data_3BPO # _model_server_result.job_id EBJf0SzBudWF-ViQNxlROg _model_server_result.datetime_utc '2024-11-28 10:19:07' _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 3bpo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 3BPO # _exptl.entry_id 3BPO _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.51 _cell.angle_gamma 90 _cell.entry_id 3BPO _cell.length_a 211.51 _cell.length_b 58.169 _cell.length_c 64.236 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BPO _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 D 1 NAG S 911 NAG 4 n D NAG 2 D 2 NAG S 912 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 29 A CYS 29 1_555 A SG CYS 58 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.622 ? disulf ? disulf2 A SG CYS 46 A CYS 45 1_555 A SG CYS 72 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 12 B CYS 9 1_555 B SG CYS 22 B CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 B SG CYS 32 B CYS 29 1_555 B SG CYS 62 B CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf5 B SG CYS 52 B CYS 49 1_555 B SG CYS 64 B CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 C SG CYS 34 C CYS 62 1_555 C SG CYS 74 C CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.696 ? disulf ? disulf7 C SG CYS 67 C CYS 95 1_555 C SG CYS 89 C CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 C SG CYS 106 C CYS 134 1_555 C SG CYS 116 C CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 C SG CYS 145 C CYS 173 1_555 C SG CYS 157 C CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf10 C SG CYS 229 C CYS 257 1_555 C SG CYS 292 C CYS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 C SG CYS 254 C CYS 282 1_555 C SG CYS 268 C CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 B ND2 ASN 106 B ASN 103 1_555 E C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 B ND2 ASN 187 B ASN 184 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale3 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 3BPO _atom_sites.fract_transf_matrix[1][1] 0.004728 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000877 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017191 _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] 0.015833 _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 B 1 901 901 NAG NAG . F 6 HOH A 1 127 12 HOH HOH . F 6 HOH A 2 128 17 HOH HOH . F 6 HOH A 3 129 21 HOH HOH . F 6 HOH A 4 130 22 HOH HOH . F 6 HOH A 5 131 27 HOH HOH . F 6 HOH A 6 132 34 HOH HOH . F 6 HOH A 7 133 41 HOH HOH . F 6 HOH A 8 134 51 HOH HOH . G 6 HOH B 1 913 3 HOH HOH . G 6 HOH B 2 914 8 HOH HOH . G 6 HOH B 3 915 14 HOH HOH . G 6 HOH B 4 916 19 HOH HOH . G 6 HOH B 5 917 24 HOH HOH . G 6 HOH B 6 918 25 HOH HOH . G 6 HOH B 7 919 28 HOH HOH . G 6 HOH B 8 920 29 HOH HOH . G 6 HOH B 9 921 31 HOH HOH . G 6 HOH B 10 922 32 HOH HOH . G 6 HOH B 11 923 35 HOH HOH . G 6 HOH B 12 924 38 HOH HOH . G 6 HOH B 13 925 40 HOH HOH . G 6 HOH B 14 926 42 HOH HOH . G 6 HOH B 15 927 44 HOH HOH . G 6 HOH B 16 928 45 HOH HOH . G 6 HOH B 17 929 50 HOH HOH . G 6 HOH B 18 930 53 HOH HOH . G 6 HOH B 19 931 56 HOH HOH . G 6 HOH B 20 932 58 HOH HOH . H 6 HOH C 1 343 1 HOH HOH . H 6 HOH C 2 344 2 HOH HOH . H 6 HOH C 3 345 4 HOH HOH . H 6 HOH C 4 346 6 HOH HOH . H 6 HOH C 5 347 9 HOH HOH . H 6 HOH C 6 348 11 HOH HOH . H 6 HOH C 7 349 13 HOH HOH . H 6 HOH C 8 350 16 HOH HOH . H 6 HOH C 9 351 18 HOH HOH . H 6 HOH C 10 352 20 HOH HOH . H 6 HOH C 11 353 23 HOH HOH . H 6 HOH C 12 354 26 HOH HOH . H 6 HOH C 13 355 30 HOH HOH . H 6 HOH C 14 356 36 HOH HOH . H 6 HOH C 15 357 37 HOH HOH . H 6 HOH C 16 358 39 HOH HOH . H 6 HOH C 17 359 43 HOH HOH . H 6 HOH C 18 360 46 HOH HOH . H 6 HOH C 19 361 47 HOH HOH . H 6 HOH C 20 362 48 HOH HOH . H 6 HOH C 21 363 49 HOH HOH . H 6 HOH C 22 364 52 HOH HOH . H 6 HOH C 23 365 54 HOH HOH . H 6 HOH C 24 366 55 HOH HOH . H 6 HOH C 25 367 57 HOH HOH . H 6 HOH C 26 368 59 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 -20.603 -11.904 -61.698 1 56.61 ? C1 NAG 901 B 1 HETATM 2 C C2 NAG . . . E 5 -19.218 -12.497 -61.483 1 57.18 ? C2 NAG 901 B 1 HETATM 3 C C3 NAG . . . E 5 -18.5 -12.055 -60.22 1 57.02 ? C3 NAG 901 B 1 HETATM 4 C C4 NAG . . . E 5 -18.602 -10.52 -60.087 1 56.08 ? C4 NAG 901 B 1 HETATM 5 C C5 NAG . . . E 5 -20.073 -10.155 -60.181 1 56.59 ? C5 NAG 901 B 1 HETATM 6 C C6 NAG . . . E 5 -20.277 -8.687 -59.881 1 56.56 ? C6 NAG 901 B 1 HETATM 7 C C7 NAG . . . E 5 -19.177 -14.812 -62.102 1 64.56 ? C7 NAG 901 B 1 HETATM 8 C C8 NAG . . . E 5 -19.405 -16.366 -61.869 1 57.28 ? C8 NAG 901 B 1 HETATM 9 N N2 NAG . . . E 5 -19.528 -14.019 -61.175 1 57.19 ? N2 NAG 901 B 1 HETATM 10 O O3 NAG . . . E 5 -17.128 -12.486 -60.267 1 56.6 ? O3 NAG 901 B 1 HETATM 11 O O4 NAG . . . E 5 -18.202 -10.357 -58.713 1 56.75 ? O4 NAG 901 B 1 HETATM 12 O O5 NAG . . . E 5 -20.493 -10.417 -61.517 1 56.17 ? O5 NAG 901 B 1 HETATM 13 O O6 NAG . . . E 5 -19.6 -7.924 -60.854 1 56.52 ? O6 NAG 901 B 1 HETATM 14 O O7 NAG . . . E 5 -18.484 -14.302 -63.033 1 57.28 ? O7 NAG 901 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #