11 HOH HOH . F 5 HOH A 9 12 12 HOH HOH . F 5 HOH A 10 13 13 HOH HOH . F 5 HOH A 11 14 14 HOH HOH . F 5 HOH A 12 15 15 HOH HOH . F 5 HOH A 13 16 16 HOH HOH . F 5 HOH A 14 17 17 HOH HOH . F 5 HOH A 15 18 18 HOH HOH . F 5 HOH A 16 19 19 HOH HOH . F 5 HOH A 17 20 20 HOH HOH . F 5 HOH A 18 255 1 HOH HOH . F 5 HOH A 19 256 2 HOH HOH . F 5 HOH A 20 257 3 HOH HOH . F 5 HOH A 21 258 21 HOH HOH . F 5 HOH A 22 259 22 HOH HOH . F 5 HOH A 23 260 23 HOH HOH . F 5 HOH A 24 261 24 HOH HOH . F 5 HOH A 25 262 25 HOH HOH . F 5 HOH A 26 263 26 HOH HOH . F 5 HOH A 27 264 27 HOH HOH . F 5 HOH A 28 265 28 HOH HOH . F 5 HOH A 29 266 29 HOH HOH . F 5 HOH A 30 267 30 HOH HOH . F 5 HOH A 31 268 31 HOH HOH . F 5 HOH A 32 269 32 HOH HOH . F 5 HOH A 33 270 33 HOH HOH . F 5 HOH A 34 271 34 HOH HOH . F 5 HOH A 35 272 35 HOH HOH . F 5 HOH A 36 273 36 HOH HOH . F 5 HOH A 37 274 37 HOH HOH . F 5 HOH A 38 275 38 HOH HOH . F 5 HOH A 39 276 39 HOH HOH . F 5 HOH A 40 277 40 HOH HOH . F 5 HOH A 41 278 41 HOH HOH . F 5 HOH A 42 279 42 HOH HOH . F 5 HOH A 43 280 43 HOH HOH . F 5 HOH A 44 281 44 HOH HOH . F 5 HOH A 45 282 45 HOH HOH . F 5 HOH A 46 283 46 HOH HOH . F 5 HOH A 47 284 47 HOH HOH . F 5 HOH A 48 285 48 HOH HOH . F 5 HOH A 49 286 49 HOH HOH . F 5 HOH A 50 287 50 HOH HOH . F 5 HOH A 51 288 51 HOH HOH . F 5 HOH A 52 289 52 HOH HOH . F 5 HOH A 53 290 53 HOH HOH . F 5 HOH A 54 291 54 HOH HOH . F 5 HOH A 55 292 55 HOH HOH . F 5 HOH A 56 293 56 HOH HOH . F 5 HOH A 57 294 57 HOH HOH . F 5 HOH A 58 295 58 HOH HOH . F 5 HOH A 59 296 59 HOH HOH . F 5 HOH A 60 297 60 HOH HOH . F 5 HOH A 61 298 61 HOH HOH . F 5 HOH A 62 299 62 HOH HOH . F 5 HOH A 63 300 63 HOH HOH . F 5 HOH A 64 301 64 HOH HOH . F 5 HOH A 65 302 65 HOH HOH . F 5 HOH A 66 303 66 HOH HOH . F 5 HOH A 67 304 67 HOH HOH . F 5 HOH A 68 305 68 HOH HOH . F 5 HOH A 69 306 69 HOH HOH . F 5 HOH A 70 307 70 HOH HOH . F 5 HOH A 71 308 71 HOH HOH . F 5 HOH A 72 309 72 HOH HOH . F 5 HOH A 73 310 73 HOH HOH . F 5 HOH A 74 311 74 HOH HOH . F 5 HOH A 75 312 75 HOH HOH . F 5 HOH A 76 313 76 HOH HOH . F 5 HOH A 77 314 77 HOH HOH . F 5 HOH A 78 315 78 HOH HOH . F 5 HOH A 79 316 79 HOH HOH . F 5 HOH A 80 317 80 HOH HOH . F 5 HOH A 81 318 81 HOH HOH . F 5 HOH A 82 319 82 HOH HOH . F 5 HOH A 83 320 83 HOH HOH . F 5 HOH A 84 321 84 HOH HOH . F 5 HOH A 85 322 85 HOH HOH . F 5 HOH A 86 323 86 HOH HOH . F 5 HOH A 87 324 87 HOH HOH . F 5 HOH A 88 325 88 HOH HOH . F 5 HOH A 89 326 89 HOH HOH . F 5 HOH A 90 327 90 HOH HOH . F 5 HOH A 91 328 91 HOH HOH . F 5 HOH A 92 329 92 HOH HOH . F 5 HOH A 93 330 93 HOH HOH . F 5 HOH A 94 331 94 HOH HOH . F 5 HOH A 95 332 95 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 . . . C 3 -18.208 -38.189 -10.702 1 41.51 ? C1 NAG 3 A 1 HETATM 2 C C2 NAG . . . C 3 -18.005 -37.413 -12.008 1 43.51 ? C2 NAG 3 A 1 HETATM 3 C C3 NAG . . . C 3 -17.393 -38.294 -13.106 1 43.35 ? C3 NAG 3 A 1 HETATM 4 C C4 NAG . . . C 3 -16.272 -39.207 -12.606 1 43.41 ? C4 NAG 3 A 1 HETATM 5 C C5 NAG . . . C 3 -16.534 -39.768 -11.205 1 43.31 ? C5 NAG 3 A 1 HETATM 6 C C6 NAG . . . C 3 -15.284 -40.4 -10.614 1 44.41 ? C6 NAG 3 A 1 HETATM 7 C C7 NAG . . . C 3 -20.421 -37.37 -12.666 1 45.26 ? C7 NAG 3 A 1 HETATM 8 C C8 NAG . . . C 3 -21.475 -36.579 -13.388 1 44.58 ? C8 NAG 3 A 1 HETATM 9 N N2 NAG . . . C 3 -19.229 -36.777 -12.486 1 43.58 ? N2 NAG 3 A 1 HETATM 10 O O3 NAG . . . C 3 -16.882 -37.468 -14.13 1 44.38 ? O3 NAG 3 A 1 HETATM 11 O O4 NAG . . . C 3 -16.141 -40.284 -13.513 1 44.53 ? O4 NAG 3 A 1 HETATM 12 O O5 NAG . . . C 3 -16.967 -38.755 -10.31 1 43.33 ? O5 NAG 3 A 1 HETATM 13 O O6 NAG . . . C 3 -15.64 -41.017 -9.398 1 44.57 ? O6 NAG 3 A 1 HETATM 14 O O7 NAG . . . C 3 -20.709 -38.494 -12.261 1 46.68 ? O7 NAG 3 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #