data_4CH5 # _model_server_result.job_id QQAYxT-B186q3yKyE5YI3A _model_server_result.datetime_utc '2025-01-11 12:39:31' _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 4ch5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 4CH5 # _exptl.entry_id 4CH5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 531.457 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(S)-2-amino-6-propionamidohexanoic(((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride' _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 4CH5 _cell.length_a 105.376 _cell.length_b 105.376 _cell.length_c 70.801 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CH5 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 4_785 -x+2,-y+3,z -1 0 0 0 -1 0 0 0 1 52.688 273.774879 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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A OE2 GLU 233 A GLU 396 1_555 C MG MG . A MG 1455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc2 B OAF YLP . A YLP 500 1_555 C MG MG . A MG 1455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc3 C MG MG . A MG 1455 1_555 I O3 POP . A POP 1461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? # _chem_comp.formula 'C19 H30 N7 O9 P' _chem_comp.formula_weight 531.457 _chem_comp.id YLP _chem_comp.mon_nstd_flag . _chem_comp.name '(S)-2-amino-6-propionamidohexanoic(((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride' _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 YLP doub 395 n n C CA YLP sing 396 n n C OAY YLP sing 397 n n N CA YLP sing 398 n n N1 C2 YLP doub 399 n y N1 C6 YLP sing 400 n y C2 N3 YLP sing 401 n y N3 C4 YLP doub 402 n y C4 C5 YLP sing 403 n y C4 N9 YLP sing 404 n y C5 C6 YLP doub 405 n y C5 N7 YLP sing 406 n y C6 N6 YLP sing 407 n n N7 C8 YLP doub 408 n y C8 N9 YLP sing 409 n y N9 C1' YLP sing 410 n n CA CB YLP sing 411 n n CB CAN YLP sing 412 n n C1' C2' YLP sing 413 n n C1' O4' YLP sing 414 n n C2' O2' YLP sing 415 n n C2' C3' YLP sing 416 n n C3' O3' YLP sing 417 n n C3' C4' YLP sing 418 n n C4' O4' YLP sing 419 n n C4' C5' YLP sing 420 n n C5' O5' YLP sing 421 n n O5' PBN YLP sing 422 n n OAD CBA YLP doub 423 n n OAF PBN YLP sing 424 n n OAI PBN YLP doub 425 n n CAM CAN YLP sing 426 n n CAM CAO YLP sing 427 n n CAO NAW YLP sing 428 n n NAW CBA YLP sing 429 n n OAY PBN YLP sing 430 n n CBA CBK YLP sing 431 n n CBF CBK YLP sing 432 n n N HN YLP sing 433 n n N HNA YLP sing 434 n n C2 H2 YLP sing 435 n n N6 HN6 YLP sing 436 n n N6 HN6A YLP sing 437 n n C8 H8 YLP sing 438 n n CA HA YLP sing 439 n n CB HB YLP sing 440 n n CB HBA YLP sing 441 n n C1' H1' YLP sing 442 n n C2' H2' YLP sing 443 n n O2' HO2' YLP sing 444 n n C3' H3' YLP sing 445 n n O3' HO3' YLP sing 446 n n C4' H4' YLP sing 447 n n C5' H5' YLP sing 448 n n C5' "H5'A" YLP sing 449 n n CAM HAM YLP sing 450 n n CAM HAMA YLP sing 451 n n CAN HAN YLP sing 452 n n CAN HANA YLP sing 453 n n CAO HAO YLP sing 454 n n CAO HAOA YLP sing 455 n n NAW HNAW YLP sing 456 n n CBF HBF YLP sing 457 n n CBF HBFA YLP sing 458 n n CBF HBFB YLP sing 459 n n CBK HBK YLP sing 460 n n CBK HBKA YLP sing 461 n n OAF HAF YLP sing 462 n n # _atom_sites.entry_id 4CH5 _atom_sites.fract_transf_matrix[1][1] 0.00949 _atom_sites.fract_transf_matrix[1][2] 0.005479 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010958 _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] 0.014124 _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 YLP A 1 500 500 YLP YLP . 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 POP A 1 1461 1461 POP POP . J 6 HOH A 1 2001 2001 HOH HOH . J 6 HOH A 2 2002 2002 HOH HOH . J 6 HOH A 3 2003 2003 HOH HOH . J 6 HOH A 4 2004 2004 HOH HOH . J 6 HOH A 5 2005 2005 HOH HOH . J 6 HOH A 6 2006 2006 HOH HOH . J 6 HOH A 7 2007 2007 HOH HOH . J 6 HOH A 8 2008 2008 HOH HOH . J 6 HOH A 9 2009 2009 HOH HOH . J 6 HOH A 10 2010 2010 HOH HOH . J 6 HOH A 11 2011 2011 HOH HOH . J 6 HOH A 12 2012 2012 HOH HOH . J 6 HOH A 13 2013 2013 HOH HOH . J 6 HOH A 14 2014 2014 HOH HOH . J 6 HOH A 15 2015 2015 HOH HOH . J 6 HOH A 16 2016 2016 HOH HOH . J 6 HOH A 17 2017 2017 HOH HOH . J 6 HOH A 18 2018 2018 HOH HOH . J 6 HOH A 19 2019 2019 HOH HOH . J 6 HOH A 20 2020 2020 HOH HOH . J 6 HOH A 21 2021 2021 HOH HOH . J 6 HOH A 22 2022 2022 HOH HOH . J 6 HOH A 23 2023 2023 HOH HOH . J 6 HOH A 24 2024 2024 HOH HOH . J 6 HOH A 25 2025 2025 HOH HOH . J 6 HOH A 26 2026 2026 HOH HOH . J 6 HOH A 27 2027 2027 HOH HOH . J 6 HOH A 28 2028 2028 HOH HOH . J 6 HOH A 29 2029 2029 HOH HOH . J 6 HOH A 30 2030 2030 HOH HOH . J 6 HOH A 31 2031 2031 HOH HOH . J 6 HOH A 32 2032 2032 HOH HOH . J 6 HOH A 33 2033 2033 HOH HOH . J 6 HOH A 34 2034 2034 HOH HOH . J 6 HOH A 35 2035 2035 HOH HOH . J 6 HOH A 36 2036 2036 HOH HOH . J 6 HOH A 37 2037 2037 HOH HOH . J 6 HOH A 38 2038 2038 HOH HOH . J 6 HOH A 39 2039 2039 HOH HOH . J 6 HOH A 40 2040 2040 HOH HOH . J 6 HOH A 41 2041 2041 HOH HOH . J 6 HOH A 42 2042 2042 HOH HOH . J 6 HOH A 43 2043 2043 HOH HOH . J 6 HOH A 44 2044 2044 HOH HOH . J 6 HOH A 45 2045 2045 HOH HOH . J 6 HOH A 46 2046 2046 HOH HOH . J 6 HOH A 47 2047 2047 HOH HOH . J 6 HOH A 48 2048 2048 HOH HOH . J 6 HOH A 49 2049 2049 HOH HOH . J 6 HOH A 50 2050 2050 HOH HOH . J 6 HOH A 51 2051 2051 HOH HOH . J 6 HOH A 52 2052 2052 HOH HOH . J 6 HOH A 53 2053 2053 HOH HOH . J 6 HOH A 54 2054 2054 HOH HOH . J 6 HOH A 55 2055 2055 HOH HOH . J 6 HOH A 56 2056 2056 HOH HOH . J 6 HOH A 57 2057 2057 HOH HOH . J 6 HOH A 58 2058 2058 HOH HOH . J 6 HOH A 59 2059 2059 HOH HOH . J 6 HOH A 60 2060 2060 HOH HOH . J 6 HOH A 61 2061 2061 HOH HOH . J 6 HOH A 62 2062 2062 HOH HOH . J 6 HOH A 63 2063 2063 HOH HOH . J 6 HOH A 64 2064 2064 HOH HOH . J 6 HOH A 65 2065 2065 HOH HOH . J 6 HOH A 66 2066 2066 HOH HOH . J 6 HOH A 67 2067 2067 HOH HOH . J 6 HOH A 68 2068 2068 HOH HOH . J 6 HOH A 69 2069 2069 HOH HOH . J 6 HOH A 70 2070 2070 HOH HOH . J 6 HOH A 71 2071 2071 HOH HOH . J 6 HOH A 72 2072 2072 HOH HOH . J 6 HOH A 73 2073 2073 HOH HOH . J 6 HOH A 74 2074 2074 HOH HOH . J 6 HOH A 75 2075 2075 HOH HOH . J 6 HOH A 76 2076 2076 HOH HOH . J 6 HOH A 77 2077 2077 HOH HOH . J 6 HOH A 78 2078 2078 HOH HOH . J 6 HOH A 79 2079 2079 HOH HOH . J 6 HOH A 80 2080 2080 HOH HOH . J 6 HOH A 81 2081 2081 HOH HOH . J 6 HOH A 82 2082 2082 HOH HOH . J 6 HOH A 83 2083 2083 HOH HOH . J 6 HOH A 84 2084 2084 HOH HOH . J 6 HOH A 85 2085 2085 HOH HOH . J 6 HOH A 86 2086 2086 HOH HOH . J 6 HOH A 87 2087 2087 HOH HOH . J 6 HOH A 88 2088 2088 HOH HOH . J 6 HOH A 89 2089 2089 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 YLP . . . B 2 43.525 133.885 -10.946 1 85.44 ? C YLP 500 A 1 HETATM 2 N N YLP . . . B 2 42.753 135.354 -9.244 1 82.8 ? N YLP 500 A 1 HETATM 3 O O YLP . . . B 2 42.631 134.152 -11.742 1 86.22 ? O YLP 500 A 1 HETATM 4 N N1 YLP . . . B 2 35.951 126.302 -11.722 1 37.25 ? N1 YLP 500 A 1 HETATM 5 C C2 YLP . . . B 2 36.128 126.345 -10.375 1 40.39 ? C2 YLP 500 A 1 HETATM 6 N N3 YLP . . . B 2 37.114 127.029 -9.77 1 38.32 ? N3 YLP 500 A 1 HETATM 7 C C4 YLP . . . B 2 37.984 127.754 -10.537 1 42.61 ? C4 YLP 500 A 1 HETATM 8 C C5 YLP . . . B 2 37.859 127.751 -12.005 1 38.93 ? C5 YLP 500 A 1 HETATM 9 C C6 YLP . . . B 2 36.759 126.963 -12.587 1 39.26 ? C6 YLP 500 A 1 HETATM 10 N N6 YLP . . . B 2 36.598 126.936 -13.932 1 35.95 ? N6 YLP 500 A 1 HETATM 11 N N7 YLP . . . B 2 38.822 128.525 -12.505 1 41.64 ? N7 YLP 500 A 1 HETATM 12 C C8 YLP . . . B 2 39.54 128.992 -11.45 1 45.18 ? C8 YLP 500 A 1 HETATM 13 N N9 YLP . . . B 2 39.047 128.517 -10.282 1 43 ? N9 YLP 500 A 1 HETATM 14 C CA YLP . . . B 2 43.946 134.978 -9.983 1 86.34 ? CA YLP 500 A 1 HETATM 15 C CB YLP . . . B 2 45.056 134.6 -8.987 1 84.54 ? CB YLP 500 A 1 HETATM 16 C C1' YLP . . . B 2 39.528 128.825 -8.924 1 42.82 ? C1' YLP 500 A 1 HETATM 17 C C2' YLP . . . B 2 40.615 127.904 -8.449 1 43.32 ? C2' YLP 500 A 1 HETATM 18 O O2' YLP . . . B 2 40.47 127.76 -7.035 1 37.13 ? O2' YLP 500 A 1 HETATM 19 C C3' YLP . . . B 2 41.888 128.653 -8.777 1 44.79 ? C3' YLP 500 A 1 HETATM 20 O O3' YLP . . . B 2 42.984 128.268 -7.958 1 46.73 ? O3' YLP 500 A 1 HETATM 21 C C4' YLP . . . B 2 41.453 130.06 -8.467 1 50.63 ? C4' YLP 500 A 1 HETATM 22 O O4' YLP . . . B 2 40.099 130.128 -8.939 1 47.35 ? O4' YLP 500 A 1 HETATM 23 C C5' YLP . . . B 2 42.326 131.127 -9.105 1 54.4 ? C5' YLP 500 A 1 HETATM 24 O O5' YLP . . . B 2 42.065 131.17 -10.497 1 60.24 ? O5' YLP 500 A 1 HETATM 25 O OAD YLP . . . B 2 44.575 140.52 -6.525 1 84.9 ? OAD YLP 500 A 1 HETATM 26 O OAF YLP . . . B 2 44.132 130.034 -11.359 1 80.87 ? OAF YLP 500 A 1 HETATM 27 O OAI YLP . . . B 2 42.739 131.678 -12.817 1 53.66 ? OAI YLP 500 A 1 HETATM 28 C CAM YLP . . . B 2 45.013 136.851 -7.723 1 76.9 ? CAM YLP 500 A 1 HETATM 29 C CAN YLP . . . B 2 45.854 135.82 -8.484 1 82.56 ? CAN YLP 500 A 1 HETATM 30 C CAO YLP . . . B 2 45.819 138.044 -7.228 1 76.68 ? CAO YLP 500 A 1 HETATM 31 N NAW YLP . . . B 2 45.627 139.231 -8.06 1 81.57 ? NAW YLP 500 A 1 HETATM 32 O OAY YLP . . . B 2 44.116 132.534 -10.954 1 79.68 ? OAY YLP 500 A 1 HETATM 33 C CBA YLP . . . B 2 45.055 140.378 -7.644 1 83.03 ? CBA YLP 500 A 1 HETATM 34 C CBF YLP . . . B 2 44.762 142.868 -8.026 1 70.54 ? CBF YLP 500 A 1 HETATM 35 C CBK YLP . . . B 2 45.058 141.522 -8.653 1 76.52 ? CBK YLP 500 A 1 HETATM 36 P PBN YLP . . . B 2 43.285 131.269 -11.511 1 58.56 ? PBN YLP 500 A 1 # _model_server_stats.io_time_ms 93 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #