data_4E05 # _model_server_result.job_id fJx5lnANDgc5V_4b266UdQ _model_server_result.datetime_utc '2024-12-27 01:14:10' _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 4e05 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 4E05 # _exptl.entry_id 4E05 _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 4E05 _cell.length_a 120.18 _cell.length_b 120.18 _cell.length_c 77.81 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4E05 _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 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,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 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 B SG CYS 28 H CYS 348 1_555 B SG CYS 44 H CYS 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf3 B SG CYS 173 H CYS 493 1_555 B SG CYS 187 H CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 201 H CYS 521 1_555 B SG CYS 231 H CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? covale ? covale1 B ND2 ASN 53 H ASN 373 1_555 D C1 NAG . H NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 B O ARG 233 H ARG 553 1_555 E NA NA . H NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc2 B O LYS 236 H LYS 556 1_555 E NA NA . H NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc3 E NA NA . H NA 602 1_555 G O HOH . H HOH 753 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc4 E NA NA . H NA 602 1_555 G O HOH . H HOH 754 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc5 E NA NA . H NA 602 1_555 G O HOH . H HOH 755 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc6 E NA NA . H NA 602 1_555 G O HOH . H HOH 756 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? # _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 4E05 _atom_sites.fract_transf_matrix[1][1] 0.008321 _atom_sites.fract_transf_matrix[1][2] 0.004804 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009608 _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] 0.012852 _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 L 1 401 16 HOH HOH . F 6 HOH L 2 402 27 HOH HOH . F 6 HOH L 3 403 37 HOH HOH . F 6 HOH L 4 404 39 HOH HOH . F 6 HOH L 5 405 62 HOH HOH . F 6 HOH L 6 406 77 HOH HOH . F 6 HOH L 7 407 90 HOH HOH . F 6 HOH L 8 408 95 HOH HOH . G 6 HOH H 1 701 2 HOH HOH . G 6 HOH H 2 702 3 HOH HOH . G 6 HOH H 3 703 4 HOH HOH . G 6 HOH H 4 704 5 HOH HOH . G 6 HOH H 5 705 6 HOH HOH . G 6 HOH H 6 706 7 HOH HOH . G 6 HOH H 7 707 8 HOH HOH . G 6 HOH H 8 708 9 HOH HOH . G 6 HOH H 9 709 10 HOH HOH . G 6 HOH H 10 710 11 HOH HOH . G 6 HOH H 11 711 12 HOH HOH . G 6 HOH H 12 712 14 HOH HOH . G 6 HOH H 13 713 15 HOH HOH . G 6 HOH H 14 714 17 HOH HOH . G 6 HOH H 15 715 18 HOH HOH . G 6 HOH H 16 716 20 HOH HOH . G 6 HOH H 17 717 21 HOH HOH . G 6 HOH H 18 718 22 HOH HOH . G 6 HOH H 19 719 23 HOH HOH . G 6 HOH H 20 720 24 HOH HOH . G 6 HOH H 21 721 25 HOH HOH . G 6 HOH H 22 722 26 HOH HOH . G 6 HOH H 23 723 28 HOH HOH . G 6 HOH H 24 724 29 HOH HOH . G 6 HOH H 25 725 30 HOH HOH . G 6 HOH H 26 726 31 HOH HOH . G 6 HOH H 27 727 32 HOH HOH . G 6 HOH H 28 728 34 HOH HOH . G 6 HOH H 29 729 35 HOH HOH . G 6 HOH H 30 730 36 HOH HOH . G 6 HOH H 31 731 41 HOH HOH . G 6 HOH H 32 732 43 HOH HOH . G 6 HOH H 33 733 45 HOH HOH . G 6 HOH H 34 734 46 HOH HOH . G 6 HOH H 35 735 48 HOH HOH . G 6 HOH H 36 736 50 HOH HOH . G 6 HOH H 37 737 51 HOH HOH . G 6 HOH H 38 738 52 HOH HOH . G 6 HOH H 39 739 54 HOH HOH . G 6 HOH H 40 740 55 HOH HOH . G 6 HOH H 41 741 56 HOH HOH . G 6 HOH H 42 742 57 HOH HOH . G 6 HOH H 43 743 59 HOH HOH . G 6 HOH H 44 744 60 HOH HOH . G 6 HOH H 45 745 61 HOH HOH . G 6 HOH H 46 746 63 HOH HOH . G 6 HOH H 47 747 64 HOH HOH . G 6 HOH H 48 748 65 HOH HOH . G 6 HOH H 49 749 66 HOH HOH . G 6 HOH H 50 750 67 HOH HOH . G 6 HOH H 51 751 68 HOH HOH . G 6 HOH H 52 752 69 HOH HOH . G 6 HOH H 53 753 70 HOH HOH . G 6 HOH H 54 754 71 HOH HOH . G 6 HOH H 55 755 72 HOH HOH . G 6 HOH H 56 756 73 HOH HOH . G 6 HOH H 57 757 74 HOH HOH . G 6 HOH H 58 758 75 HOH HOH . G 6 HOH H 59 759 76 HOH HOH . G 6 HOH H 60 760 78 HOH HOH . G 6 HOH H 61 761 79 HOH HOH . G 6 HOH H 62 762 80 HOH HOH . G 6 HOH H 63 763 81 HOH HOH . G 6 HOH H 64 764 83 HOH HOH . G 6 HOH H 65 765 84 HOH HOH . G 6 HOH H 66 766 85 HOH HOH . G 6 HOH H 67 767 86 HOH HOH . G 6 HOH H 68 768 87 HOH HOH . G 6 HOH H 69 769 88 HOH HOH . G 6 HOH H 70 770 92 HOH HOH . G 6 HOH H 71 771 93 HOH HOH . G 6 HOH H 72 772 94 HOH HOH . H 6 HOH I 1 101 13 HOH HOH . H 6 HOH I 2 102 19 HOH HOH . H 6 HOH I 3 103 40 HOH HOH . H 6 HOH I 4 104 53 HOH HOH . H 6 HOH I 5 105 58 HOH HOH . H 6 HOH I 6 106 89 HOH HOH . H 6 HOH I 7 107 91 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 37.122 2.888 -14.202 0.93 85.03 ? C1 NAG 601 H 1 HETATM 2 C C2 NAG . . . D 4 36.049 2.579 -15.247 0.93 97.92 ? C2 NAG 601 H 1 HETATM 3 C C3 NAG . . . D 4 36.495 1.527 -16.256 0.93 101.57 ? C3 NAG 601 H 1 HETATM 4 C C4 NAG . . . D 4 37.876 1.856 -16.792 0.93 98.97 ? C4 NAG 601 H 1 HETATM 5 C C5 NAG . . . D 4 38.833 2.027 -15.621 0.93 100.42 ? C5 NAG 601 H 1 HETATM 6 C C6 NAG . . . D 4 40.266 2.291 -16.084 0.93 104.69 ? C6 NAG 601 H 1 HETATM 7 C C7 NAG . . . D 4 33.711 2.817 -14.717 0.93 104.48 ? C7 NAG 601 H 1 HETATM 8 C C8 NAG . . . D 4 32.659 2.227 -15.612 0.93 103.19 ? C8 NAG 601 H 1 HETATM 9 N N2 NAG . . . D 4 34.837 2.126 -14.594 0.93 103.45 ? N2 NAG 601 H 1 HETATM 10 O O3 NAG . . . D 4 35.572 1.46 -17.323 0.93 104.79 ? O3 NAG 601 H 1 HETATM 11 O O4 NAG . . . D 4 38.304 0.809 -17.633 0.93 99.85 ? O4 NAG 601 H 1 HETATM 12 O O5 NAG . . . D 4 38.388 3.093 -14.805 0.93 96.75 ? O5 NAG 601 H 1 HETATM 13 O O6 NAG . . . D 4 40.403 3.621 -16.533 0.93 106.59 ? O6 NAG 601 H 1 HETATM 14 O O7 NAG . . . D 4 33.53 3.889 -14.142 0.93 105.07 ? O7 NAG 601 H 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #