data_4E06 # _model_server_result.job_id P3Hv06eAj46y0Pssgq5H5A _model_server_result.datetime_utc '2024-12-27 00:53:00' _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 4e06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 4E06 # _exptl.entry_id 4E06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 90 _cell.angle_gamma 120 _cell.entry_id 4E06 _cell.length_a 209.659 _cell.length_b 209.659 _cell.length_c 127.412 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4E06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 9 L CYS 293 1_555 B SG CYS 119 H CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 B SG CYS 28 H CYS 348 1_555 B SG CYS 44 H CYS 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 B SG CYS 173 H CYS 493 1_555 B SG CYS 187 H CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 201 H CYS 521 1_555 B SG CYS 231 H CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? covale ? covale1 B ND2 ASN 53 H ASN 373 1_555 D C1 NAG . H NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? metalc ? metalc1 B O ARG 233 H ARG 553 1_555 E NA NA . H NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc2 B O LYS 236 H LYS 556 1_555 E NA NA . H NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc3 E NA NA . H NA 602 1_555 F O HOH . H HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc4 E NA NA . H NA 602 1_555 F O HOH . H HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc5 E NA NA . H NA 602 1_555 F O HOH . H HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc6 E NA NA . H NA 602 1_555 F O HOH . H HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? # _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 4E06 _atom_sites.fract_transf_matrix[1][1] 0.00477 _atom_sites.fract_transf_matrix[1][2] 0.002754 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005508 _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] 0.007849 _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 D 4 NAG H 1 601 1373 NAG NAG . E 5 NA H 1 602 1 NA NA . F 6 HOH H 1 701 2 HOH HOH . F 6 HOH H 2 702 3 HOH HOH . F 6 HOH H 3 703 4 HOH HOH . F 6 HOH H 4 704 5 HOH HOH . F 6 HOH H 5 705 6 HOH HOH . F 6 HOH H 6 706 8 HOH HOH . F 6 HOH H 7 707 9 HOH HOH . F 6 HOH H 8 708 10 HOH HOH . F 6 HOH H 9 709 12 HOH HOH . F 6 HOH H 10 710 14 HOH HOH . F 6 HOH H 11 711 15 HOH HOH . F 6 HOH H 12 712 16 HOH HOH . F 6 HOH H 13 713 17 HOH HOH . F 6 HOH H 14 714 18 HOH HOH . F 6 HOH H 15 715 19 HOH HOH . F 6 HOH H 16 716 20 HOH HOH . F 6 HOH H 17 717 21 HOH HOH . F 6 HOH H 18 718 22 HOH HOH . F 6 HOH H 19 719 23 HOH HOH . F 6 HOH H 20 720 24 HOH HOH . G 6 HOH I 1 101 7 HOH HOH . G 6 HOH I 2 102 11 HOH HOH . G 6 HOH I 3 103 13 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 . . . D 4 -61.199 -43 -0.432 0.93 109.29 ? C1 NAG 601 H 1 HETATM 2 C C2 NAG . . . D 4 -59.841 -43.344 -1.066 0.93 122.18 ? C2 NAG 601 H 1 HETATM 3 C C3 NAG . . . D 4 -59.159 -42.128 -1.694 0.93 125.83 ? C3 NAG 601 H 1 HETATM 4 C C4 NAG . . . D 4 -60.143 -41.482 -2.664 0.93 123.23 ? C4 NAG 601 H 1 HETATM 5 C C5 NAG . . . D 4 -61.38 -41.068 -1.858 0.93 124.68 ? C5 NAG 601 H 1 HETATM 6 C C6 NAG . . . D 4 -62.376 -40.261 -2.684 0.93 128.95 ? C6 NAG 601 H 1 HETATM 7 C C7 NAG . . . D 4 -58.944 -45.286 0.031 0.93 128.74 ? C7 NAG 601 H 1 HETATM 8 C C8 NAG . . . D 4 -57.593 -45.929 0.152 0.93 127.45 ? C8 NAG 601 H 1 HETATM 9 N N2 NAG . . . D 4 -58.972 -43.962 -0.088 0.93 127.71 ? N2 NAG 601 H 1 HETATM 10 O O3 NAG . . . D 4 -57.965 -42.489 -2.357 0.93 129.05 ? O3 NAG 601 H 1 HETATM 11 O O4 NAG . . . D 4 -59.549 -40.407 -3.376 0.93 124.11 ? O4 NAG 601 H 1 HETATM 12 O O5 NAG . . . D 4 -62.006 -42.226 -1.318 0.93 121.01 ? O5 NAG 601 H 1 HETATM 13 O O6 NAG . . . D 4 -62.764 -41.019 -3.805 0.93 130.85 ? O6 NAG 601 H 1 HETATM 14 O O7 NAG . . . D 4 -59.966 -45.973 0.034 0.93 129.33 ? O7 NAG 601 H 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #