data_5VRM # _model_server_result.job_id RjilC4v25vR_l4_VOH63Wg _model_server_result.datetime_utc '2024-10-19 17:41:34' _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 5vrm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":300}' # _entry.id 5VRM # _exptl.entry_id 5VRM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 957.459 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3-oxidanyl-4-[[1-oxidanyl-6-[4-(trifluoromethyl)phenoxy]-3~{H}-2,1$l^{4}-benzoxaborol-1-yl]oxy]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' _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 105.59 _cell.angle_gamma 90 _cell.entry_id 5VRM _cell.length_a 125.35 _cell.length_b 92.68 _cell.length_c 101.93 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VRM _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 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 PISA tetrameric 4 software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 1 A,B,C,D,E,F,G,H,I,J,K,L 5 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C35 H37 B F3 N7 O17 P2 1' _chem_comp.formula_weight 957.459 _chem_comp.id 9JJ _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3-oxidanyl-4-[[1-oxidanyl-6-[4-(trifluoromethyl)phenoxy]-3~{H}-2,1$l^{4}-benzoxaborol-1-yl]oxy]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' _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 N1A C2A 9JJ doub 1 n y N1A C6A 9JJ sing 2 n y C2A N3A 9JJ sing 3 n y N6A C6A 9JJ sing 4 n n C6A C5A 9JJ doub 5 n y N3A C4A 9JJ doub 6 n y C5A C4A 9JJ sing 7 n y C5A N7A 9JJ sing 8 n y C4A N9A 9JJ sing 9 n y O3D C3D 9JJ sing 10 n n N7A C8A 9JJ doub 11 n y N9A C8A 9JJ sing 12 n y N9A C1B 9JJ sing 13 n n O4D C4D 9JJ sing 14 n n O4D C1D 9JJ sing 15 n n C4D C3D 9JJ sing 16 n n C4D C5D 9JJ sing 17 n n C1B O4B 9JJ sing 18 n n C1B C2B 9JJ sing 19 n n C3D C2D 9JJ sing 20 n n C1D N1N 9JJ sing 21 n n C1D C2D 9JJ sing 22 n n O4B C4B 9JJ sing 23 n n C6N C5N 9JJ doub 24 n y C6N N1N 9JJ sing 25 n y O2B C2B 9JJ sing 26 n n C5D O5D 9JJ sing 27 n n C5N C4N 9JJ sing 28 n y N1N C2N 9JJ doub 29 n y C2D O2D 9JJ sing 30 n n C2B C3B 9JJ sing 31 n n C4B C3B 9JJ sing 32 n n C4B C5B 9JJ sing 33 n n O2D B1 9JJ sing 34 n n O5D PN 9JJ sing 35 n n C3B O3B 9JJ sing 36 n n O2 C3 9JJ sing 37 n n O2 B1 9JJ sing 38 n n C3 C4 9JJ sing 39 n n C2N C3N 9JJ sing 40 n y C4N C3N 9JJ doub 41 n y C5B O5B 9JJ sing 42 n n B1 C5 9JJ sing 43 n n B1 O1 9JJ sing 44 n n C4 C5 9JJ doub 45 n y C4 C15 9JJ sing 46 n y C5 C12 9JJ sing 47 n y C15 C14 9JJ doub 48 n y F26 C23 9JJ sing 49 n n C3N C7N 9JJ sing 50 n n C12 C13 9JJ doub 51 n y O5B PA 9JJ sing 52 n n C14 C13 9JJ sing 53 n y C13 O16 9JJ sing 54 n n O2N PN 9JJ doub 55 n n PN O1N 9JJ sing 56 n n PN O3 9JJ sing 57 n n C22 C21 9JJ doub 58 n y C22 C17 9JJ sing 59 n y C21 C20 9JJ sing 60 n y O16 C17 9JJ sing 61 n n C17 C18 9JJ doub 62 n y C20 C23 9JJ sing 63 n n C20 C19 9JJ doub 64 n y C23 F25 9JJ sing 65 n n C23 F24 9JJ sing 66 n n C18 C19 9JJ sing 67 n y O3 PA 9JJ sing 68 n n C7N O7N 9JJ doub 69 n n C7N N7N 9JJ sing 70 n n PA O2A 9JJ doub 71 n n PA O1A 9JJ sing 72 n n O1A H1 9JJ sing 73 n n C5B H2 9JJ sing 74 n n C5B H3 9JJ sing 75 n n C4B H4 9JJ sing 76 n n C3B H5 9JJ sing 77 n n O3B H6 9JJ sing 78 n n C2B H7 9JJ sing 79 n n O2B H8 9JJ sing 80 n n C1B H9 9JJ sing 81 n n C8A H10 9JJ sing 82 n n N6A H11 9JJ sing 83 n n N6A H12 9JJ sing 84 n n C2A H13 9JJ sing 85 n n O1N H14 9JJ sing 86 n n C5D H15 9JJ sing 87 n n C5D H16 9JJ sing 88 n n C4D H17 9JJ sing 89 n n C3D H18 9JJ sing 90 n n O3D H19 9JJ sing 91 n n C2D H20 9JJ sing 92 n n C1D H21 9JJ sing 93 n n C2N H22 9JJ sing 94 n n N7N H23 9JJ sing 95 n n N7N H24 9JJ sing 96 n n C4N H25 9JJ sing 97 n n C5N H26 9JJ sing 98 n n C6N H27 9JJ sing 99 n n C3 H28 9JJ sing 100 n n C3 H29 9JJ sing 101 n n C12 H30 9JJ sing 102 n n C14 H31 9JJ sing 103 n n C15 H32 9JJ sing 104 n n C18 H33 9JJ sing 105 n n C19 H34 9JJ sing 106 n n C21 H35 9JJ sing 107 n n C22 H36 9JJ sing 108 n n O1 H37 9JJ sing 109 n n # _atom_sites.entry_id 5VRM _atom_sites.fract_transf_matrix[1][1] 0.007978 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002226 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01079 _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] 0.010186 _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 E 2 9JJ A 1 300 300 9JJ NAD . F 2 9JJ B 1 300 300 9JJ NAD . G 2 9JJ C 1 300 300 9JJ NAD . H 2 9JJ D 1 300 300 9JJ NAD . I 3 HOH A 1 401 58 HOH HOH . I 3 HOH A 2 402 12 HOH HOH . I 3 HOH A 3 403 19 HOH HOH . I 3 HOH A 4 404 10 HOH HOH . I 3 HOH A 5 405 6 HOH HOH . I 3 HOH A 6 406 15 HOH HOH . I 3 HOH A 7 407 17 HOH HOH . I 3 HOH A 8 408 13 HOH HOH . I 3 HOH A 9 409 23 HOH HOH . I 3 HOH A 10 410 3 HOH HOH . I 3 HOH A 11 411 9 HOH HOH . I 3 HOH A 12 412 16 HOH HOH . I 3 HOH A 13 413 21 HOH HOH . I 3 HOH A 14 414 2 HOH HOH . I 3 HOH A 15 415 61 HOH HOH . I 3 HOH A 16 416 20 HOH HOH . I 3 HOH A 17 417 8 HOH HOH . I 3 HOH A 18 418 55 HOH HOH . I 3 HOH A 19 419 11 HOH HOH . I 3 HOH A 20 420 56 HOH HOH . I 3 HOH A 21 421 7 HOH HOH . I 3 HOH A 22 422 5 HOH HOH . I 3 HOH A 23 423 4 HOH HOH . J 3 HOH B 1 401 29 HOH HOH . J 3 HOH B 2 402 27 HOH HOH . J 3 HOH B 3 403 25 HOH HOH . J 3 HOH B 4 404 59 HOH HOH . J 3 HOH B 5 405 31 HOH HOH . J 3 HOH B 6 406 18 HOH HOH . J 3 HOH B 7 407 26 HOH HOH . J 3 HOH B 8 408 33 HOH HOH . J 3 HOH B 9 409 28 HOH HOH . J 3 HOH B 10 410 57 HOH HOH . J 3 HOH B 11 411 30 HOH HOH . J 3 HOH B 12 412 32 HOH HOH . J 3 HOH B 13 413 14 HOH HOH . K 3 HOH C 1 401 39 HOH HOH . K 3 HOH C 2 402 35 HOH HOH . K 3 HOH C 3 403 43 HOH HOH . K 3 HOH C 4 404 34 HOH HOH . K 3 HOH C 5 405 38 HOH HOH . K 3 HOH C 6 406 36 HOH HOH . K 3 HOH C 7 407 42 HOH HOH . K 3 HOH C 8 408 40 HOH HOH . K 3 HOH C 9 409 46 HOH HOH . K 3 HOH C 10 410 45 HOH HOH . K 3 HOH C 11 411 47 HOH HOH . K 3 HOH C 12 412 37 HOH HOH . L 3 HOH D 1 401 54 HOH HOH . L 3 HOH D 2 402 41 HOH HOH . L 3 HOH D 3 403 22 HOH HOH . L 3 HOH D 4 404 1 HOH HOH . L 3 HOH D 5 405 52 HOH HOH . L 3 HOH D 6 406 48 HOH HOH . L 3 HOH D 7 407 44 HOH HOH . L 3 HOH D 8 408 53 HOH HOH . L 3 HOH D 9 409 50 HOH HOH . L 3 HOH D 10 410 51 HOH HOH . L 3 HOH D 11 411 49 HOH HOH . L 3 HOH D 12 412 24 HOH HOH . L 3 HOH D 13 413 60 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 PA 9JJ . . . H 2 273.464 45.24 136.557 1 96.03 ? PA 9JJ 300 D 1 HETATM 2 O O1A 9JJ . . . H 2 274.318 44.27 137.346 1 88.8 ? O1A 9JJ 300 D 1 HETATM 3 O O2A 9JJ . . . H 2 273.222 46.631 137.097 1 90.92 ? O2A 9JJ 300 D 1 HETATM 4 O O5B 9JJ . . . H 2 274.106 45.334 135.084 1 99.11 ? O5B 9JJ 300 D 1 HETATM 5 C C5B 9JJ . . . H 2 274.016 46.503 134.273 1 100.66 ? C5B 9JJ 300 D 1 HETATM 6 C C4B 9JJ . . . H 2 275.128 46.415 133.237 1 101.47 ? C4B 9JJ 300 D 1 HETATM 7 O O4B 9JJ . . . H 2 275.004 47.431 132.238 1 100.8 ? O4B 9JJ 300 D 1 HETATM 8 C C3B 9JJ . . . H 2 276.494 46.598 133.888 1 106.28 ? C3B 9JJ 300 D 1 HETATM 9 O O3B 9JJ . . . H 2 277.228 45.368 133.907 1 107.97 ? O3B 9JJ 300 D 1 HETATM 10 C C2B 9JJ . . . H 2 277.2 47.656 133.056 1 107.53 ? C2B 9JJ 300 D 1 HETATM 11 O O2B 9JJ . . . H 2 278.533 47.262 132.706 1 112.78 ? O2B 9JJ 300 D 1 HETATM 12 C C1B 9JJ . . . H 2 276.319 47.81 131.822 1 103.4 ? C1B 9JJ 300 D 1 HETATM 13 N N9A 9JJ . . . H 2 276.374 49.193 131.276 1 99.63 ? N9A 9JJ 300 D 1 HETATM 14 C C8A 9JJ . . . H 2 275.762 50.281 131.769 1 98.73 ? C8A 9JJ 300 D 1 HETATM 15 N N7A 9JJ . . . H 2 276.061 51.346 130.987 1 95.18 ? N7A 9JJ 300 D 1 HETATM 16 C C5A 9JJ . . . H 2 276.869 50.912 129.998 1 95.44 ? C5A 9JJ 300 D 1 HETATM 17 C C6A 9JJ . . . H 2 277.489 51.531 128.918 1 95.97 ? C6A 9JJ 300 D 1 HETATM 18 N N6A 9JJ . . . H 2 277.312 52.988 128.674 1 95.65 ? N6A 9JJ 300 D 1 HETATM 19 N N1A 9JJ . . . H 2 278.26 50.792 128.087 1 96.05 ? N1A 9JJ 300 D 1 HETATM 20 C C2A 9JJ . . . H 2 278.432 49.476 128.29 1 95.14 ? C2A 9JJ 300 D 1 HETATM 21 N N3A 9JJ . . . H 2 277.845 48.856 129.324 1 92.84 ? N3A 9JJ 300 D 1 HETATM 22 C C4A 9JJ . . . H 2 277.062 49.552 130.187 1 95.58 ? C4A 9JJ 300 D 1 HETATM 23 O O3 9JJ . . . H 2 272.014 44.598 136.236 1 90.59 ? O3 9JJ 300 D 1 HETATM 24 P PN 9JJ . . . H 2 271.789 43.24 135.387 1 82.53 ? PN 9JJ 300 D 1 HETATM 25 O O1N 9JJ . . . H 2 270.552 42.576 135.942 1 85.58 ? O1N 9JJ 300 D 1 HETATM 26 O O2N 9JJ . . . H 2 273.085 42.464 135.342 1 81.62 ? O2N 9JJ 300 D 1 HETATM 27 O O5D 9JJ . . . H 2 271.439 43.732 133.885 1 86.59 ? O5D 9JJ 300 D 1 HETATM 28 C C5D 9JJ . . . H 2 270.954 42.811 132.893 1 83.49 ? C5D 9JJ 300 D 1 HETATM 29 C C4D 9JJ . . . H 2 270.205 43.509 131.754 1 82.7 ? C4D 9JJ 300 D 1 HETATM 30 O O4D 9JJ . . . H 2 268.915 42.919 131.527 1 79.8 ? O4D 9JJ 300 D 1 HETATM 31 C C3D 9JJ . . . H 2 269.839 44.934 132.101 1 84.42 ? C3D 9JJ 300 D 1 HETATM 32 O O3D 9JJ . . . H 2 269.444 45.584 130.885 1 86.34 ? O3D 9JJ 300 D 1 HETATM 33 C C2D 9JJ . . . H 2 268.654 44.691 133.012 1 77.26 ? C2D 9JJ 300 D 1 HETATM 34 O O2D 9JJ . . . H 2 267.946 45.87 133.376 1 74.6 ? O2D 9JJ 300 D 1 HETATM 35 C C1D 9JJ . . . H 2 267.883 43.688 132.173 1 71.83 ? C1D 9JJ 300 D 1 HETATM 36 N N1N 9JJ . . . H 2 267.034 42.781 132.945 1 66.7 ? N1N 9JJ 300 D 1 HETATM 37 C C2N 9JJ . . . H 2 266.751 42.988 134.243 1 63.77 ? C2N 9JJ 300 D 1 HETATM 38 C C3N 9JJ . . . H 2 265.971 42.131 134.907 1 61.82 ? C3N 9JJ 300 D 1 HETATM 39 C C7N 9JJ . . . H 2 265.653 42.351 136.352 1 66.66 ? C7N 9JJ 300 D 1 HETATM 40 O O7N 9JJ . . . H 2 264.504 42.22 136.744 1 66.12 ? O7N 9JJ 300 D 1 HETATM 41 N N7N 9JJ . . . H 2 266.707 42.707 137.24 1 71.46 ? N7N 9JJ 300 D 1 HETATM 42 C C4N 9JJ . . . H 2 265.455 41.027 134.256 1 57.78 ? C4N 9JJ 300 D 1 HETATM 43 C C5N 9JJ . . . H 2 265.764 40.84 132.922 1 58.93 ? C5N 9JJ 300 D 1 HETATM 44 C C6N 9JJ . . . H 2 266.546 41.721 132.296 1 61.41 ? C6N 9JJ 300 D 1 HETATM 45 B B1 9JJ . . . H 2 268.57 46.667 134.378 0.7 74.3 ? B1 9JJ 300 D 1 HETATM 46 O O2 9JJ . . . H 2 269.897 47.088 134.06 0.7 77.47 ? O2 9JJ 300 D 1 HETATM 47 C C3 9JJ . . . H 2 270.097 48.508 134.119 0.7 77.51 ? C3 9JJ 300 D 1 HETATM 48 C C4 9JJ . . . H 2 268.75 49.016 134.544 0.7 74.03 ? C4 9JJ 300 D 1 HETATM 49 C C5 9JJ . . . H 2 267.863 47.996 134.694 0.7 72.1 ? C5 9JJ 300 D 1 HETATM 50 C C12 9JJ . . . H 2 266.552 48.201 135.081 0.7 69.93 ? C12 9JJ 300 D 1 HETATM 51 C C13 9JJ . . . H 2 266.157 49.514 135.309 0.7 67.87 ? C13 9JJ 300 D 1 HETATM 52 C C14 9JJ . . . H 2 267.08 50.555 135.148 0.7 69.31 ? C14 9JJ 300 D 1 HETATM 53 C C15 9JJ . . . H 2 268.386 50.323 134.762 0.7 70.88 ? C15 9JJ 300 D 1 HETATM 54 O O16 9JJ . . . H 2 264.866 49.773 135.691 0.7 67.11 ? O16 9JJ 300 D 1 HETATM 55 C C17 9JJ . . . H 2 264.374 51.053 135.752 0.7 70.07 ? C17 9JJ 300 D 1 HETATM 56 C C18 9JJ . . . H 2 263.056 51.269 136.125 0.7 72.23 ? C18 9JJ 300 D 1 HETATM 57 C C19 9JJ . . . H 2 262.557 52.568 136.189 0.7 74.5 ? C19 9JJ 300 D 1 HETATM 58 C C20 9JJ . . . H 2 263.369 53.652 135.885 0.7 75.66 ? C20 9JJ 300 D 1 HETATM 59 C C21 9JJ . . . H 2 264.684 53.439 135.513 0.7 73.58 ? C21 9JJ 300 D 1 HETATM 60 C C22 9JJ . . . H 2 265.174 52.152 135.45 0.7 70.61 ? C22 9JJ 300 D 1 HETATM 61 C C23 9JJ . . . H 2 262.825 55.047 135.955 0.7 78.49 ? C23 9JJ 300 D 1 HETATM 62 F F24 9JJ . . . H 2 262.064 55.156 137.031 0.7 77.27 ? F24 9JJ 300 D 1 HETATM 63 F F25 9JJ . . . H 2 263.817 55.915 136.058 0.7 81.13 ? F25 9JJ 300 D 1 HETATM 64 F F26 9JJ . . . H 2 262.136 55.277 134.843 0.7 75.94 ? F26 9JJ 300 D 1 HETATM 65 O O1 9JJ . . . H 2 268.666 45.874 135.689 0.7 72.29 ? O1 9JJ 300 D 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 65 #