data_6XPX # _model_server_result.job_id hQTb4xKs4ryP14M8NiRywQ _model_server_result.datetime_utc '2024-10-17 09:24:06' _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 6xpx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 6XPX # _exptl.entry_id 6XPX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 108.01 _cell.angle_gamma 90 _cell.entry_id 6XPX _cell.length_a 68.42 _cell.length_b 101.56 _cell.length_c 77.41 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XPX _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,K,L,M,N,O,P,Q,R,S _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 ? 5 E N N ? 5 F N N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 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 4 n D NAG 1 D 1 NAG A 802 NAG 4 n D NAG 2 D 2 NAG A 803 NAG 4 n D BMA 3 D 3 BMA A 804 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 16 A CYS 52 1_555 A SG CYS 241 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? disulf ? disulf2 A SG CYS 28 A CYS 64 1_555 A SG CYS 40 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? disulf ? disulf3 A SG CYS 61 A CYS 97 1_555 A SG CYS 103 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf4 A SG CYS 245 A CYS 281 1_555 A SG CYS 269 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf5 B SG CYS 23 C CYS 23 1_555 B SG CYS 94 C CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf6 B SG CYS 140 C CYS 140 1_555 B SG CYS 200 C CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf7 C SG CYS 22 B CYS 22 1_555 C SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? disulf ? disulf8 C SG CYS 143 B CYS 143 1_555 C SG CYS 199 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? covale ? covale1 A ND2 ASN 45 A ASN 81 1_555 F C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 A ND2 ASN 129 A ASN 165 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale3 A ND2 ASN 249 A ASN 285 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 334 n n C1 O1 NAG sing 335 n n C1 O5 NAG sing 336 n n C1 H1 NAG sing 337 n n C2 C3 NAG sing 338 n n C2 N2 NAG sing 339 n n C2 H2 NAG sing 340 n n C3 C4 NAG sing 341 n n C3 O3 NAG sing 342 n n C3 H3 NAG sing 343 n n C4 C5 NAG sing 344 n n C4 O4 NAG sing 345 n n C4 H4 NAG sing 346 n n C5 C6 NAG sing 347 n n C5 O5 NAG sing 348 n n C5 H5 NAG sing 349 n n C6 O6 NAG sing 350 n n C6 H61 NAG sing 351 n n C6 H62 NAG sing 352 n n C7 C8 NAG sing 353 n n C7 N2 NAG sing 354 n n C7 O7 NAG doub 355 n n C8 H81 NAG sing 356 n n C8 H82 NAG sing 357 n n C8 H83 NAG sing 358 n n N2 HN2 NAG sing 359 n n O1 HO1 NAG sing 360 n n O3 HO3 NAG sing 361 n n O4 HO4 NAG sing 362 n n O6 HO6 NAG sing 363 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 6XPX _atom_sites.fract_transf_matrix[1][1] 0.014616 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004753 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009846 _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] 0.013584 _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 5 NAG A 1 401 312 NAG NAG . F 5 NAG A 1 402 313 NAG NAG . G 6 BCN A 1 403 401 BCN BCN . H 7 GOL A 1 404 501 GOL GOL . I 7 GOL A 1 405 601 GOL GOL . J 6 BCN A 1 406 701 BCN BCN . K 7 GOL A 1 407 801 GOL GOL . L 8 1PE C 1 301 301 1PE 1PE . M 7 GOL C 1 302 401 GOL GOL . N 7 GOL C 1 303 601 GOL GOL . O 7 GOL C 1 304 701 GOL GOL . P 7 GOL B 1 501 501 GOL GOL . Q 9 HOH A 1 501 3 HOH HOH . Q 9 HOH A 2 502 2 HOH HOH . Q 9 HOH A 3 503 13 HOH HOH . Q 9 HOH A 4 504 4 HOH HOH . Q 9 HOH A 5 505 8 HOH HOH . Q 9 HOH A 6 506 9 HOH HOH . Q 9 HOH A 7 507 12 HOH HOH . R 9 HOH C 1 401 5 HOH HOH . R 9 HOH C 2 402 11 HOH HOH . R 9 HOH C 3 403 10 HOH HOH . R 9 HOH C 4 404 6 HOH HOH . R 9 HOH C 5 405 16 HOH HOH . R 9 HOH C 6 406 1 HOH HOH . R 9 HOH C 7 407 15 HOH HOH . S 9 HOH B 1 601 14 HOH HOH . S 9 HOH B 2 602 7 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 . . . E 5 -28.669 0.612 -32.279 1 92.21 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . E 5 -28.936 0.447 -33.802 1 99.96 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . E 5 -28.332 1.624 -34.578 1 104.63 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . E 5 -28.904 2.939 -34.06 1 104.73 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . E 5 -28.565 3.082 -32.567 1 103.67 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . E 5 -29.131 4.326 -31.927 1 106.45 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . E 5 -29.175 -1.736 -34.886 1 108.14 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . E 5 -28.481 -2.991 -35.342 1 106.74 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . E 5 -28.407 -0.813 -34.299 1 103.62 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . E 5 -28.527 1.494 -35.987 1 105.21 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . E 5 -28.398 4.018 -34.842 1 103.75 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . E 5 -29.113 1.975 -31.831 1 100.45 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . E 5 -29.239 5.383 -32.873 1 111.07 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . E 5 -30.378 -1.566 -35.041 1 113.19 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #