data_9N3R # _model_server_result.job_id 6-rgEXSPjZlUY-fHCn8hmQ _model_server_result.datetime_utc '2025-07-05 09:51:52' _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 9n3r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 9N3R # _exptl.entry_id 9N3R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 9N3R _cell.length_a 98.21 _cell.length_b 136.6 _cell.length_c 178.01 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9N3R _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,I,J,K,L,M,N,O,P,Q,R,S _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 I N N # _chem_comp.formula 'C11 H15 N5 O3 S' _chem_comp.formula_weight 297.334 _chem_comp.id MTA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 CS S5' MTA sing 323 n n CS HCS1 MTA sing 324 n n CS HCS2 MTA sing 325 n n CS HCS3 MTA sing 326 n n S5' C5' MTA sing 327 n n C5' C4' MTA sing 328 n n C5' "H5'1" MTA sing 329 n n C5' "H5'2" MTA sing 330 n n C4' O4' MTA sing 331 n n C4' C3' MTA sing 332 n n C4' H4' MTA sing 333 n n O4' C1' MTA sing 334 n n C2' O2' MTA sing 335 n n C2' C3' MTA sing 336 n n C2' C1' MTA sing 337 n n C2' H2' MTA sing 338 n n O2' HO2' MTA sing 339 n n C3' O3' MTA sing 340 n n C3' H3' MTA sing 341 n n O3' H3T MTA sing 342 n n C1' N9 MTA sing 343 n n C1' H1' MTA sing 344 n n N9 C8 MTA sing 345 n y N9 C4 MTA sing 346 n y C8 N7 MTA doub 347 n y C8 H8 MTA sing 348 n n N7 C5 MTA sing 349 n y C5 C6 MTA sing 350 n y C5 C4 MTA doub 351 n y C6 N6 MTA sing 352 n n C6 N1 MTA doub 353 n y N6 H61 MTA sing 354 n n N6 H62 MTA sing 355 n n N1 C2 MTA sing 356 n y C2 N3 MTA doub 357 n y C2 H2 MTA sing 358 n n N3 C4 MTA sing 359 n y # _atom_sites.entry_id 9N3R _atom_sites.fract_transf_matrix[1][1] 0.010182 _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] 0.007321 _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] 0.005618 _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 3 MTA A 1 701 1 MTA MTA . F 4 A1BV0 A 1 702 1 A1BV0 LIG . G 5 CL A 1 703 4 CL CL . H 5 CL A 1 704 5 CL CL . I 3 MTA C 1 701 2 MTA MTA . J 4 A1BV0 C 1 702 2 A1BV0 LIG . K 5 CL C 1 703 1 CL CL . L 5 CL C 1 704 2 CL CL . M 5 CL C 1 705 3 CL CL . N 6 EDO C 1 706 2 EDO EDO . O 6 EDO D 1 401 1 EDO EDO . P 7 HOH A 1 801 66 HOH HOH . P 7 HOH A 2 802 100 HOH HOH . P 7 HOH A 3 803 46 HOH HOH . P 7 HOH A 4 804 63 HOH HOH . P 7 HOH A 5 805 7 HOH HOH . P 7 HOH A 6 806 43 HOH HOH . P 7 HOH A 7 807 103 HOH HOH . P 7 HOH A 8 808 1 HOH HOH . P 7 HOH A 9 809 90 HOH HOH . P 7 HOH A 10 810 65 HOH HOH . P 7 HOH A 11 811 37 HOH HOH . P 7 HOH A 12 812 49 HOH HOH . P 7 HOH A 13 813 36 HOH HOH . P 7 HOH A 14 814 20 HOH HOH . P 7 HOH A 15 815 38 HOH HOH . P 7 HOH A 16 816 96 HOH HOH . P 7 HOH A 17 817 8 HOH HOH . P 7 HOH A 18 818 54 HOH HOH . P 7 HOH A 19 819 94 HOH HOH . P 7 HOH A 20 820 10 HOH HOH . P 7 HOH A 21 821 51 HOH HOH . P 7 HOH A 22 822 93 HOH HOH . P 7 HOH A 23 823 77 HOH HOH . P 7 HOH A 24 824 21 HOH HOH . P 7 HOH A 25 825 98 HOH HOH . P 7 HOH A 26 826 56 HOH HOH . P 7 HOH A 27 827 41 HOH HOH . P 7 HOH A 28 828 79 HOH HOH . P 7 HOH A 29 829 47 HOH HOH . P 7 HOH A 30 830 60 HOH HOH . P 7 HOH A 31 831 14 HOH HOH . P 7 HOH A 32 832 42 HOH HOH . P 7 HOH A 33 833 70 HOH HOH . P 7 HOH A 34 834 74 HOH HOH . P 7 HOH A 35 835 33 HOH HOH . P 7 HOH A 36 836 3 HOH HOH . P 7 HOH A 37 837 44 HOH HOH . P 7 HOH A 38 838 9 HOH HOH . P 7 HOH A 39 839 35 HOH HOH . Q 7 HOH B 1 401 45 HOH HOH . Q 7 HOH B 2 402 73 HOH HOH . Q 7 HOH B 3 403 55 HOH HOH . Q 7 HOH B 4 404 59 HOH HOH . Q 7 HOH B 5 405 75 HOH HOH . R 7 HOH C 1 801 97 HOH HOH . R 7 HOH C 2 802 34 HOH HOH . R 7 HOH C 3 803 80 HOH HOH . R 7 HOH C 4 804 50 HOH HOH . R 7 HOH C 5 805 62 HOH HOH . R 7 HOH C 6 806 99 HOH HOH . R 7 HOH C 7 807 53 HOH HOH . R 7 HOH C 8 808 81 HOH HOH . R 7 HOH C 9 809 89 HOH HOH . R 7 HOH C 10 810 82 HOH HOH . R 7 HOH C 11 811 30 HOH HOH . R 7 HOH C 12 812 28 HOH HOH . R 7 HOH C 13 813 48 HOH HOH . R 7 HOH C 14 814 13 HOH HOH . R 7 HOH C 15 815 69 HOH HOH . R 7 HOH C 16 816 78 HOH HOH . R 7 HOH C 17 817 11 HOH HOH . R 7 HOH C 18 818 52 HOH HOH . R 7 HOH C 19 819 5 HOH HOH . R 7 HOH C 20 820 64 HOH HOH . R 7 HOH C 21 821 4 HOH HOH . R 7 HOH C 22 822 101 HOH HOH . R 7 HOH C 23 823 95 HOH HOH . R 7 HOH C 24 824 68 HOH HOH . R 7 HOH C 25 825 84 HOH HOH . R 7 HOH C 26 826 102 HOH HOH . R 7 HOH C 27 827 19 HOH HOH . R 7 HOH C 28 828 32 HOH HOH . R 7 HOH C 29 829 87 HOH HOH . R 7 HOH C 30 830 2 HOH HOH . R 7 HOH C 31 831 72 HOH HOH . R 7 HOH C 32 832 27 HOH HOH . R 7 HOH C 33 833 25 HOH HOH . R 7 HOH C 34 834 58 HOH HOH . R 7 HOH C 35 835 86 HOH HOH . R 7 HOH C 36 836 83 HOH HOH . R 7 HOH C 37 837 57 HOH HOH . R 7 HOH C 38 838 88 HOH HOH . R 7 HOH C 39 839 39 HOH HOH . R 7 HOH C 40 840 12 HOH HOH . R 7 HOH C 41 841 61 HOH HOH . R 7 HOH C 42 842 29 HOH HOH . R 7 HOH C 43 843 6 HOH HOH . R 7 HOH C 44 844 40 HOH HOH . R 7 HOH C 45 845 31 HOH HOH . R 7 HOH C 46 846 26 HOH HOH . R 7 HOH C 47 847 67 HOH HOH . S 7 HOH D 1 501 85 HOH HOH . S 7 HOH D 2 502 17 HOH HOH . S 7 HOH D 3 503 71 HOH HOH . S 7 HOH D 4 504 15 HOH HOH . S 7 HOH D 5 505 23 HOH HOH . S 7 HOH D 6 506 18 HOH HOH . S 7 HOH D 7 507 76 HOH HOH . S 7 HOH D 8 508 22 HOH HOH . S 7 HOH D 9 509 16 HOH HOH . S 7 HOH D 10 510 24 HOH HOH . S 7 HOH D 11 511 91 HOH HOH . S 7 HOH D 12 512 92 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 CS MTA . . . E 3 23.113 -28.812 51.181 1 60.14 ? CS MTA 701 A 1 HETATM 2 S S5' MTA . . . E 3 21.778 -27.622 50.929 1 66.02 ? S5' MTA 701 A 1 HETATM 3 C C5' MTA . . . E 3 20.397 -28.777 50.7 1 67.19 ? C5' MTA 701 A 1 HETATM 4 C C4' MTA . . . E 3 20.653 -29.683 49.507 1 71.26 ? C4' MTA 701 A 1 HETATM 5 O O4' MTA . . . E 3 19.699 -30.749 49.455 1 71.44 ? O4' MTA 701 A 1 HETATM 6 C C2' MTA . . . E 3 19.176 -29.374 47.653 1 70.36 ? C2' MTA 701 A 1 HETATM 7 O O2' MTA . . . E 3 19.068 -29.412 46.262 1 62.94 ? O2' MTA 701 A 1 HETATM 8 C C3' MTA . . . E 3 20.553 -28.943 48.175 1 73.3 ? C3' MTA 701 A 1 HETATM 9 O O3' MTA . . . E 3 21.567 -29.405 47.325 1 64.33 ? O3' MTA 701 A 1 HETATM 10 C C1' MTA . . . E 3 19.066 -30.792 48.213 1 65.07 ? C1' MTA 701 A 1 HETATM 11 N N9 MTA . . . E 3 17.705 -31.242 48.392 1 65.13 ? N9 MTA 701 A 1 HETATM 12 C C8 MTA . . . E 3 16.714 -30.614 49.097 1 64.92 ? C8 MTA 701 A 1 HETATM 13 N N7 MTA . . . E 3 15.586 -31.26 49.082 1 58.98 ? N7 MTA 701 A 1 HETATM 14 C C5 MTA . . . E 3 15.84 -32.375 48.328 1 54.58 ? C5 MTA 701 A 1 HETATM 15 C C6 MTA . . . E 3 15.043 -33.465 47.936 1 56.01 ? C6 MTA 701 A 1 HETATM 16 N N6 MTA . . . E 3 13.763 -33.581 48.29 1 66.14 ? N6 MTA 701 A 1 HETATM 17 N N1 MTA . . . E 3 15.606 -34.414 47.179 1 62.64 ? N1 MTA 701 A 1 HETATM 18 C C2 MTA . . . E 3 16.885 -34.292 46.83 1 69.75 ? C2 MTA 701 A 1 HETATM 19 N N3 MTA . . . E 3 17.729 -33.321 47.134 1 73.75 ? N3 MTA 701 A 1 HETATM 20 C C4 MTA . . . E 3 17.154 -32.385 47.887 1 65.07 ? C4 MTA 701 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #