data_3KPD # _model_server_result.job_id r84RoNX4a_D0zqSCsSrylw _model_server_result.datetime_utc '2024-11-26 09:35:33' _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":"G","auth_seq_id":1000}' # _entry.id 3KPD # _exptl.entry_id 3KPD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 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 ? 3 G N N ? 3 H N N # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 N CA SAM sing 299 n n N HN1 SAM sing 300 n n N HN2 SAM sing 301 n n CA C SAM sing 302 n n CA CB SAM sing 303 n n CA HA SAM sing 304 n n C O SAM doub 305 n n C OXT SAM sing 306 n n CB CG SAM sing 307 n n CB HB1 SAM sing 308 n n CB HB2 SAM sing 309 n n CG SD SAM sing 310 n n CG HG1 SAM sing 311 n n CG HG2 SAM sing 312 n n SD CE SAM sing 313 n n SD C5' SAM sing 314 n n CE HE1 SAM sing 315 n n CE HE2 SAM sing 316 n n CE HE3 SAM sing 317 n n C5' C4' SAM sing 318 n n C5' "H5'1" SAM sing 319 n n C5' "H5'2" SAM sing 320 n n C4' O4' SAM sing 321 n n C4' C3' SAM sing 322 n n C4' H4' SAM sing 323 n n O4' C1' SAM sing 324 n n C3' O3' SAM sing 325 n n C3' C2' SAM sing 326 n n C3' H3' SAM sing 327 n n O3' HO3' SAM sing 328 n n C2' O2' SAM sing 329 n n C2' C1' SAM sing 330 n n C2' H2' SAM sing 331 n n O2' HO2' SAM sing 332 n n C1' N9 SAM sing 333 n n C1' H1' SAM sing 334 n n N9 C8 SAM sing 335 n y N9 C4 SAM sing 336 n y C8 N7 SAM doub 337 n y C8 H8 SAM sing 338 n n N7 C5 SAM sing 339 n y C5 C6 SAM sing 340 n y C5 C4 SAM doub 341 n y C6 N6 SAM sing 342 n n C6 N1 SAM doub 343 n y N6 HN61 SAM sing 344 n n N6 HN62 SAM sing 345 n n N1 C2 SAM sing 346 n y C2 N3 SAM doub 347 n y C2 H2 SAM sing 348 n n N3 C4 SAM sing 349 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 N N SAM . . . G 3 -8.054 38.274 -19.65 1 74.83 ? N SAM 1000 B 1 HETATM 2 C CA SAM . . . G 3 -7.852 37.23 -18.628 1 74.74 ? CA SAM 1000 B 1 HETATM 3 C C SAM . . . G 3 -6.377 36.886 -18.455 1 75.15 ? C SAM 1000 B 1 HETATM 4 O O SAM . . . G 3 -5.513 37.604 -18.971 1 75.59 ? O SAM 1000 B 1 HETATM 5 O OXT SAM . . . G 3 -6.026 35.897 -17.803 1 75.28 -1 OXT SAM 1000 B 1 HETATM 6 C CB SAM . . . G 3 -8.634 35.945 -18.894 1 74.34 ? CB SAM 1000 B 1 HETATM 7 C CG SAM . . . G 3 -8.722 35.541 -20.362 1 72.43 ? CG SAM 1000 B 1 HETATM 8 S SD SAM . . . G 3 -7.458 34.35 -20.879 1 69.4 ? SD SAM 1000 B 1 HETATM 9 C CE SAM . . . G 3 -8.135 33.904 -22.504 1 70.1 ? CE SAM 1000 B 1 HETATM 10 C C5' SAM . . . G 3 -7.958 32.912 -19.883 1 61.87 ? C5' SAM 1000 B 1 HETATM 11 C C4' SAM . . . G 3 -7.014 31.719 -19.925 1 55.24 ? C4' SAM 1000 B 1 HETATM 12 O O4' SAM . . . G 3 -5.674 32.155 -19.913 1 52.92 ? O4' SAM 1000 B 1 HETATM 13 C C3' SAM . . . G 3 -7.157 30.876 -18.663 1 54.19 ? C3' SAM 1000 B 1 HETATM 14 O O3' SAM . . . G 3 -7.88 29.684 -18.885 1 52.53 ? O3' SAM 1000 B 1 HETATM 15 C C2' SAM . . . G 3 -5.741 30.597 -18.187 1 52.98 ? C2' SAM 1000 B 1 HETATM 16 O O2' SAM . . . G 3 -5.544 29.216 -17.943 1 52.09 ? O2' SAM 1000 B 1 HETATM 17 C C1' SAM . . . G 3 -4.908 31.125 -19.342 1 51.05 ? C1' SAM 1000 B 1 HETATM 18 N N9 SAM . . . G 3 -3.551 31.549 -18.96 1 48.95 ? N9 SAM 1000 B 1 HETATM 19 C C8 SAM . . . G 3 -3.155 32.288 -17.88 1 48.13 ? C8 SAM 1000 B 1 HETATM 20 N N7 SAM . . . G 3 -1.803 32.441 -17.93 1 46.86 ? N7 SAM 1000 B 1 HETATM 21 C C5 SAM . . . G 3 -1.33 31.799 -19.016 1 46 ? C5 SAM 1000 B 1 HETATM 22 C C6 SAM . . . G 3 -0.049 31.621 -19.524 1 45.06 ? C6 SAM 1000 B 1 HETATM 23 N N6 SAM . . . G 3 0.988 32.152 -18.896 1 46.98 ? N6 SAM 1000 B 1 HETATM 24 N N1 SAM . . . G 3 0.165 30.902 -20.676 1 42.88 ? N1 SAM 1000 B 1 HETATM 25 C C2 SAM . . . G 3 -0.93 30.365 -21.319 1 45.85 ? C2 SAM 1000 B 1 HETATM 26 N N3 SAM . . . G 3 -2.215 30.532 -20.816 1 46.82 ? N3 SAM 1000 B 1 HETATM 27 C C4 SAM . . . G 3 -2.414 31.236 -19.673 1 47.74 ? C4 SAM 1000 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #