data_3QD6 # _model_server_result.job_id HQJsa0XdfoA-gVpNb_jTSQ _model_server_result.datetime_utc '2024-12-26 15:27:21' _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 3qd6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":1411}' # _entry.id 3QD6 # _exptl.entry_id 3QD6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _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 3QD6 _cell.length_a 133.212 _cell.length_b 133.212 _cell.length_c 211.151 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QD6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? pentameric 5 author_defined_assembly 1 ? pentameric 5 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,K,L,M 1 1 D,E,F,I,J,N,O,P 2 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 ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N # 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 66 A CYS 178 1_555 A SG CYS 106 A CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 B SG CYS 66 B CYS 178 1_555 B SG CYS 106 B CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 C SG CYS 66 C CYS 178 1_555 C SG CYS 106 C CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 D SG CYS 66 D CYS 178 1_555 D SG CYS 106 D CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 E SG CYS 66 E CYS 178 1_555 E SG CYS 106 E CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 F SG CYS 66 F CYS 178 1_555 F SG CYS 106 F CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 G SG CYS 6 R CYS 26 1_555 G SG CYS 17 R CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf8 G SG CYS 18 R CYS 38 1_555 G SG CYS 31 R CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 G SG CYS 21 R CYS 41 1_555 G SG CYS 39 R CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 G SG CYS 42 R CYS 62 1_555 G SG CYS 57 R CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf11 G SG CYS 63 R CYS 83 1_555 G SG CYS 83 R CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 G SG CYS 85 R CYS 105 1_555 G SG CYS 99 R CYS 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 G SG CYS 91 R CYS 111 1_555 G SG CYS 96 R CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 G SG CYS 105 R CYS 125 1_555 G SG CYS 123 R CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 H SG CYS 6 S CYS 26 1_555 H SG CYS 17 S CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf16 H SG CYS 18 S CYS 38 1_555 H SG CYS 31 S CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf17 H SG CYS 21 S CYS 41 1_555 H SG CYS 39 S CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf18 H SG CYS 42 S CYS 62 1_555 H SG CYS 57 S CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf19 H SG CYS 63 S CYS 83 1_555 H SG CYS 83 S CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf20 H SG CYS 85 S CYS 105 1_555 H SG CYS 99 S CYS 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf21 H SG CYS 91 S CYS 111 1_555 H SG CYS 96 S CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf22 H SG CYS 105 S CYS 125 1_555 H SG CYS 123 S CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf23 I SG CYS 6 T CYS 26 1_555 I SG CYS 17 T CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf24 I SG CYS 18 T CYS 38 1_555 I SG CYS 31 T CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf25 I SG CYS 21 T CYS 41 1_555 I SG CYS 39 T CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf26 I SG CYS 42 T CYS 62 1_555 I SG CYS 57 T CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf27 I SG CYS 63 T CYS 83 1_555 I SG CYS 83 T CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf28 I SG CYS 85 T CYS 105 1_555 I SG CYS 99 T CYS 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf29 I SG CYS 91 T CYS 111 1_555 I SG CYS 96 T CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf30 I SG CYS 105 T CYS 125 1_555 I SG CYS 123 T CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf31 J SG CYS 6 U CYS 26 1_555 J SG CYS 17 U CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf32 J SG CYS 18 U CYS 38 1_555 J SG CYS 31 U CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf33 J SG CYS 21 U CYS 41 1_555 J SG CYS 39 U CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf34 J SG CYS 42 U CYS 62 1_555 J SG CYS 57 U CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf35 J SG CYS 63 U CYS 83 1_555 J SG CYS 83 U CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf36 J SG CYS 85 U CYS 105 1_555 J SG CYS 99 U CYS 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf37 J SG CYS 91 U CYS 111 1_555 J SG CYS 96 U CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf38 J SG CYS 105 U CYS 125 1_555 J SG CYS 123 U CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 128 A ASN 240 1_555 K C1 NAG . A NAG 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 B ND2 ASN 128 B ASN 240 1_555 L C1 NAG . B NAG 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 C ND2 ASN 128 C ASN 240 1_555 M C1 NAG . C NAG 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 D ND2 ASN 128 D ASN 240 1_555 N C1 NAG . D NAG 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale5 E ND2 ASN 128 E ASN 240 1_555 O C1 NAG . E NAG 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 F ND2 ASN 128 F ASN 240 1_555 P C1 NAG . F NAG 1411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? # _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 3QD6 _atom_sites.fract_transf_matrix[1][1] 0.007507 _atom_sites.fract_transf_matrix[1][2] 0.004334 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008668 _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] 0.004736 _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 K 3 NAG A 1 1411 1411 NAG NAG . L 3 NAG B 1 1411 1411 NAG NAG . M 3 NAG C 1 1411 1411 NAG NAG . N 3 NAG D 1 1411 1411 NAG NAG . O 3 NAG E 1 1411 1411 NAG NAG . P 3 NAG F 1 1411 1411 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 . . . K 3 -64.434 89.839 -42.478 1 78.9 ? C1 NAG 1411 A 1 HETATM 2 C C2 NAG . . . K 3 -63.662 91.178 -42.347 1 81.45 ? C2 NAG 1411 A 1 HETATM 3 C C3 NAG . . . K 3 -64.545 92.342 -41.865 1 81.45 ? C3 NAG 1411 A 1 HETATM 4 C C4 NAG . . . K 3 -65.827 92.383 -42.686 1 82.46 ? C4 NAG 1411 A 1 HETATM 5 C C5 NAG . . . K 3 -66.506 91.03 -42.487 1 82.76 ? C5 NAG 1411 A 1 HETATM 6 C C6 NAG . . . K 3 -67.912 90.875 -43.036 1 83.79 ? C6 NAG 1411 A 1 HETATM 7 C C7 NAG . . . K 3 -62.704 91.265 -40.127 1 86.14 ? C7 NAG 1411 A 1 HETATM 8 C C8 NAG . . . K 3 -63.524 90.278 -39.294 1 86.39 ? C8 NAG 1411 A 1 HETATM 9 N N2 NAG . . . K 3 -62.556 90.998 -41.422 1 84.2 ? N2 NAG 1411 A 1 HETATM 10 O O3 NAG . . . K 3 -63.843 93.571 -41.992 1 79.65 ? O3 NAG 1411 A 1 HETATM 11 O O4 NAG . . . K 3 -66.66 93.446 -42.239 1 84.65 ? O4 NAG 1411 A 1 HETATM 12 O O5 NAG . . . K 3 -65.711 90.019 -43.104 1 80.3 ? O5 NAG 1411 A 1 HETATM 13 O O6 NAG . . . K 3 -68.314 89.507 -43.018 1 82.48 ? O6 NAG 1411 A 1 HETATM 14 O O7 NAG . . . K 3 -62.206 92.261 -39.592 1 87.03 ? O7 NAG 1411 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #