data_4XTD # _model_server_result.job_id D6vp53UrsG0Ox06yG-vNfw _model_server_result.datetime_utc '2024-11-18 17:44:46' _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 4xtd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 4XTD # _exptl.entry_id 4XTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 348.206 _entity.id 2 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 'INOSINIC ACID' _entity.pdbx_number_of_molecules 2 _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 4XTD _cell.length_a 117.201 _cell.length_b 117.201 _cell.length_c 56.095 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XTD _symmetry.cell_setting ? _symmetry.Int_Tables_number 75 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 4' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1,2,4,6 B,D,F 2 1,3,5,7 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_575 -x,-y+2,z -1 0 0 0 -1 0 0 0 1 0 234.402 0 3 'crystal symmetry operation' 2_685 -x+1,-y+3,z -1 0 0 0 -1 0 0 0 1 117.201 351.603 0 4 'crystal symmetry operation' 3_665 -y+1,x+1,z 0 -1 0 1 0 0 0 0 1 117.201 117.201 0 5 'crystal symmetry operation' 3_765 -y+2,x+1,z 0 -1 0 1 0 0 0 0 1 234.402 117.201 0 6 'crystal symmetry operation' 4_465 y-1,-x+1,z 0 1 0 -1 0 0 0 0 1 -117.201 117.201 0 7 'crystal symmetry operation' 4_475 y-1,-x+2,z 0 1 0 -1 0 0 0 0 1 -117.201 234.402 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D 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 covale ? covale1 A SG CYS 225 A CYS 334 1_555 C C2 IMP . A IMP 601 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.765 ? covale ? covale2 B SG CYS 225 B CYS 334 1_555 D C2 IMP . B IMP 601 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.766 ? # _chem_comp.formula 'C10 H13 N4 O8 P' _chem_comp.formula_weight 348.206 _chem_comp.id IMP _chem_comp.mon_nstd_flag n _chem_comp.name 'INOSINIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 P O1P IMP doub 173 n n P O2P IMP sing 174 n n P O3P IMP sing 175 n n P O5' IMP sing 176 n n O2P HOP2 IMP sing 177 n n O3P HOP3 IMP sing 178 n n O5' C5' IMP sing 179 n n C5' C4' IMP sing 180 n n C5' "H5'1" IMP sing 181 n n C5' "H5'2" IMP sing 182 n n C4' O4' IMP sing 183 n n C4' C3' IMP sing 184 n n C4' H4' IMP sing 185 n n O4' C1' IMP sing 186 n n C3' O3' IMP sing 187 n n C3' C2' IMP sing 188 n n C3' H3' IMP sing 189 n n O3' HO3' IMP sing 190 n n C2' O2' IMP sing 191 n n C2' C1' IMP sing 192 n n C2' H2' IMP sing 193 n n O2' HO2' IMP sing 194 n n C1' N9 IMP sing 195 n n C1' H1' IMP sing 196 n n N9 C8 IMP sing 197 n y N9 C4 IMP sing 198 n y C8 N7 IMP doub 199 n y C8 H8 IMP sing 200 n n N7 C5 IMP sing 201 n y C5 C6 IMP sing 202 n n C5 C4 IMP doub 203 n y C6 O6 IMP doub 204 n n C6 N1 IMP sing 205 n n N1 C2 IMP sing 206 n n N1 HN1 IMP sing 207 n n C2 N3 IMP doub 208 n n C2 H2 IMP sing 209 n n N3 C4 IMP sing 210 n n # _atom_sites.entry_id 4XTD _atom_sites.fract_transf_matrix[1][1] 0.008532 _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] 0.008532 _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] 0.017827 _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 C 2 IMP A 1 601 601 IMP IMP . D 2 IMP B 1 601 601 IMP IMP . E 3 HOH A 1 701 70 HOH HOH . E 3 HOH A 2 702 18 HOH HOH . E 3 HOH A 3 703 32 HOH HOH . E 3 HOH A 4 704 93 HOH HOH . E 3 HOH A 5 705 132 HOH HOH . E 3 HOH A 6 706 6 HOH HOH . E 3 HOH A 7 707 37 HOH HOH . E 3 HOH A 8 708 41 HOH HOH . E 3 HOH A 9 709 76 HOH HOH . E 3 HOH A 10 710 35 HOH HOH . E 3 HOH A 11 711 38 HOH HOH . E 3 HOH A 12 712 142 HOH HOH . E 3 HOH A 13 713 47 HOH HOH . E 3 HOH A 14 714 109 HOH HOH . E 3 HOH A 15 715 65 HOH HOH . E 3 HOH A 16 716 40 HOH HOH . E 3 HOH A 17 717 126 HOH HOH . E 3 HOH A 18 718 62 HOH HOH . E 3 HOH A 19 719 49 HOH HOH . E 3 HOH A 20 720 150 HOH HOH . E 3 HOH A 21 721 145 HOH HOH . E 3 HOH A 22 722 153 HOH HOH . E 3 HOH A 23 723 169 HOH HOH . E 3 HOH A 24 724 147 HOH HOH . E 3 HOH A 25 725 165 HOH HOH . E 3 HOH A 26 726 120 HOH HOH . E 3 HOH A 27 727 2 HOH HOH . E 3 HOH A 28 728 3 HOH HOH . E 3 HOH A 29 729 4 HOH HOH . E 3 HOH A 30 730 5 HOH HOH . E 3 HOH A 31 731 15 HOH HOH . E 3 HOH A 32 732 17 HOH HOH . E 3 HOH A 33 733 20 HOH HOH . E 3 HOH A 34 734 21 HOH HOH . E 3 HOH A 35 735 23 HOH HOH . E 3 HOH A 36 736 29 HOH HOH . E 3 HOH A 37 737 31 HOH HOH . E 3 HOH A 38 738 33 HOH HOH . E 3 HOH A 39 739 34 HOH HOH . E 3 HOH A 40 740 43 HOH HOH . E 3 HOH A 41 741 45 HOH HOH . E 3 HOH A 42 742 50 HOH HOH . E 3 HOH A 43 743 63 HOH HOH . E 3 HOH A 44 744 68 HOH HOH . E 3 HOH A 45 745 71 HOH HOH . E 3 HOH A 46 746 77 HOH HOH . E 3 HOH A 47 747 78 HOH HOH . E 3 HOH A 48 748 79 HOH HOH . E 3 HOH A 49 749 80 HOH HOH . E 3 HOH A 50 750 81 HOH HOH . E 3 HOH A 51 751 84 HOH HOH . E 3 HOH A 52 752 86 HOH HOH . E 3 HOH A 53 753 87 HOH HOH . E 3 HOH A 54 754 88 HOH HOH . E 3 HOH A 55 755 92 HOH HOH . E 3 HOH A 56 756 94 HOH HOH . E 3 HOH A 57 757 108 HOH HOH . E 3 HOH A 58 758 112 HOH HOH . E 3 HOH A 59 759 118 HOH HOH . E 3 HOH A 60 760 123 HOH HOH . E 3 HOH A 61 761 144 HOH HOH . E 3 HOH A 62 762 146 HOH HOH . E 3 HOH A 63 763 149 HOH HOH . E 3 HOH A 64 764 151 HOH HOH . E 3 HOH A 65 765 157 HOH HOH . E 3 HOH A 66 766 158 HOH HOH . E 3 HOH A 67 767 159 HOH HOH . E 3 HOH A 68 768 160 HOH HOH . E 3 HOH A 69 769 164 HOH HOH . F 3 HOH B 1 701 74 HOH HOH . F 3 HOH B 2 702 85 HOH HOH . F 3 HOH B 3 703 75 HOH HOH . F 3 HOH B 4 704 27 HOH HOH . F 3 HOH B 5 705 16 HOH HOH . F 3 HOH B 6 706 82 HOH HOH . F 3 HOH B 7 707 1 HOH HOH . F 3 HOH B 8 708 90 HOH HOH . F 3 HOH B 9 709 99 HOH HOH . F 3 HOH B 10 710 148 HOH HOH . F 3 HOH B 11 711 12 HOH HOH . F 3 HOH B 12 712 44 HOH HOH . F 3 HOH B 13 713 48 HOH HOH . F 3 HOH B 14 714 46 HOH HOH . F 3 HOH B 15 715 170 HOH HOH . F 3 HOH B 16 716 135 HOH HOH . F 3 HOH B 17 717 100 HOH HOH . F 3 HOH B 18 718 128 HOH HOH . F 3 HOH B 19 719 171 HOH HOH . F 3 HOH B 20 720 53 HOH HOH . F 3 HOH B 21 721 129 HOH HOH . F 3 HOH B 22 722 162 HOH HOH . F 3 HOH B 23 723 161 HOH HOH . F 3 HOH B 24 724 7 HOH HOH . F 3 HOH B 25 725 8 HOH HOH . F 3 HOH B 26 726 9 HOH HOH . F 3 HOH B 27 727 10 HOH HOH . F 3 HOH B 28 728 11 HOH HOH . F 3 HOH B 29 729 13 HOH HOH . F 3 HOH B 30 730 14 HOH HOH . F 3 HOH B 31 731 19 HOH HOH . F 3 HOH B 32 732 22 HOH HOH . F 3 HOH B 33 733 24 HOH HOH . F 3 HOH B 34 734 25 HOH HOH . F 3 HOH B 35 735 26 HOH HOH . F 3 HOH B 36 736 28 HOH HOH . F 3 HOH B 37 737 30 HOH HOH . F 3 HOH B 38 738 36 HOH HOH . F 3 HOH B 39 739 39 HOH HOH . F 3 HOH B 40 740 42 HOH HOH . F 3 HOH B 41 741 52 HOH HOH . F 3 HOH B 42 742 54 HOH HOH . F 3 HOH B 43 743 55 HOH HOH . F 3 HOH B 44 744 57 HOH HOH . F 3 HOH B 45 745 58 HOH HOH . F 3 HOH B 46 746 60 HOH HOH . F 3 HOH B 47 747 64 HOH HOH . F 3 HOH B 48 748 67 HOH HOH . F 3 HOH B 49 749 69 HOH HOH . F 3 HOH B 50 750 73 HOH HOH . F 3 HOH B 51 751 83 HOH HOH . F 3 HOH B 52 752 95 HOH HOH . F 3 HOH B 53 753 113 HOH HOH . F 3 HOH B 54 754 114 HOH HOH . F 3 HOH B 55 755 115 HOH HOH . F 3 HOH B 56 756 127 HOH HOH . F 3 HOH B 57 757 138 HOH HOH . F 3 HOH B 58 758 139 HOH HOH . F 3 HOH B 59 759 141 HOH HOH . F 3 HOH B 60 760 154 HOH HOH . F 3 HOH B 61 761 155 HOH HOH . F 3 HOH B 62 762 156 HOH HOH . F 3 HOH B 63 763 163 HOH HOH . F 3 HOH B 64 764 166 HOH HOH . F 3 HOH B 65 765 168 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 P P IMP . . . D 2 36.385 178.799 4.82 1 45.81 ? P IMP 601 B 1 HETATM 2 O O1P IMP . . . D 2 36.408 179.125 3.351 1 39.49 ? O1P IMP 601 B 1 HETATM 3 O O2P IMP . . . D 2 37.669 178.347 5.456 1 42.97 ? O2P IMP 601 B 1 HETATM 4 O O3P IMP . . . D 2 35.334 177.74 5.042 1 39.53 ? O3P IMP 601 B 1 HETATM 5 O O5' IMP . . . D 2 35.958 180.109 5.622 1 46.52 ? O5' IMP 601 B 1 HETATM 6 C C5' IMP . . . D 2 34.723 180.763 5.365 1 40.41 ? C5' IMP 601 B 1 HETATM 7 C C4' IMP . . . D 2 34.371 181.726 6.471 1 43.11 ? C4' IMP 601 B 1 HETATM 8 O O4' IMP . . . D 2 35.266 182.873 6.426 1 44.78 ? O4' IMP 601 B 1 HETATM 9 C C3' IMP . . . D 2 32.98 182.338 6.396 1 44.66 ? C3' IMP 601 B 1 HETATM 10 O O3' IMP . . . D 2 31.981 181.491 6.931 1 42 ? O3' IMP 601 B 1 HETATM 11 C C2' IMP . . . D 2 33.153 183.641 7.166 1 46.97 ? C2' IMP 601 B 1 HETATM 12 O O2' IMP . . . D 2 33.169 183.41 8.568 1 46.12 ? O2' IMP 601 B 1 HETATM 13 C C1' IMP . . . D 2 34.554 184.056 6.725 1 45.56 ? C1' IMP 601 B 1 HETATM 14 N N9 IMP . A . D 2 34.517 184.881 5.502 0.16 48.83 ? N9 IMP 601 B 1 HETATM 15 N N9 IMP . B . D 2 34.52 184.894 5.509 0.84 48.56 ? N9 IMP 601 B 1 HETATM 16 C C8 IMP . A . D 2 34.116 184.852 4.219 0.16 51.07 ? C8 IMP 601 B 1 HETATM 17 C C8 IMP . B . D 2 33.918 185.009 4.31 0.84 51.4 ? C8 IMP 601 B 1 HETATM 18 N N7 IMP . A . D 2 34.43 186.03 3.655 0.16 51.46 ? N7 IMP 601 B 1 HETATM 19 N N7 IMP . B . D 2 34.427 186.086 3.687 0.84 52.03 ? N7 IMP 601 B 1 HETATM 20 C C5 IMP . A . D 2 35.015 186.783 4.577 0.16 47.94 ? C5 IMP 601 B 1 HETATM 21 C C5 IMP . B . D 2 35.335 186.635 4.484 0.84 48.17 ? C5 IMP 601 B 1 HETATM 22 C C6 IMP . A . D 2 35.575 188.205 4.509 0.16 51.94 ? C6 IMP 601 B 1 HETATM 23 C C6 IMP . B . D 2 36.228 187.869 4.3 0.84 50.37 ? C6 IMP 601 B 1 HETATM 24 O O6 IMP . A . D 2 35.517 188.805 3.494 0.16 49.67 ? O6 IMP 601 B 1 HETATM 25 O O6 IMP . B . D 2 36.16 188.502 3.3 0.84 47.29 ? O6 IMP 601 B 1 HETATM 26 N N1 IMP . A . D 2 36.168 188.806 5.661 0.16 49.36 ? N1 IMP 601 B 1 HETATM 27 N N1 IMP . B . D 2 37.139 188.256 5.33 0.84 49.28 ? N1 IMP 601 B 1 HETATM 28 C C2 IMP . A . D 2 36.231 188.059 6.89 0.16 50.13 ? C2 IMP 601 B 1 HETATM 29 C C2 IMP . B . D 2 37.211 187.477 6.54 0.84 49.27 ? C2 IMP 601 B 1 HETATM 30 N N3 IMP . A . D 2 35.696 186.699 6.948 0.16 48.52 ? N3 IMP 601 B 1 HETATM 31 N N3 IMP . B . D 2 36.356 186.301 6.705 0.84 47.74 ? N3 IMP 601 B 1 HETATM 32 C C4 IMP . A . D 2 35.076 186.072 5.739 0.16 51.4 ? C4 IMP 601 B 1 HETATM 33 C C4 IMP . B . D 2 35.401 185.895 5.628 0.84 52.16 ? C4 IMP 601 B 1 HETATM 34 H "H5'1" IMP . . . D 2 34.79 181.251 4.529 1 48.49 ? "H5'1" IMP 601 B 1 HETATM 35 H "H5'2" IMP . . . D 2 34.021 180.098 5.289 1 48.49 ? "H5'2" IMP 601 B 1 HETATM 36 H H4' IMP . . . D 2 34.474 181.278 7.325 1 51.74 ? H4' IMP 601 B 1 HETATM 37 H H3' IMP . . . D 2 32.767 182.539 5.471 1 53.6 ? H3' IMP 601 B 1 HETATM 38 H HO3' IMP . . . D 2 31.725 181.795 7.683 1 50.4 ? HO3' IMP 601 B 1 HETATM 39 H H2' IMP . . . D 2 32.487 184.299 6.914 1 56.37 ? H2' IMP 601 B 1 HETATM 40 H HO2' IMP . . . D 2 32.547 183.857 8.936 1 55.35 ? HO2' IMP 601 B 1 HETATM 41 H H1' IMP . . . D 2 34.997 184.536 7.442 1 54.68 ? H1' IMP 601 B 1 HETATM 42 H H8 IMP . A . D 2 33.699 184.137 3.793 0.16 61.28 ? H8 IMP 601 B 1 HETATM 43 H H8 IMP . B . D 2 33.263 184.442 3.972 0.84 61.68 ? H8 IMP 601 B 1 HETATM 44 H HN1 IMP . A . D 2 36.482 189.605 5.622 0.16 59.23 ? HN1 IMP 601 B 1 HETATM 45 H HN1 IMP . B . D 2 37.64 188.948 5.229 0.84 59.13 ? HN1 IMP 601 B 1 HETATM 46 H H2 IMP . A . D 2 36.616 188.439 7.646 0.16 60.16 ? H2 IMP 601 B 1 HETATM 47 H H2 IMP . B . D 2 37.802 187.721 7.215 0.84 59.13 ? H2 IMP 601 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 47 #