data_2YP0 # _model_server_result.job_id yGmyoPqvqzpoC4x85uAQDw _model_server_result.datetime_utc '2024-11-25 06:29:10' _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 2yp0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 2YP0 # _exptl.entry_id 2YP0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.287 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-O-(sulfidophosphinato)adenosine" _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 97.87 _cell.angle_gamma 90 _cell.entry_id 2YP0 _cell.length_a 39.83 _cell.length_b 47.74 _cell.length_c 50.93 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YP0 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 B N N ? 2 D N N # _chem_comp.formula 'C10 H14 N5 O6 P S' _chem_comp.formula_weight 363.287 _chem_comp.id OVE _chem_comp.mon_nstd_flag . _chem_comp.name "2'-O-(sulfidophosphinato)adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-2'-MONOPHOSPHOROTHIOATE" # 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 O1P P OVE sing 294 n n P S2P OVE sing 295 n n P O3P OVE doub 296 n n P O2' OVE sing 297 n n O2' C2' OVE sing 298 n n C2' C3' OVE sing 299 n n C2' C1' OVE sing 300 n n C3' O3' OVE sing 301 n n C3' C4' OVE sing 302 n n C1' O4' OVE sing 303 n n C1' N9 OVE sing 304 n n O4' C4' OVE sing 305 n n C4' C5' OVE sing 306 n n C5' O5' OVE sing 307 n n N9 C8 OVE sing 308 n y N9 C4 OVE sing 309 n y C8 N7 OVE doub 310 n y N7 C5 OVE sing 311 n y C5 C6 OVE doub 312 n y C5 C4 OVE sing 313 n y C6 N6 OVE sing 314 n n C6 N1 OVE sing 315 n y C4 N3 OVE doub 316 n y N3 C2 OVE sing 317 n y H2 C2 OVE sing 318 n n N1 C2 OVE doub 319 n y O1P H1P OVE sing 320 n n S2P H2P OVE sing 321 n n C2' H2' OVE sing 322 n n C3' H3' OVE sing 323 n n C1' H1' OVE sing 324 n n O3' HA OVE sing 325 n n C4' H4' OVE sing 326 n n C5' "H5'1" OVE sing 327 n n C5' "H5'2" OVE sing 328 n n O5' H5' OVE sing 329 n n C8 H8 OVE sing 330 n n N6 H61N OVE sing 331 n n N6 H62N OVE sing 332 n n # _atom_sites.entry_id 2YP0 _atom_sites.fract_transf_matrix[1][1] 0.025107 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00347 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020947 _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] 0.019821 _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 B 2 OVE A 1 401 1379 OVE OVE . C 3 GOL A 1 402 1380 GOL GOL . D 2 OVE A 1 403 1381 OVE OVE . E 4 1PE A 1 404 1382 1PE 1PE . F 5 ACY A 1 405 1383 ACY ACY . G 6 HOH A 1 501 2022 HOH HOH . G 6 HOH A 2 502 2039 HOH HOH . G 6 HOH A 3 503 2006 HOH HOH . G 6 HOH A 4 504 2061 HOH HOH . G 6 HOH A 5 505 2065 HOH HOH . G 6 HOH A 6 506 2041 HOH HOH . G 6 HOH A 7 507 2040 HOH HOH . G 6 HOH A 8 508 2033 HOH HOH . G 6 HOH A 9 509 2060 HOH HOH . G 6 HOH A 10 510 2072 HOH HOH . G 6 HOH A 11 511 2009 HOH HOH . G 6 HOH A 12 512 2049 HOH HOH . G 6 HOH A 13 513 2018 HOH HOH . G 6 HOH A 14 514 2071 HOH HOH . G 6 HOH A 15 515 2031 HOH HOH . G 6 HOH A 16 516 2001 HOH HOH . G 6 HOH A 17 517 2046 HOH HOH . G 6 HOH A 18 518 2066 HOH HOH . G 6 HOH A 19 519 2044 HOH HOH . G 6 HOH A 20 520 2048 HOH HOH . G 6 HOH A 21 521 2005 HOH HOH . G 6 HOH A 22 522 2015 HOH HOH . G 6 HOH A 23 523 2020 HOH HOH . G 6 HOH A 24 524 2069 HOH HOH . G 6 HOH A 25 525 2050 HOH HOH . G 6 HOH A 26 526 2024 HOH HOH . G 6 HOH A 27 527 2053 HOH HOH . G 6 HOH A 28 528 2021 HOH HOH . G 6 HOH A 29 529 2011 HOH HOH . G 6 HOH A 30 530 2014 HOH HOH . G 6 HOH A 31 531 2062 HOH HOH . G 6 HOH A 32 532 2017 HOH HOH . G 6 HOH A 33 533 2038 HOH HOH . G 6 HOH A 34 534 2013 HOH HOH . G 6 HOH A 35 535 2059 HOH HOH . G 6 HOH A 36 536 2010 HOH HOH . G 6 HOH A 37 537 2056 HOH HOH . G 6 HOH A 38 538 2025 HOH HOH . G 6 HOH A 39 539 2007 HOH HOH . G 6 HOH A 40 540 2070 HOH HOH . G 6 HOH A 41 541 2067 HOH HOH . G 6 HOH A 42 542 2030 HOH HOH . G 6 HOH A 43 543 2016 HOH HOH . G 6 HOH A 44 544 2019 HOH HOH . G 6 HOH A 45 545 2023 HOH HOH . G 6 HOH A 46 546 2064 HOH HOH . G 6 HOH A 47 547 2027 HOH HOH . G 6 HOH A 48 548 2057 HOH HOH . G 6 HOH A 49 549 2045 HOH HOH . G 6 HOH A 50 550 2068 HOH HOH . G 6 HOH A 51 551 2042 HOH HOH . G 6 HOH A 52 552 2076 HOH HOH . G 6 HOH A 53 553 2026 HOH HOH . G 6 HOH A 54 554 2063 HOH HOH . G 6 HOH A 55 555 2012 HOH HOH . G 6 HOH A 56 556 2074 HOH HOH . G 6 HOH A 57 557 2003 HOH HOH . G 6 HOH A 58 558 2035 HOH HOH . G 6 HOH A 59 559 2047 HOH HOH . G 6 HOH A 60 560 2028 HOH HOH . G 6 HOH A 61 561 2032 HOH HOH . G 6 HOH A 62 562 2043 HOH HOH . G 6 HOH A 63 563 2008 HOH HOH . G 6 HOH A 64 564 2034 HOH HOH . G 6 HOH A 65 565 2054 HOH HOH . G 6 HOH A 66 566 2073 HOH HOH . G 6 HOH A 67 567 2058 HOH HOH . G 6 HOH A 68 568 2075 HOH HOH . G 6 HOH A 69 569 2002 HOH HOH . G 6 HOH A 70 570 2004 HOH HOH . G 6 HOH A 71 571 2029 HOH HOH . G 6 HOH A 72 572 2051 HOH HOH . G 6 HOH A 73 573 2052 HOH HOH . G 6 HOH A 74 574 2055 HOH HOH . G 6 HOH A 75 575 2037 HOH HOH . G 6 HOH A 76 576 2036 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 O O1P OVE . . . D 2 32.53 -14.279 54.332 1 14.51 ? O1P OVE 403 A 1 HETATM 2 P P OVE . . . D 2 31.718 -13.984 53.115 1 43.91 ? P OVE 403 A 1 HETATM 3 S S2P OVE . . . D 2 32.623 -12.581 52.067 1 60.99 ? S2P OVE 403 A 1 HETATM 4 O O3P OVE . . . D 2 30.338 -13.497 53.529 1 38.82 ? O3P OVE 403 A 1 HETATM 5 O O2' OVE . . . D 2 31.567 -15.254 52.231 1 26.91 ? O2' OVE 403 A 1 HETATM 6 C C2' OVE . . . D 2 31.189 -16.512 52.619 1 29.02 ? C2' OVE 403 A 1 HETATM 7 C C3' OVE . . . D 2 32.386 -17.318 52.961 1 33.43 ? C3' OVE 403 A 1 HETATM 8 O O3' OVE . . . D 2 33.497 -16.864 52.251 1 32.75 ? O3' OVE 403 A 1 HETATM 9 C C1' OVE . . . D 2 30.82 -17.143 51.327 1 28.17 ? C1' OVE 403 A 1 HETATM 10 O O4' OVE . . . D 2 31.132 -18.493 51.441 1 25.72 ? O4' OVE 403 A 1 HETATM 11 C C4' OVE . . . D 2 32.044 -18.666 52.478 1 33.12 ? C4' OVE 403 A 1 HETATM 12 C C5' OVE . . . D 2 31.49 -19.53 53.563 1 32.79 ? C5' OVE 403 A 1 HETATM 13 O O5' OVE . . . D 2 30.371 -18.926 54.1 1 29.41 ? O5' OVE 403 A 1 HETATM 14 N N9 OVE . . . D 2 29.455 -16.987 50.867 1 27.43 ? N9 OVE 403 A 1 HETATM 15 C C8 OVE . . . D 2 29.005 -16.486 49.628 1 22.53 ? C8 OVE 403 A 1 HETATM 16 N N7 OVE . . . D 2 27.617 -16.523 49.643 1 29.24 ? N7 OVE 403 A 1 HETATM 17 C C5 OVE . . . D 2 27.221 -17.049 50.899 1 30.56 ? C5 OVE 403 A 1 HETATM 18 C C6 OVE . . . D 2 25.977 -17.281 51.387 1 35.81 ? C6 OVE 403 A 1 HETATM 19 N N6 OVE . . . D 2 24.819 -16.975 50.584 1 23.08 ? N6 OVE 403 A 1 HETATM 20 C C4 OVE . . . D 2 28.319 -17.342 51.667 1 28.59 ? C4 OVE 403 A 1 HETATM 21 N N3 OVE . . . D 2 28.236 -17.85 52.895 1 36.6 ? N3 OVE 403 A 1 HETATM 22 C C2 OVE . . . D 2 26.981 -18.092 53.408 1 31.74 ? C2 OVE 403 A 1 HETATM 23 N N1 OVE . . . D 2 25.863 -17.802 52.638 1 28.62 ? N1 OVE 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #