data_3KPD # _model_server_result.job_id mraLMc3SX9KYXgr5Z5GF0w _model_server_result.datetime_utc '2025-02-18 12:13:28' _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 3kpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2}' # _entry.id 3KPD # _exptl.entry_id 3KPD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _entity.pdbx_number_of_molecules 5 _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 3KPD _cell.length_a 58.671 _cell.length_b 165.794 _cell.length_c 122.997 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F 1 1,2 B,C,G,H,I 2 1 D,J,K 3 1,3 # 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' 3_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 58.671 0 -61.4985 3 'crystal symmetry operation' 4_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 ? 2 E N N ? 2 F N N ? 2 I N N ? 2 J N N ? 2 K 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 222 n n CS HCS1 MTA sing 223 n n CS HCS2 MTA sing 224 n n CS HCS3 MTA sing 225 n n S5' C5' MTA sing 226 n n C5' C4' MTA sing 227 n n C5' "H5'1" MTA sing 228 n n C5' "H5'2" MTA sing 229 n n C4' O4' MTA sing 230 n n C4' C3' MTA sing 231 n n C4' H4' MTA sing 232 n n O4' C1' MTA sing 233 n n C2' O2' MTA sing 234 n n C2' C3' MTA sing 235 n n C2' C1' MTA sing 236 n n C2' H2' MTA sing 237 n n O2' HO2' MTA sing 238 n n C3' O3' MTA sing 239 n n C3' H3' MTA sing 240 n n O3' H3T MTA sing 241 n n C1' N9 MTA sing 242 n n C1' H1' MTA sing 243 n n N9 C8 MTA sing 244 n y N9 C4 MTA sing 245 n y C8 N7 MTA doub 246 n y C8 H8 MTA sing 247 n n N7 C5 MTA sing 248 n y C5 C6 MTA sing 249 n y C5 C4 MTA doub 250 n y C6 N6 MTA sing 251 n n C6 N1 MTA doub 252 n y N6 H61 MTA sing 253 n n N6 H62 MTA sing 254 n n N1 C2 MTA sing 255 n y C2 N3 MTA doub 256 n y C2 H2 MTA sing 257 n n N3 C4 MTA sing 258 n y # _atom_sites.entry_id 3KPD _atom_sites.fract_transf_matrix[1][1] 0.017044 _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] 0.006032 _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] 0.00813 _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 MTA A 1 1 1 MTA MTA . F 2 MTA A 1 2 2 MTA MTA . G 3 SAM B 1 1000 1000 SAM SAM . H 3 SAM C 1 1000 1000 SAM SAM . I 2 MTA C 1 1 1 MTA MTA . J 2 MTA D 1 1 1 MTA MTA . K 2 MTA D 1 2 2 MTA MTA . # 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 . . . F 2 27.105 15.129 -23.911 1 74.69 ? CS MTA 2 A 1 HETATM 2 S S5' MTA . . . F 2 27.201 13.393 -24.229 1 76.11 ? S5' MTA 2 A 1 HETATM 3 C C5' MTA . . . F 2 26.916 12.531 -22.722 1 69.83 ? C5' MTA 2 A 1 HETATM 4 C C4' MTA . . . F 2 25.427 12.224 -22.651 1 65.45 ? C4' MTA 2 A 1 HETATM 5 O O4' MTA . . . F 2 24.69 13.33 -23.155 1 62.64 ? O4' MTA 2 A 1 HETATM 6 C C2' MTA . . . F 2 23.83 11.509 -24.333 1 61.46 ? C2' MTA 2 A 1 HETATM 7 O O2' MTA . . . F 2 22.767 10.547 -24.365 1 58.56 ? O2' MTA 2 A 1 HETATM 8 C C3' MTA . . . F 2 25.009 11.024 -23.497 1 63.36 ? C3' MTA 2 A 1 HETATM 9 O O3' MTA . . . F 2 24.662 9.93 -22.628 1 63.14 ? O3' MTA 2 A 1 HETATM 10 C C1' MTA . . . F 2 23.456 12.797 -23.605 1 61.18 ? C1' MTA 2 A 1 HETATM 11 N N9 MTA . . . F 2 22.707 13.839 -24.35 1 60.29 ? N9 MTA 2 A 1 HETATM 12 C C8 MTA . . . F 2 22.92 14.295 -25.589 1 60.58 ? C8 MTA 2 A 1 HETATM 13 N N7 MTA . . . F 2 22.018 15.262 -25.912 1 61.43 ? N7 MTA 2 A 1 HETATM 14 C C5 MTA . . . F 2 21.211 15.445 -24.854 1 61.69 ? C5 MTA 2 A 1 HETATM 15 C C6 MTA . . . F 2 20.041 16.302 -24.511 1 62.53 ? C6 MTA 2 A 1 HETATM 16 N N6 MTA . . . F 2 19.535 17.203 -25.393 1 63.46 ? N6 MTA 2 A 1 HETATM 17 N N1 MTA . . . F 2 19.494 16.157 -23.281 1 61.31 ? N1 MTA 2 A 1 HETATM 18 C C2 MTA . . . F 2 19.979 15.269 -22.393 1 60.3 ? C2 MTA 2 A 1 HETATM 19 N N3 MTA . . . F 2 21.026 14.468 -22.636 1 60.19 ? N3 MTA 2 A 1 HETATM 20 C C4 MTA . . . F 2 21.676 14.505 -23.827 1 60.82 ? C4 MTA 2 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #