data_4DKD # _model_server_result.job_id 48OxkdbdQKddR_DFMXLk3Q _model_server_result.datetime_utc '2024-11-04 22:36:33' _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 4dkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":403}' # _entry.id 4DKD # _exptl.entry_id 4DKD _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 120 _cell.entry_id 4DKD _cell.length_a 101.361 _cell.length_b 101.361 _cell.length_c 175.252 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I,J,K,L,M,N _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 H N N ? 5 I N N ? 5 J N N ? 5 K 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 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 3 n D NAG 1 D 1 NAG A 201 NAG 3 n D NAG 2 D 2 NAG A 202 NAG 3 n E NAG 1 E 1 NAG B 201 NAG 3 n E NAG 2 E 2 NAG B 202 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 18 A CYS 35 1_555 A SG CYS 163 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 160 A CYS 177 1_555 A SG CYS 174 A CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 18 B CYS 35 1_555 B SG CYS 163 B CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 160 B CYS 177 1_555 B SG CYS 174 B CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 C SG CYS 26 C CYS 42 1_555 C SG CYS 68 C CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? disulf ? disulf6 C SG CYS 111 C CYS 127 1_555 C SG CYS 161 C CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf7 C SG CYS 208 C CYS 224 1_555 C SG CYS 262 C CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 59 A ASN 76 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 B ND2 ASN 59 B ASN 76 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 C ND2 ASN 57 C ASN 73 1_555 H C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 C ND2 ASN 137 C ASN 153 1_555 I C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 C ND2 ASN 224 C ASN 240 1_555 J C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 C ND2 ASN 259 C ASN 275 1_555 K C1 NAG . C NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 ? # 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 4DKD _atom_sites.fract_transf_matrix[1][1] 0.009866 _atom_sites.fract_transf_matrix[1][2] 0.005696 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011392 _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] 0.005706 _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 4 BMA A 1 303 203 BMA BMA . G 4 BMA B 1 303 203 BMA BMA . H 5 NAG C 1 401 401 NAG NAG . I 5 NAG C 1 402 402 NAG NAG . J 5 NAG C 1 403 403 NAG NAG . K 5 NAG C 1 404 404 NAG NAG . L 6 HOH A 1 401 1 HOH HOH . L 6 HOH A 2 402 4 HOH HOH . L 6 HOH A 3 403 5 HOH HOH . L 6 HOH A 4 404 9 HOH HOH . M 6 HOH B 1 401 7 HOH HOH . M 6 HOH B 2 402 8 HOH HOH . M 6 HOH B 3 403 11 HOH HOH . M 6 HOH B 4 404 12 HOH HOH . M 6 HOH B 5 405 13 HOH HOH . M 6 HOH B 6 406 14 HOH HOH . M 6 HOH B 7 407 15 HOH HOH . M 6 HOH B 8 408 16 HOH HOH . N 6 HOH C 1 501 2 HOH HOH . N 6 HOH C 2 502 3 HOH HOH . N 6 HOH C 3 503 6 HOH HOH . N 6 HOH C 4 504 10 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 . . . J 5 -5.347 -15.806 36.979 1 139.32 ? C1 NAG 403 C 1 HETATM 2 C C2 NAG . . . J 5 -4.829 -17.094 37.608 1 141.7 ? C2 NAG 403 C 1 HETATM 3 C C3 NAG . . . J 5 -3.74 -16.824 38.645 1 146.19 ? C3 NAG 403 C 1 HETATM 4 C C4 NAG . . . J 5 -2.722 -15.796 38.157 1 147.11 ? C4 NAG 403 C 1 HETATM 5 C C5 NAG . . . J 5 -3.416 -14.587 37.536 1 144.94 ? C5 NAG 403 C 1 HETATM 6 C C6 NAG . . . J 5 -2.41 -13.588 36.972 1 141.48 ? C6 NAG 403 C 1 HETATM 7 C C7 NAG . . . J 5 -6.661 -18.687 37.548 1 129.17 ? C7 NAG 403 C 1 HETATM 8 C C8 NAG . . . J 5 -7.771 -19.357 38.301 1 125.86 ? C8 NAG 403 C 1 HETATM 9 N N2 NAG . . . J 5 -5.932 -17.805 38.228 1 133.91 ? N2 NAG 403 C 1 HETATM 10 O O3 NAG . . . J 5 -3.076 -18.028 38.968 1 151.09 ? O3 NAG 403 C 1 HETATM 11 O O4 NAG . . . J 5 -1.927 -15.379 39.246 1 147.15 ? O4 NAG 403 C 1 HETATM 12 O O5 NAG . . . J 5 -4.272 -15.023 36.501 1 143.11 ? O5 NAG 403 C 1 HETATM 13 O O6 NAG . . . J 5 -1.218 -13.63 37.733 1 138.7 ? O6 NAG 403 C 1 HETATM 14 O O7 NAG . . . J 5 -6.458 -18.959 36.365 1 125.13 ? O7 NAG 403 C 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #