data_4YV2 # _model_server_result.job_id RcQ0sYTUmyY3LD_H-5FUsQ _model_server_result.datetime_utc '2024-11-05 06:53:11' _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 4yv2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 4YV2 # _exptl.entry_id 4YV2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.444 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE" _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 107.7 _cell.angle_gamma 90 _cell.entry_id 4YV2 _cell.length_a 43.658 _cell.length_b 100.315 _cell.length_c 71.365 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YV2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 C N N ? 2 D N N # _chem_comp.formula 'C14 H24 N6 O3 S' _chem_comp.formula_weight 356.444 _chem_comp.id S4M _chem_comp.mon_nstd_flag . _chem_comp.name "5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE" _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 CA N S4M sing 300 n n CA CB S4M sing 301 n n CA HA1 S4M sing 302 n n CA HA2 S4M sing 303 n n N HN1 S4M sing 304 n n N HN2 S4M sing 305 n n CB CG S4M sing 306 n n CB HB1 S4M sing 307 n n CB HB2 S4M sing 308 n n CG SD S4M sing 309 n n CG HG1 S4M sing 310 n n CG HG2 S4M sing 311 n n SD CE S4M sing 312 n n SD C5' S4M sing 313 n n SD HSD S4M sing 314 n n CE HE1 S4M sing 315 n n CE HE2 S4M sing 316 n n CE HE3 S4M sing 317 n n C5' C4' S4M sing 318 n n C5' "H5'1" S4M sing 319 n n C5' "H5'2" S4M sing 320 n n C4' C3' S4M sing 321 n n C4' O4' S4M sing 322 n n C4' H4' S4M sing 323 n n O4' C1' S4M sing 324 n n C1' C2' S4M sing 325 n n C1' N9 S4M sing 326 n n C1' H1' S4M sing 327 n n C2' O2' S4M sing 328 n n C2' C3' S4M sing 329 n n C2' H2' S4M sing 330 n n O2' HO2' S4M sing 331 n n C3' O3' S4M sing 332 n n C3' H3' S4M sing 333 n n O3' HO3' S4M sing 334 n n N9 C4 S4M sing 335 n y N9 C8 S4M sing 336 n y C8 N7 S4M doub 337 n y C8 H8 S4M sing 338 n n N7 C5 S4M sing 339 n y C5 C4 S4M doub 340 n y C5 C6 S4M sing 341 n y C6 N1 S4M doub 342 n y C6 N6 S4M sing 343 n n N6 HN61 S4M sing 344 n n N6 HN62 S4M sing 345 n n C4 N3 S4M sing 346 n y N3 C2 S4M doub 347 n y C2 N1 S4M sing 348 n y C2 H2 S4M sing 349 n n # _atom_sites.entry_id 4YV2 _atom_sites.fract_transf_matrix[1][1] 0.022905 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007309 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009969 _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] 0.014709 _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 C 2 S4M A 1 301 1 S4M S4M . D 2 S4M B 1 301 1 S4M S4M . E 3 4K3 B 1 302 1 4K3 UNL . F 3 4K3 B 1 303 1 4K3 UNL . G 4 HOH A 1 401 11 HOH HOH . G 4 HOH A 2 402 21 HOH HOH . G 4 HOH A 3 403 6 HOH HOH . G 4 HOH A 4 404 35 HOH HOH . G 4 HOH A 5 405 33 HOH HOH . G 4 HOH A 6 406 20 HOH HOH . G 4 HOH A 7 407 46 HOH HOH . G 4 HOH A 8 408 8 HOH HOH . G 4 HOH A 9 409 9 HOH HOH . G 4 HOH A 10 410 18 HOH HOH . G 4 HOH A 11 411 5 HOH HOH . G 4 HOH A 12 412 12 HOH HOH . G 4 HOH A 13 413 36 HOH HOH . G 4 HOH A 14 414 3 HOH HOH . G 4 HOH A 15 415 49 HOH HOH . G 4 HOH A 16 416 15 HOH HOH . G 4 HOH A 17 417 27 HOH HOH . G 4 HOH A 18 418 1 HOH HOH . G 4 HOH A 19 419 28 HOH HOH . G 4 HOH A 20 420 37 HOH HOH . G 4 HOH A 21 421 40 HOH HOH . G 4 HOH A 22 422 48 HOH HOH . G 4 HOH A 23 423 10 HOH HOH . G 4 HOH A 24 424 29 HOH HOH . G 4 HOH A 25 425 47 HOH HOH . G 4 HOH A 26 426 44 HOH HOH . H 4 HOH B 1 401 42 HOH HOH . H 4 HOH B 2 402 50 HOH HOH . H 4 HOH B 3 403 25 HOH HOH . H 4 HOH B 4 404 39 HOH HOH . H 4 HOH B 5 405 34 HOH HOH . H 4 HOH B 6 406 32 HOH HOH . H 4 HOH B 7 407 26 HOH HOH . H 4 HOH B 8 408 41 HOH HOH . H 4 HOH B 9 409 4 HOH HOH . H 4 HOH B 10 410 52 HOH HOH . H 4 HOH B 11 411 38 HOH HOH . H 4 HOH B 12 412 31 HOH HOH . H 4 HOH B 13 413 16 HOH HOH . H 4 HOH B 14 414 22 HOH HOH . H 4 HOH B 15 415 45 HOH HOH . H 4 HOH B 16 416 17 HOH HOH . H 4 HOH B 17 417 51 HOH HOH . H 4 HOH B 18 418 19 HOH HOH . H 4 HOH B 19 419 2 HOH HOH . H 4 HOH B 20 420 30 HOH HOH . H 4 HOH B 21 421 14 HOH HOH . H 4 HOH B 22 422 13 HOH HOH . H 4 HOH B 23 423 7 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 CA S4M . . . C 2 12.678 13.517 28.205 1 44.56 ? CA S4M 301 A 1 HETATM 2 N N S4M . . . C 2 11.608 13.848 29.215 1 32.55 ? N S4M 301 A 1 HETATM 3 C CB S4M . . . C 2 13.031 14.675 27.296 1 39.63 ? CB S4M 301 A 1 HETATM 4 C CG S4M . . . C 2 14.401 15.259 27.612 1 48.68 ? CG S4M 301 A 1 HETATM 5 S SD S4M . . . C 2 14.445 16.417 29.059 1 52.39 ? SD S4M 301 A 1 HETATM 6 C CE S4M . . . C 2 13.487 17.832 28.372 1 42.39 ? CE S4M 301 A 1 HETATM 7 C C5' S4M . . . C 2 16.177 16.947 28.797 1 39.84 ? C5' S4M 301 A 1 HETATM 8 C C4' S4M . . . C 2 16.573 17.924 29.91 1 40.33 ? C4' S4M 301 A 1 HETATM 9 O O4' S4M . . . C 2 17.949 17.784 30.295 1 37.26 ? O4' S4M 301 A 1 HETATM 10 C C1' S4M . . . C 2 18.351 19.066 30.756 1 35.68 ? C1' S4M 301 A 1 HETATM 11 C C2' S4M . . . C 2 17.759 20.017 29.697 1 39.27 ? C2' S4M 301 A 1 HETATM 12 O O2' S4M . . . C 2 17.579 21.365 30.132 1 31.75 ? O2' S4M 301 A 1 HETATM 13 C C3' S4M . . . C 2 16.436 19.352 29.384 1 35.69 ? C3' S4M 301 A 1 HETATM 14 O O3' S4M . . . C 2 15.296 19.891 30.013 1 32.92 ? O3' S4M 301 A 1 HETATM 15 N N9 S4M . . . C 2 19.79 19.109 30.916 1 33.92 ? N9 S4M 301 A 1 HETATM 16 C C8 S4M . . . C 2 20.708 19.116 29.898 1 35.25 ? C8 S4M 301 A 1 HETATM 17 N N7 S4M . . . C 2 21.937 19.147 30.389 1 33.71 ? N7 S4M 301 A 1 HETATM 18 C C5 S4M . . . C 2 21.807 19.159 31.766 1 32.54 ? C5 S4M 301 A 1 HETATM 19 C C6 S4M . . . C 2 22.724 19.218 32.813 1 33.61 ? C6 S4M 301 A 1 HETATM 20 N N6 S4M . . . C 2 24.084 19.278 32.604 1 31.78 ? N6 S4M 301 A 1 HETATM 21 C C4 S4M . . . C 2 20.484 19.127 32.112 1 31.59 ? C4 S4M 301 A 1 HETATM 22 N N3 S4M . . . C 2 20.024 19.135 33.367 1 34.42 ? N3 S4M 301 A 1 HETATM 23 C C2 S4M . . . C 2 20.982 19.168 34.289 1 30.97 ? C2 S4M 301 A 1 HETATM 24 N N1 S4M . . . C 2 22.3 19.212 34.079 1 31.88 ? N1 S4M 301 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 137 _model_server_stats.create_model_time_ms 119 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 24 #