data_3O4O # _model_server_result.job_id KzLt6zZ0wXfTvK-tXeoVpw _model_server_result.datetime_utc '2024-11-26 17:00:48' _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 3o4o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":340}' # _entry.id 3O4O # _exptl.entry_id 3O4O _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 4 _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 3O4O _cell.length_a 44.83 _cell.length_b 177.47 _cell.length_c 180.66 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3O4O _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 F N N ? 5 G N N ? 5 H N N ? 5 I N 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 B 338 NAG 4 n D NAG 2 D 2 NAG B 339 NAG 4 n E NAG 1 E 1 NAG B 341 NAG 4 n E NAG 2 E 2 NAG B 342 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 B SG CYS 18 C CYS 15 1_555 B SG CYS 106 C CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? disulf ? disulf2 B SG CYS 40 C CYS 37 1_555 B SG CYS 98 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? disulf ? disulf3 B SG CYS 142 C CYS 139 1_555 B SG CYS 197 C CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? disulf ? disulf4 B SG CYS 248 C CYS 245 1_555 B SG CYS 316 C CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? disulf ? disulf5 C SG CYS 7 B CYS 4 1_555 C SG CYS 105 B CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? disulf ? disulf6 C SG CYS 30 B CYS 27 1_555 C SG CYS 97 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf7 C SG CYS 120 B CYS 117 1_555 C SG CYS 164 B CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? disulf ? disulf8 C SG CYS 143 B CYS 140 1_555 C SG CYS 195 B CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? disulf ? disulf9 C SG CYS 249 B CYS 246 1_555 C SG CYS 315 B CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 B ND2 ASN 102 C ASN 99 1_555 F C1 NAG . C NAG 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B ND2 ASN 209 C ASN 206 1_555 G C1 NAG . C NAG 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 C ND2 ASN 90 B ASN 87 1_555 H C1 NAG . B NAG 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 C ND2 ASN 94 B ASN 91 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale5 C ND2 ASN 101 B ASN 98 1_555 I C1 NAG . B NAG 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 C ND2 ASN 192 B ASN 189 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 3O4O _atom_sites.fract_transf_matrix[1][1] 0.022306 _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] 0.005635 _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] 0.005535 _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 5 NAG C 1 337 337 NAG NAG . G 5 NAG C 1 338 338 NAG NAG . H 5 NAG B 1 337 337 NAG NAG . I 5 NAG B 1 340 340 NAG NAG . # 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 . . . I 5 -6.976 12.865 25.497 1 164.72 ? C1 NAG 340 B 1 HETATM 2 C C2 NAG . . . I 5 -7.82 13.558 26.574 1 165 ? C2 NAG 340 B 1 HETATM 3 C C3 NAG . . . I 5 -8.832 12.619 27.2 1 162.26 ? C3 NAG 340 B 1 HETATM 4 C C4 NAG . . . I 5 -9.63 11.913 26.097 1 158.71 ? C4 NAG 340 B 1 HETATM 5 C C5 NAG . . . I 5 -8.743 11.273 25.025 1 158.71 ? C5 NAG 340 B 1 HETATM 6 C C6 NAG . . . I 5 -9.51 10.751 23.823 1 155.29 ? C6 NAG 340 B 1 HETATM 7 C C7 NAG . . . I 5 -7.065 15.505 27.708 1 170.84 ? C7 NAG 340 B 1 HETATM 8 C C8 NAG . . . I 5 -8.358 16.063 28.233 1 170.1 ? C8 NAG 340 B 1 HETATM 9 N N2 NAG . . . I 5 -6.999 14.185 27.584 1 168.45 ? N2 NAG 340 B 1 HETATM 10 O O3 NAG . . . I 5 -9.693 13.396 28.009 1 162.32 ? O3 NAG 340 B 1 HETATM 11 O O4 NAG . . . I 5 -10.438 10.919 26.699 1 156.28 ? O4 NAG 340 B 1 HETATM 12 O O5 NAG . . . I 5 -7.782 12.172 24.532 1 161.32 ? O5 NAG 340 B 1 HETATM 13 O O6 NAG . . . I 5 -10.661 11.538 23.575 1 154.54 ? O6 NAG 340 B 1 HETATM 14 O O7 NAG . . . I 5 -6.151 16.268 27.385 1 173.55 ? O7 NAG 340 B 1 # _model_server_stats.io_time_ms 114 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 415 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #