data_4CH3 # _model_server_result.job_id lelWow4T4ABfvXSH_N7kuQ _model_server_result.datetime_utc '2025-01-11 15:40:03' _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 4ch3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 4CH3 # _exptl.entry_id 4CH3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 545.483 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine" _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 4CH3 _cell.length_a 105.257 _cell.length_b 105.257 _cell.length_c 71.382 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CH3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64' # _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,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id OAI _struct_conn.ptnr1_label_comp_id YLB _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id YLB _struct_conn.ptnr1_auth_seq_id 500 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id MG _struct_conn.ptnr2_label_comp_id MG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id MG _struct_conn.ptnr2_auth_seq_id 1455 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.771 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C20 H32 N7 O9 P' _chem_comp.formula_weight 545.483 _chem_comp.id YLB _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine" _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 C O YLB doub 385 n n C CA YLB sing 386 n n C OAY YLB sing 387 n n N CA YLB sing 388 n n N1 C2 YLB doub 389 n y N1 C6 YLB sing 390 n y C2 N3 YLB sing 391 n y C3 CBF YLB sing 392 n n N3 C4 YLB doub 393 n y C4 C5 YLB sing 394 n y C4 N9 YLB sing 395 n y C5 C6 YLB doub 396 n y C5 N7 YLB sing 397 n y C6 N6 YLB sing 398 n n N7 C8 YLB doub 399 n y C8 N9 YLB sing 400 n y N9 C1' YLB sing 401 n n CA CB YLB sing 402 n n CB CAN YLB sing 403 n n C1' C2' YLB sing 404 n n C1' O4' YLB sing 405 n n C2' O2' YLB sing 406 n n C2' C3' YLB sing 407 n n C3' O3' YLB sing 408 n n C3' C4' YLB sing 409 n n C4' O4' YLB sing 410 n n C4' C5' YLB sing 411 n n C5' O5' YLB sing 412 n n O5' PBN YLB sing 413 n n OAD CBA YLB doub 414 n n OAF PBN YLB doub 415 n n OAI PBN YLB sing 416 n n CAM CAN YLB sing 417 n n CAM CAO YLB sing 418 n n CAO NAW YLB sing 419 n n NAW CBA YLB sing 420 n n OAY PBN YLB sing 421 n n CBA CBK YLB sing 422 n n CBF CBK YLB sing 423 n n N HN YLB sing 424 n n N HNA YLB sing 425 n n C2 H2 YLB sing 426 n n C3 H3 YLB sing 427 n n C3 H3A YLB sing 428 n n C3 H3B YLB sing 429 n n N6 HN6 YLB sing 430 n n N6 HN6A YLB sing 431 n n C8 H8 YLB sing 432 n n CA HA YLB sing 433 n n CB HB YLB sing 434 n n CB HBA YLB sing 435 n n C1' H1' YLB sing 436 n n C2' H2' YLB sing 437 n n O2' HO2' YLB sing 438 n n C3' H3' YLB sing 439 n n O3' HO3' YLB sing 440 n n C4' H4' YLB sing 441 n n C5' H5' YLB sing 442 n n C5' "H5'A" YLB sing 443 n n CAM HAM YLB sing 444 n n CAM HAMA YLB sing 445 n n CAN HAN YLB sing 446 n n CAN HANA YLB sing 447 n n CAO HAO YLB sing 448 n n CAO HAOA YLB sing 449 n n NAW HNAW YLB sing 450 n n CBF HBF YLB sing 451 n n CBF HBFA YLB sing 452 n n CBK HBK YLB sing 453 n n CBK HBKA YLB sing 454 n n OAI HAI YLB sing 455 n n # _atom_sites.entry_id 4CH3 _atom_sites.fract_transf_matrix[1][1] 0.009501 _atom_sites.fract_transf_matrix[1][2] 0.005485 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01097 _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] 0.014009 _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 YLB A 1 500 500 YLB YLB . C 3 MG A 1 1455 1455 MG MG . D 4 EDO A 1 1456 1456 EDO EDO . E 4 EDO A 1 1457 1457 EDO EDO . F 4 EDO A 1 1458 1458 EDO EDO . G 4 EDO A 1 1459 1459 EDO EDO . H 4 EDO A 1 1460 1460 EDO EDO . I 5 HOH A 1 2001 2001 HOH HOH . I 5 HOH A 2 2002 2002 HOH HOH . I 5 HOH A 3 2003 2003 HOH HOH . I 5 HOH A 4 2004 2004 HOH HOH . I 5 HOH A 5 2005 2005 HOH HOH . I 5 HOH A 6 2006 2006 HOH HOH . I 5 HOH A 7 2007 2007 HOH HOH . I 5 HOH A 8 2008 2008 HOH HOH . I 5 HOH A 9 2009 2009 HOH HOH . I 5 HOH A 10 2010 2010 HOH HOH . I 5 HOH A 11 2011 2011 HOH HOH . I 5 HOH A 12 2012 2012 HOH HOH . I 5 HOH A 13 2013 2013 HOH HOH . I 5 HOH A 14 2014 2014 HOH HOH . I 5 HOH A 15 2015 2015 HOH HOH . I 5 HOH A 16 2016 2016 HOH HOH . I 5 HOH A 17 2017 2017 HOH HOH . I 5 HOH A 18 2018 2018 HOH HOH . I 5 HOH A 19 2019 2019 HOH HOH . I 5 HOH A 20 2020 2020 HOH HOH . I 5 HOH A 21 2021 2021 HOH HOH . I 5 HOH A 22 2022 2022 HOH HOH . I 5 HOH A 23 2023 2023 HOH HOH . I 5 HOH A 24 2024 2024 HOH HOH . I 5 HOH A 25 2025 2025 HOH HOH . I 5 HOH A 26 2026 2026 HOH HOH . I 5 HOH A 27 2027 2027 HOH HOH . I 5 HOH A 28 2028 2028 HOH HOH . I 5 HOH A 29 2029 2029 HOH HOH . I 5 HOH A 30 2030 2030 HOH HOH . I 5 HOH A 31 2031 2031 HOH HOH . I 5 HOH A 32 2032 2032 HOH HOH . I 5 HOH A 33 2033 2033 HOH HOH . I 5 HOH A 34 2034 2034 HOH HOH . I 5 HOH A 35 2035 2035 HOH HOH . I 5 HOH A 36 2036 2036 HOH HOH . I 5 HOH A 37 2037 2037 HOH HOH . I 5 HOH A 38 2038 2038 HOH HOH . I 5 HOH A 39 2039 2039 HOH HOH . I 5 HOH A 40 2040 2040 HOH HOH . I 5 HOH A 41 2041 2041 HOH HOH . I 5 HOH A 42 2042 2042 HOH HOH . I 5 HOH A 43 2043 2043 HOH HOH . I 5 HOH A 44 2044 2044 HOH HOH . I 5 HOH A 45 2045 2045 HOH HOH . I 5 HOH A 46 2046 2046 HOH HOH . I 5 HOH A 47 2047 2047 HOH HOH . I 5 HOH A 48 2048 2048 HOH HOH . I 5 HOH A 49 2049 2049 HOH HOH . I 5 HOH A 50 2050 2050 HOH HOH . I 5 HOH A 51 2051 2051 HOH HOH . I 5 HOH A 52 2052 2052 HOH HOH . I 5 HOH A 53 2053 2053 HOH HOH . I 5 HOH A 54 2054 2054 HOH HOH . I 5 HOH A 55 2055 2055 HOH HOH . I 5 HOH A 56 2056 2056 HOH HOH . I 5 HOH A 57 2057 2057 HOH HOH . I 5 HOH A 58 2058 2058 HOH HOH . I 5 HOH A 59 2059 2059 HOH HOH . I 5 HOH A 60 2060 2060 HOH HOH . I 5 HOH A 61 2061 2061 HOH HOH . I 5 HOH A 62 2062 2062 HOH HOH . I 5 HOH A 63 2063 2063 HOH HOH . I 5 HOH A 64 2064 2064 HOH HOH . I 5 HOH A 65 2065 2065 HOH HOH . I 5 HOH A 66 2066 2066 HOH HOH . I 5 HOH A 67 2067 2067 HOH HOH . I 5 HOH A 68 2068 2068 HOH HOH . I 5 HOH A 69 2069 2069 HOH HOH . I 5 HOH A 70 2070 2070 HOH HOH . I 5 HOH A 71 2071 2071 HOH HOH . I 5 HOH A 72 2072 2072 HOH HOH . I 5 HOH A 73 2073 2073 HOH HOH . I 5 HOH A 74 2074 2074 HOH HOH . I 5 HOH A 75 2075 2075 HOH HOH . I 5 HOH A 76 2076 2076 HOH HOH . I 5 HOH A 77 2077 2077 HOH HOH . I 5 HOH A 78 2078 2078 HOH HOH . I 5 HOH A 79 2079 2079 HOH HOH . I 5 HOH A 80 2080 2080 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 C YLB . . . B 2 42.97 133.81 -11.193 1 73.93 ? C YLB 500 A 1 HETATM 2 N N YLB . . . B 2 43.897 136 -11.154 1 74.09 ? N YLB 500 A 1 HETATM 3 O O YLB . . . B 2 42.052 133.827 -11.992 1 77.06 ? O YLB 500 A 1 HETATM 4 N N1 YLB . . . B 2 36.047 126.091 -11.75 1 40.64 ? N1 YLB 500 A 1 HETATM 5 C C2 YLB . . . B 2 36.216 126.145 -10.405 1 41.67 ? C2 YLB 500 A 1 HETATM 6 C C3 YLB . . . B 2 44.606 143.198 -8.231 1 69.23 ? C3 YLB 500 A 1 HETATM 7 N N3 YLB . . . B 2 37.194 126.863 -9.805 1 40.74 ? N3 YLB 500 A 1 HETATM 8 C C4 YLB . . . B 2 38.052 127.587 -10.577 1 44.74 ? C4 YLB 500 A 1 HETATM 9 C C5 YLB . . . B 2 37.932 127.582 -12.055 1 43.77 ? C5 YLB 500 A 1 HETATM 10 C C6 YLB . . . B 2 36.84 126.762 -12.625 1 41.1 ? C6 YLB 500 A 1 HETATM 11 N N6 YLB . . . B 2 36.651 126.691 -13.96 1 38.17 ? N6 YLB 500 A 1 HETATM 12 N N7 YLB . . . B 2 38.912 128.369 -12.543 1 47.54 ? N7 YLB 500 A 1 HETATM 13 C C8 YLB . . . B 2 39.611 128.849 -11.474 1 51.33 ? C8 YLB 500 A 1 HETATM 14 N N9 YLB . . . B 2 39.093 128.367 -10.305 1 49.17 ? N9 YLB 500 A 1 HETATM 15 C CA YLB . . . B 2 43.226 135.008 -10.327 1 75.35 ? CA YLB 500 A 1 HETATM 16 C CB YLB . . . B 2 43.978 134.598 -9.039 1 73.93 ? CB YLB 500 A 1 HETATM 17 C C1' YLB . . . B 2 39.519 128.656 -8.922 1 45.38 ? C1' YLB 500 A 1 HETATM 18 C C2' YLB . . . B 2 40.58 127.722 -8.438 1 44.66 ? C2' YLB 500 A 1 HETATM 19 O O2' YLB . . . B 2 40.433 127.592 -7.023 1 41.32 ? O2' YLB 500 A 1 HETATM 20 C C3' YLB . . . B 2 41.863 128.458 -8.755 1 46.63 ? C3' YLB 500 A 1 HETATM 21 O O3' YLB . . . B 2 42.989 128.053 -7.983 1 46.91 ? O3' YLB 500 A 1 HETATM 22 C C4' YLB . . . B 2 41.452 129.862 -8.397 1 52.59 ? C4' YLB 500 A 1 HETATM 23 O O4' YLB . . . B 2 40.092 129.961 -8.859 1 50.03 ? O4' YLB 500 A 1 HETATM 24 C C5' YLB . . . B 2 42.366 130.885 -9.032 1 56 ? C5' YLB 500 A 1 HETATM 25 O O5' YLB . . . B 2 42.155 130.859 -10.428 1 57.11 ? O5' YLB 500 A 1 HETATM 26 O OAD YLB . . . B 2 44.961 139.381 -6.227 1 74.52 ? OAD YLB 500 A 1 HETATM 27 O OAF YLB . . . B 2 42.821 131.166 -12.807 1 48.97 ? OAF YLB 500 A 1 HETATM 28 O OAI YLB . . . B 2 44.528 130.273 -11.06 1 70.22 ? OAI YLB 500 A 1 HETATM 29 C CAM YLB . . . B 2 45.149 136.289 -7.616 1 67.1 ? CAM YLB 500 A 1 HETATM 30 C CAN YLB . . . B 2 45.316 135.296 -8.762 1 73.67 ? CAN YLB 500 A 1 HETATM 31 C CAO YLB . . . B 2 46.299 137.271 -7.53 1 68.09 ? CAO YLB 500 A 1 HETATM 32 N NAW YLB . . . B 2 45.923 138.548 -8.105 1 72.62 ? NAW YLB 500 A 1 HETATM 33 O OAY YLB . . . B 2 43.831 132.643 -11.073 1 70.34 ? OAY YLB 500 A 1 HETATM 34 C CBA YLB . . . B 2 45.276 139.496 -7.416 1 75.55 ? CBA YLB 500 A 1 HETATM 35 C CBF YLB . . . B 2 44.853 141.986 -7.36 1 70.73 ? CBF YLB 500 A 1 HETATM 36 C CBK YLB . . . B 2 44.939 140.737 -8.227 1 72.23 ? CBK YLB 500 A 1 HETATM 37 P PBN YLB . . . B 2 43.356 131.161 -11.425 1 59.88 ? PBN YLB 500 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 37 #