data_5VRM # _model_server_result.job_id Vn6anJYKaelmM_KZg4RIhg _model_server_result.datetime_utc '2024-10-19 17:35:02' _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":"E","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 . . . E 2 253.609 12.021 110.927 1 39.94 ? PA 9JJ 300 A 1 HETATM 2 O O1A 9JJ . . . E 2 254.984 11.433 111.059 1 45.37 ? O1A 9JJ 300 A 1 HETATM 3 O O2A 9JJ . . . E 2 252.598 11.313 110.077 1 44.37 ? O2A 9JJ 300 A 1 HETATM 4 O O5B 9JJ . . . E 2 253.035 12.224 112.401 1 43.32 ? O5B 9JJ 300 A 1 HETATM 5 C C5B 9JJ . . . E 2 251.669 11.953 112.697 1 41.43 ? C5B 9JJ 300 A 1 HETATM 6 C C4B 9JJ . . . E 2 251.686 10.93 113.818 1 40.37 ? C4B 9JJ 300 A 1 HETATM 7 O O4B 9JJ . . . E 2 250.493 11.028 114.596 1 40.17 ? O4B 9JJ 300 A 1 HETATM 8 C C3B 9JJ . . . E 2 251.775 9.519 113.236 1 40.41 ? C3B 9JJ 300 A 1 HETATM 9 O O3B 9JJ . . . E 2 252.877 8.784 113.775 1 37.67 ? O3B 9JJ 300 A 1 HETATM 10 C C2B 9JJ . . . E 2 250.469 8.903 113.667 1 41.35 ? C2B 9JJ 300 A 1 HETATM 11 O O2B 9JJ . . . E 2 250.586 7.5 113.911 1 44.59 ? O2B 9JJ 300 A 1 HETATM 12 C C1B 9JJ . . . E 2 250.117 9.699 114.916 1 40.56 ? C1B 9JJ 300 A 1 HETATM 13 N N9A 9JJ . . . E 2 248.687 9.448 115.196 1 40.98 ? N9A 9JJ 300 A 1 HETATM 14 C C8A 9JJ . . . E 2 247.636 9.688 114.392 1 40.25 ? C8A 9JJ 300 A 1 HETATM 15 N N7A 9JJ . . . E 2 246.514 9.278 115.028 1 40.88 ? N7A 9JJ 300 A 1 HETATM 16 C C5A 9JJ . . . E 2 246.887 8.772 116.228 1 40.23 ? C5A 9JJ 300 A 1 HETATM 17 C C6A 9JJ . . . E 2 246.205 8.211 117.289 1 40.33 ? C6A 9JJ 300 A 1 HETATM 18 N N6A 9JJ . . . E 2 244.732 8.07 117.24 1 41.76 ? N6A 9JJ 300 A 1 HETATM 19 N N1A 9JJ . . . E 2 246.89 7.796 118.373 1 41.14 ? N1A 9JJ 300 A 1 HETATM 20 C C2A 9JJ . . . E 2 248.222 7.916 118.438 1 40.42 ? C2A 9JJ 300 A 1 HETATM 21 N N3A 9JJ . . . E 2 248.909 8.451 117.425 1 38.59 ? N3A 9JJ 300 A 1 HETATM 22 C C4A 9JJ . . . E 2 248.258 8.881 116.322 1 39.63 ? C4A 9JJ 300 A 1 HETATM 23 O O3 9JJ . . . E 2 253.66 13.59 110.562 1 37.71 ? O3 9JJ 300 A 1 HETATM 24 P PN 9JJ . . . E 2 254.653 14.627 111.292 1 34.15 ? PN 9JJ 300 A 1 HETATM 25 O O1N 9JJ . . . E 2 254.839 15.73 110.294 1 33.68 ? O1N 9JJ 300 A 1 HETATM 26 O O2N 9JJ . . . E 2 255.892 13.903 111.789 1 34.41 ? O2N 9JJ 300 A 1 HETATM 27 O O5D 9JJ . . . E 2 253.797 15.181 112.54 1 33.64 ? O5D 9JJ 300 A 1 HETATM 28 C C5D 9JJ . . . E 2 254.262 15.167 113.893 1 33.34 ? C5D 9JJ 300 A 1 HETATM 29 C C4D 9JJ . . . E 2 253.765 16.371 114.693 1 33.43 ? C4D 9JJ 300 A 1 HETATM 30 O O4D 9JJ . . . E 2 254.444 17.576 114.327 1 34.11 ? O4D 9JJ 300 A 1 HETATM 31 C C3D 9JJ . . . E 2 252.292 16.677 114.491 1 32.87 ? C3D 9JJ 300 A 1 HETATM 32 O O3D 9JJ . . . E 2 251.755 17.122 115.741 1 31.5 ? O3D 9JJ 300 A 1 HETATM 33 C C2D 9JJ . . . E 2 252.283 17.804 113.482 1 32.17 ? C2D 9JJ 300 A 1 HETATM 34 O O2D 9JJ . . . E 2 251.078 18.56 113.541 1 34.37 ? O2D 9JJ 300 A 1 HETATM 35 C C1D 9JJ . . . E 2 253.5 18.58 113.946 1 32.73 ? C1D 9JJ 300 A 1 HETATM 36 N N1N 9JJ . . . E 2 254.05 19.497 112.937 1 33.95 ? N1N 9JJ 300 A 1 HETATM 37 C C2N 9JJ . . . E 2 254.362 19.071 111.697 1 35.05 ? C2N 9JJ 300 A 1 HETATM 38 C C3N 9JJ . . . E 2 254.869 19.916 110.78 1 35.6 ? C3N 9JJ 300 A 1 HETATM 39 C C7N 9JJ . . . E 2 255.23 19.455 109.393 1 36.87 ? C7N 9JJ 300 A 1 HETATM 40 O O7N 9JJ . . . E 2 255.322 20.263 108.489 1 38.31 ? O7N 9JJ 300 A 1 HETATM 41 N N7N 9JJ . . . E 2 255.486 18.092 109.108 1 37.05 ? N7N 9JJ 300 A 1 HETATM 42 C C4N 9JJ . . . E 2 255.066 21.248 111.126 1 35.38 ? C4N 9JJ 300 A 1 HETATM 43 C C5N 9JJ . . . E 2 254.739 21.665 112.417 1 35.28 ? C5N 9JJ 300 A 1 HETATM 44 C C6N 9JJ . . . E 2 254.24 20.779 113.291 1 33.86 ? C6N 9JJ 300 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #