data_5VDR # _model_server_result.job_id 6V2YH13g_AHgXHt7eF-zcQ _model_server_result.datetime_utc '2024-10-15 12:23:30' _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 5vdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 5VDR # _exptl.entry_id 5VDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 660.381 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3',3'-cdIMP" _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 109.89 _cell.angle_gamma 90 _cell.entry_id 5VDR _cell.length_a 215.528 _cell.length_b 48.395 _cell.length_c 89.099 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,D,I 1 1 B,E,F,G,H,J 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 D N N ? 3 F N N ? 3 G N N ? 3 H 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 metalc ? metalc1 A NE2 HIS 231 A HIS 390 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc2 A SG CYS 237 A CYS 396 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc3 A SG CYS 238 A CYS 397 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc4 A SG CYS 245 A CYS 404 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc5 B NE2 HIS 231 B HIS 390 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc6 B SG CYS 237 B CYS 396 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc7 B SG CYS 238 B CYS 397 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc8 B SG CYS 245 B CYS 404 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _chem_comp.formula 'C20 H22 N8 O14 P2' _chem_comp.formula_weight 660.381 _chem_comp.id 9B7 _chem_comp.mon_nstd_flag . _chem_comp.name "3',3'-cdIMP" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-3,5,10,12-tetrahydroxy-2,9-bis(6-oxo-3,6-dihydro-9H-purin-9-yl)octahydro-2H,5H, 7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-5,12-dione" # 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 O01 C02 9B7 doub 1 n n N03 C02 9B7 sing 2 n n N03 C04 9B7 doub 3 n n O36 C35 9B7 doub 4 n n C02 C07 9B7 sing 5 n n N34 C35 9B7 sing 6 n n N34 C33 9B7 doub 7 n n C35 C37 9B7 sing 8 n n C04 N05 9B7 sing 9 n n C33 N32 9B7 sing 10 n n C07 N08 9B7 sing 11 n y C07 C06 9B7 doub 12 n y N08 C09 9B7 doub 13 n y C37 N38 9B7 sing 14 n y C37 C31 9B7 doub 15 n y N05 C06 9B7 sing 16 n n N32 C31 9B7 sing 17 n n C06 N10 9B7 sing 18 n y N38 C39 9B7 doub 19 n y C31 N30 9B7 sing 20 n y C09 N10 9B7 sing 21 n y N10 C11 9B7 sing 22 n n C39 N30 9B7 sing 23 n y N30 C29 9B7 sing 24 n n C11 C43 9B7 sing 25 n n C11 O12 9B7 sing 26 n n O17 P16 9B7 doub 27 n n C29 C27 9B7 sing 28 n n C29 O40 9B7 sing 29 n n C43 O44 9B7 sing 30 n n C43 C19 9B7 sing 31 n n O12 C13 9B7 sing 32 n n C27 O28 9B7 sing 33 n n C27 C25 9B7 sing 34 n n C19 C13 9B7 sing 35 n n C19 O20 9B7 sing 36 n n O40 C24 9B7 sing 37 n n O42 P21 9B7 doub 38 n n O15 P16 9B7 sing 39 n n O15 C14 9B7 sing 40 n n C25 C24 9B7 sing 41 n n C25 O26 9B7 sing 42 n n P16 O26 9B7 sing 43 n n P16 O18 9B7 sing 44 n n C13 C14 9B7 sing 45 n n O22 P21 9B7 sing 46 n n O22 C23 9B7 sing 47 n n C24 C23 9B7 sing 48 n n O20 P21 9B7 sing 49 n n P21 O41 9B7 sing 50 n n C11 H1 9B7 sing 51 n n C13 H2 9B7 sing 52 n n C14 H3 9B7 sing 53 n n C14 H4 9B7 sing 54 n n C19 H5 9B7 sing 55 n n C23 H6 9B7 sing 56 n n C23 H7 9B7 sing 57 n n C24 H8 9B7 sing 58 n n C25 H9 9B7 sing 59 n n C27 H10 9B7 sing 60 n n C29 H11 9B7 sing 61 n n C39 H12 9B7 sing 62 n n C04 H13 9B7 sing 63 n n N05 H14 9B7 sing 64 n n C09 H15 9B7 sing 65 n n O18 H16 9B7 sing 66 n n O28 H17 9B7 sing 67 n n N32 H18 9B7 sing 68 n n C33 H19 9B7 sing 69 n n O41 H20 9B7 sing 70 n n C43 H21 9B7 sing 71 n n O44 H22 9B7 sing 72 n n # _atom_sites.entry_id 5VDR _atom_sites.fract_transf_matrix[1][1] 0.00464 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001679 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020663 _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] 0.011936 _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 ZN A 1 601 601 ZN ZN . D 3 9B7 A 1 602 2 9B7 3II . E 2 ZN B 1 601 601 ZN ZN . F 3 9B7 B 1 602 3 9B7 3II . G 3 9B7 B 1 603 3 9B7 3II . H 3 9B7 B 1 604 3 9B7 3II . I 4 HOH A 1 701 30 HOH HOH . I 4 HOH A 2 702 3 HOH HOH . I 4 HOH A 3 703 28 HOH HOH . I 4 HOH A 4 704 6 HOH HOH . I 4 HOH A 5 705 31 HOH HOH . I 4 HOH A 6 706 10 HOH HOH . I 4 HOH A 7 707 27 HOH HOH . I 4 HOH A 8 708 12 HOH HOH . I 4 HOH A 9 709 11 HOH HOH . I 4 HOH A 10 710 4 HOH HOH . I 4 HOH A 11 711 7 HOH HOH . I 4 HOH A 12 712 26 HOH HOH . I 4 HOH A 13 713 13 HOH HOH . I 4 HOH A 14 714 16 HOH HOH . I 4 HOH A 15 715 1 HOH HOH . I 4 HOH A 16 716 5 HOH HOH . J 4 HOH B 1 701 18 HOH HOH . J 4 HOH B 2 702 20 HOH HOH . J 4 HOH B 3 703 22 HOH HOH . J 4 HOH B 4 704 17 HOH HOH . J 4 HOH B 5 705 25 HOH HOH . J 4 HOH B 6 706 8 HOH HOH . J 4 HOH B 7 707 24 HOH HOH . J 4 HOH B 8 708 21 HOH HOH . J 4 HOH B 9 709 2 HOH HOH . J 4 HOH B 10 710 9 HOH HOH . J 4 HOH B 11 711 15 HOH HOH . J 4 HOH B 12 712 14 HOH HOH . J 4 HOH B 13 713 23 HOH HOH . J 4 HOH B 14 714 29 HOH HOH . J 4 HOH B 15 715 19 HOH HOH . J 4 HOH B 16 716 32 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 C11 9B7 . . . D 3 -29.423 -1.227 25.311 1 88.41 ? C11 9B7 602 A 1 HETATM 2 C C13 9B7 . . . D 3 -29.238 -0.266 27.348 1 93.42 ? C13 9B7 602 A 1 HETATM 3 C C14 9B7 . . . D 3 -28.928 1.04 28.03 1 94.56 ? C14 9B7 602 A 1 HETATM 4 O O17 9B7 . . . D 3 -28.545 4.276 25.941 1 103.98 -1 O17 9B7 602 A 1 HETATM 5 C C19 9B7 . . . D 3 -27.832 -1.029 26.878 1 97.92 ? C19 9B7 602 A 1 HETATM 6 O O22 9B7 . . . D 3 -25.056 0.179 27.728 1 102.69 ? O22 9B7 602 A 1 HETATM 7 C C23 9B7 . . . D 3 -25.235 1.228 28.675 1 102.66 ? C23 9B7 602 A 1 HETATM 8 C C24 9B7 . . . D 3 -24.959 2.555 27.997 1 103.2 ? C24 9B7 602 A 1 HETATM 9 C C25 9B7 . . . D 3 -25.945 2.898 27.235 1 104.15 ? C25 9B7 602 A 1 HETATM 10 C C27 9B7 . . . D 3 -25.285 3.947 26.356 1 102.87 ? C27 9B7 602 A 1 HETATM 11 C C29 9B7 . . . D 3 -23.959 3.234 25.983 1 97.61 ? C29 9B7 602 A 1 HETATM 12 C C31 9B7 . . . D 3 -24.463 2.961 23.521 1 86.35 ? C31 9B7 602 A 1 HETATM 13 C C35 9B7 . . . D 3 -24.934 2.14 21.177 1 83.06 ? C35 9B7 602 A 1 HETATM 14 C C37 9B7 . . . D 3 -24.62 1.889 22.656 1 83.23 ? C37 9B7 602 A 1 HETATM 15 C C39 9B7 . . . D 3 -24.191 1.124 24.631 1 81.47 ? C39 9B7 602 A 1 HETATM 16 O O01 9B7 . . . D 3 -27.688 -0.361 19.822 1 67.35 ? O01 9B7 602 A 1 HETATM 17 C C02 9B7 . . . D 3 -28.064 -1.112 20.655 1 69.9 ? C02 9B7 602 A 1 HETATM 18 N N03 9B7 . . . D 3 -28.228 -2.506 20.346 1 68.12 ? N03 9B7 602 A 1 HETATM 19 C C04 9B7 . . . D 3 -28.691 -3.422 21.375 1 68.55 ? C04 9B7 602 A 1 HETATM 20 N N05 9B7 . . . D 3 -28.988 -2.921 22.723 1 69.26 ? N05 9B7 602 A 1 HETATM 21 C C06 9B7 . . . D 3 -28.815 -1.475 23.04 1 73.94 ? C06 9B7 602 A 1 HETATM 22 C C07 9B7 . . . D 3 -28.375 -0.599 22.064 1 72.84 ? C07 9B7 602 A 1 HETATM 23 N N08 9B7 . . . D 3 -28.319 0.613 22.632 1 74.24 ? N08 9B7 602 A 1 HETATM 24 C C09 9B7 . . . D 3 -28.702 0.506 23.895 1 78.71 ? C09 9B7 602 A 1 HETATM 25 N N10 9B7 . . . D 3 -29.006 -0.756 24.155 1 81.41 ? N10 9B7 602 A 1 HETATM 26 O O12 9B7 . . . D 3 -29.872 -0.066 26.249 1 90.84 ? O12 9B7 602 A 1 HETATM 27 O O15 9B7 . . . D 3 -29.356 2.082 27.192 1 98.09 ? O15 9B7 602 A 1 HETATM 28 P P16 9B7 . . . D 3 -28.572 3.545 27.262 1 101.23 ? P16 9B7 602 A 1 HETATM 29 O O18 9B7 . . . D 3 -29.431 4.401 28.159 1 103.58 ? O18 9B7 602 A 1 HETATM 30 O O20 9B7 . . . D 3 -27.156 -1.628 28.018 1 102.13 ? O20 9B7 602 A 1 HETATM 31 P P21 9B7 . . . D 3 -25.522 -1.359 28.173 1 100.86 ? P21 9B7 602 A 1 HETATM 32 O O26 9B7 . . . D 3 -27.093 3.486 28.017 1 103.96 ? O26 9B7 602 A 1 HETATM 33 O O28 9B7 . . . D 3 -25.033 5.074 27.071 1 104.79 ? O28 9B7 602 A 1 HETATM 34 N N30 9B7 . . . D 3 -24.195 2.445 24.733 1 87.96 ? N30 9B7 602 A 1 HETATM 35 N N32 9B7 . . . D 3 -24.6 4.358 23.017 1 87.41 ? N32 9B7 602 A 1 HETATM 36 C C33 9B7 . . . D 3 -24.902 4.602 21.599 1 88.18 ? C33 9B7 602 A 1 HETATM 37 N N34 9B7 . . . D 3 -25.067 3.485 20.688 1 86.16 ? N34 9B7 602 A 1 HETATM 38 O O36 9B7 . . . D 3 -25.068 1.226 20.438 1 79.5 ? O36 9B7 602 A 1 HETATM 39 N N38 9B7 . . . D 3 -24.445 0.772 23.375 1 79.82 ? N38 9B7 602 A 1 HETATM 40 O O40 9B7 . . . D 3 -23.7 2.451 26.969 1 101.72 ? O40 9B7 602 A 1 HETATM 41 O O41 9B7 . . . D 3 -24.952 -1.813 29.495 1 102.93 -1 O41 9B7 602 A 1 HETATM 42 O O42 9B7 . . . D 3 -24.885 -2.264 27.149 1 92.56 ? O42 9B7 602 A 1 HETATM 43 C C43 9B7 . . . D 3 -28.237 -1.922 26.074 1 93.91 ? C43 9B7 602 A 1 HETATM 44 O O44 9B7 . . . D 3 -28.739 -3.111 26.836 1 93.3 ? O44 9B7 602 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #