data_6PGQ # _model_server_result.job_id 2-e2SNuXIQUiFJuw6qQ2Mw _model_server_result.datetime_utc '2024-11-23 18:02:08' _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 6pgq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6PGQ # _exptl.entry_id 6PGQ _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 3 _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 6PGQ _cell.length_a 181.288 _cell.length_b 181.288 _cell.length_c 181.288 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PGQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 3 2' # _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,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 D N N ? 4 E N N ? 4 F N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 GLC _pdbx_entity_branch_link.comp_id_2 GLC _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 3 n C GLC 1 C 1 GLC A 500 MAL 3 n C GLC 2 C 2 GLC A 500 MAL # 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 390 A CYS 55 1_555 A SG CYS 416 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? disulf ? disulf2 A SG CYS 407 A CYS 72 1_555 A SG CYS 447 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf3 A SG CYS 430 A CYS 95 1_555 A SG CYS 469 A CYS 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? covale ? covale1 A ND2 ASN 408 A ASN 73 1_555 D C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale2 A ND2 ASN 460 A ASN 125 1_555 E C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale3 A ND2 ASN 465 A ASN 130 1_555 F C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale4 B C PRO 11 B PRO 32 1_555 B N NH2 12 B NH2 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale5 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 sing # _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 267 n n C1 O1 NAG sing 268 n n C1 O5 NAG sing 269 n n C1 H1 NAG sing 270 n n C2 C3 NAG sing 271 n n C2 N2 NAG sing 272 n n C2 H2 NAG sing 273 n n C3 C4 NAG sing 274 n n C3 O3 NAG sing 275 n n C3 H3 NAG sing 276 n n C4 C5 NAG sing 277 n n C4 O4 NAG sing 278 n n C4 H4 NAG sing 279 n n C5 C6 NAG sing 280 n n C5 O5 NAG sing 281 n n C5 H5 NAG sing 282 n n C6 O6 NAG sing 283 n n C6 H61 NAG sing 284 n n C6 H62 NAG sing 285 n n C7 C8 NAG sing 286 n n C7 N2 NAG sing 287 n n C7 O7 NAG doub 288 n n C8 H81 NAG sing 289 n n C8 H82 NAG sing 290 n n C8 H83 NAG sing 291 n n N2 HN2 NAG sing 292 n n O1 HO1 NAG sing 293 n n O3 HO3 NAG sing 294 n n O4 HO4 NAG sing 295 n n O6 HO6 NAG sing 296 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 6PGQ _atom_sites.fract_transf_matrix[1][1] 0.005516 _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] 0.005516 _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] 0.005516 _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 D 4 NAG A 1 501 501 NAG NAG . E 4 NAG A 1 502 502 NAG NAG . F 4 NAG A 1 503 503 NAG NAG . G 5 ACT A 1 504 504 ACT ACT . H 6 HOH A 1 601 1 HOH HOH . H 6 HOH A 2 602 2 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 . . . D 4 -33.352 -29.084 -7.696 1 128.23 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . D 4 -34.379 -29.975 -8.406 1 133.7 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . D 4 -33.911 -30.255 -9.831 1 140.98 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . D 4 -33.52 -28.963 -10.547 1 144.96 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . D 4 -32.462 -28.22 -9.735 1 132.68 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . D 4 -31.997 -26.918 -10.356 1 123.4 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . D 4 -33.769 -31.972 -7.053 1 138.11 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . D 4 -34.304 -33.097 -6.209 1 130.45 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . D 4 -34.673 -31.213 -7.703 1 139.91 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . D 4 -34.951 -30.931 -10.529 1 147.22 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . D 4 -32.997 -29.253 -11.842 1 159.28 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . D 4 -33.052 -27.916 -8.452 1 131.93 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . D 4 -33.06 -25.976 -10.446 1 111.04 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . D 4 -32.564 -31.74 -7.132 1 128.78 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #