data_4CLW # _model_server_result.job_id jESj1LE0nFriohtD4I8-Sw _model_server_result.datetime_utc '2024-11-24 14:12:21' _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 4clw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1467}' # _entry.id 4CLW # _exptl.entry_id 4CLW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 4CLW _cell.length_a 100.57 _cell.length_b 100.57 _cell.length_c 97.17 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CLW _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -50.285 87.096175 0 3 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 50.285 87.096175 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 covale ? covale1 A C ALA 252 A ALA 252 1_555 A N CME 253 A CME 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale2 A C CME 253 A CME 253 1_555 A N THR 254 A THR 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? metalc ? metalc1 A OD1 ASP 47 A ASP 47 1_555 I CA CA . A CA 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc2 A O ILE 48 A ILE 48 1_555 I CA CA . A CA 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc3 A OD1 ASP 99 A ASP 99 1_555 I CA CA . A CA 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc4 B O1B APC . A APC 1467 1_555 I CA CA . A CA 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc5 B O1G APC . A APC 1467 1_555 I CA CA . A CA 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc6 I CA CA . A CA 1474 1_555 K O HOH . A HOH 2027 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 PG O1G APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 4CLW _atom_sites.fract_transf_matrix[1][1] 0.009943 _atom_sites.fract_transf_matrix[1][2] 0.005741 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011482 _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] 0.010291 _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 APC A 1 1467 1467 APC APC . C 3 SO3 A 1 1468 1468 SO3 SO3 . D 4 PEG A 1 1469 1469 PEG PEG . E 5 EDO A 1 1470 1470 EDO EDO . F 5 EDO A 1 1471 1471 EDO EDO . G 5 EDO A 1 1472 1472 EDO EDO . H 5 EDO A 1 1473 1473 EDO EDO . I 6 CA A 1 1474 1474 CA CA . J 7 GOL A 1 1475 1475 GOL GOL . K 8 HOH A 1 2001 2001 HOH HOH . K 8 HOH A 2 2002 2002 HOH HOH . K 8 HOH A 3 2003 2003 HOH HOH . K 8 HOH A 4 2004 2004 HOH HOH . K 8 HOH A 5 2005 2005 HOH HOH . K 8 HOH A 6 2006 2006 HOH HOH . K 8 HOH A 7 2007 2007 HOH HOH . K 8 HOH A 8 2008 2008 HOH HOH . K 8 HOH A 9 2009 2009 HOH HOH . K 8 HOH A 10 2010 2010 HOH HOH . K 8 HOH A 11 2011 2011 HOH HOH . K 8 HOH A 12 2012 2012 HOH HOH . K 8 HOH A 13 2013 2013 HOH HOH . K 8 HOH A 14 2014 2014 HOH HOH . K 8 HOH A 15 2015 2015 HOH HOH . K 8 HOH A 16 2016 2016 HOH HOH . K 8 HOH A 17 2017 2017 HOH HOH . K 8 HOH A 18 2018 2018 HOH HOH . K 8 HOH A 19 2019 2019 HOH HOH . K 8 HOH A 20 2020 2020 HOH HOH . K 8 HOH A 21 2021 2021 HOH HOH . K 8 HOH A 22 2022 2022 HOH HOH . K 8 HOH A 23 2023 2023 HOH HOH . K 8 HOH A 24 2024 2024 HOH HOH . K 8 HOH A 25 2025 2025 HOH HOH . K 8 HOH A 26 2026 2026 HOH HOH . K 8 HOH A 27 2027 2027 HOH HOH . K 8 HOH A 28 2028 2028 HOH HOH . K 8 HOH A 29 2029 2029 HOH HOH . K 8 HOH A 30 2030 2030 HOH HOH . K 8 HOH A 31 2031 2031 HOH HOH . K 8 HOH A 32 2032 2032 HOH HOH . K 8 HOH A 33 2033 2033 HOH HOH . K 8 HOH A 34 2034 2034 HOH HOH . K 8 HOH A 35 2035 2035 HOH HOH . K 8 HOH A 36 2036 2036 HOH HOH . K 8 HOH A 37 2037 2037 HOH HOH . K 8 HOH A 38 2038 2038 HOH HOH . K 8 HOH A 39 2039 2039 HOH HOH . K 8 HOH A 40 2040 2040 HOH HOH . K 8 HOH A 41 2041 2041 HOH HOH . K 8 HOH A 42 2042 2042 HOH HOH . K 8 HOH A 43 2043 2043 HOH HOH . K 8 HOH A 44 2044 2044 HOH HOH . K 8 HOH A 45 2045 2045 HOH HOH . K 8 HOH A 46 2046 2046 HOH HOH . K 8 HOH A 47 2047 2047 HOH HOH . K 8 HOH A 48 2048 2048 HOH HOH . K 8 HOH A 49 2049 2049 HOH HOH . K 8 HOH A 50 2050 2050 HOH HOH . K 8 HOH A 51 2051 2051 HOH HOH . K 8 HOH A 52 2052 2052 HOH HOH . K 8 HOH A 53 2053 2053 HOH HOH . K 8 HOH A 54 2054 2054 HOH HOH . K 8 HOH A 55 2055 2055 HOH HOH . K 8 HOH A 56 2056 2056 HOH HOH . K 8 HOH A 57 2057 2057 HOH HOH . K 8 HOH A 58 2058 2058 HOH HOH . K 8 HOH A 59 2059 2059 HOH HOH . K 8 HOH A 60 2060 2060 HOH HOH . K 8 HOH A 61 2061 2061 HOH HOH . K 8 HOH A 62 2062 2062 HOH HOH . K 8 HOH A 63 2063 2063 HOH HOH . K 8 HOH A 64 2064 2064 HOH HOH . K 8 HOH A 65 2065 2065 HOH HOH . K 8 HOH A 66 2066 2066 HOH HOH . K 8 HOH A 67 2067 2067 HOH HOH . K 8 HOH A 68 2068 2068 HOH HOH . K 8 HOH A 69 2069 2069 HOH HOH . K 8 HOH A 70 2070 2070 HOH HOH . K 8 HOH A 71 2071 2071 HOH HOH . K 8 HOH A 72 2072 2072 HOH HOH . K 8 HOH A 73 2073 2073 HOH HOH . K 8 HOH A 74 2074 2074 HOH HOH . K 8 HOH A 75 2075 2075 HOH HOH . K 8 HOH A 76 2076 2076 HOH HOH . K 8 HOH A 77 2077 2077 HOH HOH . K 8 HOH A 78 2078 2078 HOH HOH . K 8 HOH A 79 2079 2079 HOH HOH . K 8 HOH A 80 2080 2080 HOH HOH . K 8 HOH A 81 2081 2081 HOH HOH . K 8 HOH A 82 2082 2082 HOH HOH . K 8 HOH A 83 2083 2083 HOH HOH . K 8 HOH A 84 2084 2084 HOH HOH . K 8 HOH A 85 2085 2085 HOH HOH . K 8 HOH A 86 2086 2086 HOH HOH . K 8 HOH A 87 2087 2087 HOH HOH . K 8 HOH A 88 2088 2088 HOH HOH . K 8 HOH A 89 2089 2089 HOH HOH . K 8 HOH A 90 2090 2090 HOH HOH . K 8 HOH A 91 2091 2091 HOH HOH . K 8 HOH A 92 2092 2092 HOH HOH . K 8 HOH A 93 2093 2093 HOH HOH . K 8 HOH A 94 2094 2094 HOH HOH . K 8 HOH A 95 2095 2095 HOH HOH . K 8 HOH A 96 2096 2096 HOH HOH . K 8 HOH A 97 2097 2097 HOH HOH . K 8 HOH A 98 2098 2098 HOH HOH . K 8 HOH A 99 2099 2099 HOH HOH . K 8 HOH A 100 2100 2100 HOH HOH . K 8 HOH A 101 2101 2101 HOH HOH . K 8 HOH A 102 2102 2102 HOH HOH . K 8 HOH A 103 2103 2103 HOH HOH . K 8 HOH A 104 2104 2104 HOH HOH . K 8 HOH A 105 2105 2105 HOH HOH . K 8 HOH A 106 2106 2106 HOH HOH . K 8 HOH A 107 2107 2107 HOH HOH . K 8 HOH A 108 2108 2108 HOH HOH . K 8 HOH A 109 2109 2109 HOH HOH . K 8 HOH A 110 2110 2110 HOH HOH . K 8 HOH A 111 2111 2111 HOH HOH . K 8 HOH A 112 2112 2112 HOH HOH . K 8 HOH A 113 2113 2113 HOH HOH . K 8 HOH A 114 2114 2114 HOH HOH . K 8 HOH A 115 2115 2115 HOH HOH . K 8 HOH A 116 2116 2116 HOH HOH . K 8 HOH A 117 2117 2117 HOH HOH . K 8 HOH A 118 2118 2118 HOH HOH . K 8 HOH A 119 2119 2119 HOH HOH . K 8 HOH A 120 2120 2120 HOH HOH . K 8 HOH A 121 2121 2121 HOH HOH . K 8 HOH A 122 2122 2122 HOH HOH . K 8 HOH A 123 2123 2123 HOH HOH . K 8 HOH A 124 2124 2124 HOH HOH . K 8 HOH A 125 2125 2125 HOH HOH . K 8 HOH A 126 2126 2126 HOH HOH . K 8 HOH A 127 2127 2127 HOH HOH . K 8 HOH A 128 2128 2128 HOH HOH . K 8 HOH A 129 2129 2129 HOH HOH . K 8 HOH A 130 2130 2130 HOH HOH . K 8 HOH A 131 2131 2131 HOH HOH . K 8 HOH A 132 2132 2132 HOH HOH . K 8 HOH A 133 2133 2133 HOH HOH . K 8 HOH A 134 2134 2134 HOH HOH . K 8 HOH A 135 2135 2135 HOH HOH . K 8 HOH A 136 2136 2136 HOH HOH . K 8 HOH A 137 2137 2137 HOH HOH . K 8 HOH A 138 2138 2138 HOH HOH . K 8 HOH A 139 2139 2139 HOH HOH . K 8 HOH A 140 2140 2140 HOH HOH . K 8 HOH A 141 2141 2141 HOH HOH . K 8 HOH A 142 2142 2142 HOH HOH . K 8 HOH A 143 2143 2143 HOH HOH . K 8 HOH A 144 2144 2144 HOH HOH . K 8 HOH A 145 2145 2145 HOH HOH . K 8 HOH A 146 2146 2146 HOH HOH . K 8 HOH A 147 2147 2147 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 P PG APC . . . B 2 24.124 36.03 1.26 1 55.78 ? PG APC 1467 A 1 HETATM 2 O O1G APC . . . B 2 22.657 35.715 0.959 1 54.7 ? O1G APC 1467 A 1 HETATM 3 O O2G APC . . . B 2 24.616 37.453 0.937 1 50.83 ? O2G APC 1467 A 1 HETATM 4 O O3G APC . . . B 2 24.339 35.671 2.697 1 53.37 ? O3G APC 1467 A 1 HETATM 5 P PB APC . . . B 2 24.683 33.511 0.001 1 57.19 ? PB APC 1467 A 1 HETATM 6 O O1B APC . . . B 2 23.658 33.423 -1.065 1 52.09 ? O1B APC 1467 A 1 HETATM 7 O O2B APC . . . B 2 26.025 32.937 -0.697 1 61.58 ? O2B APC 1467 A 1 HETATM 8 O O3B APC . . . B 2 24.98 35.098 0.265 1 55.21 ? O3B APC 1467 A 1 HETATM 9 P PA APC . . . B 2 23.615 30.899 1.36 1 67.13 ? PA APC 1467 A 1 HETATM 10 O O1A APC . . . B 2 24.791 30.057 0.682 1 68.61 ? O1A APC 1467 A 1 HETATM 11 O O2A APC . . . B 2 22.339 30.752 0.596 1 58.23 ? O2A APC 1467 A 1 HETATM 12 C C3A APC . . . B 2 24.173 32.651 1.533 1 57.37 ? C3A APC 1467 A 1 HETATM 13 O O5' APC . . . B 2 23.335 30.372 2.868 1 61.28 ? O5' APC 1467 A 1 HETATM 14 C C5' APC . . . B 2 22.296 30.977 3.623 1 68.17 ? C5' APC 1467 A 1 HETATM 15 C C4' APC . . . B 2 21.239 29.977 4.018 1 68.73 ? C4' APC 1467 A 1 HETATM 16 O O4' APC . . . B 2 20.269 30.682 4.789 1 71.29 ? O4' APC 1467 A 1 HETATM 17 C C3' APC . . . B 2 20.487 29.331 2.856 1 70.12 ? C3' APC 1467 A 1 HETATM 18 O O3' APC . . . B 2 20.294 27.966 3.216 1 73.74 ? O3' APC 1467 A 1 HETATM 19 C C2' APC . . . B 2 19.129 29.987 2.823 1 71.5 ? C2' APC 1467 A 1 HETATM 20 O O2' APC . . . B 2 18.077 29.077 2.473 1 69.06 ? O2' APC 1467 A 1 HETATM 21 C C1' APC . . . B 2 18.946 30.469 4.266 1 65.74 ? C1' APC 1467 A 1 HETATM 22 N N9 APC . . . B 2 18.136 31.707 4.318 1 65.85 ? N9 APC 1467 A 1 HETATM 23 C C8 APC . . . B 2 18.587 32.943 4.63 1 67.33 ? C8 APC 1467 A 1 HETATM 24 N N7 APC . . . B 2 17.599 33.864 4.574 1 62.67 ? N7 APC 1467 A 1 HETATM 25 C C5 APC . . . B 2 16.477 33.201 4.241 1 53.59 ? C5 APC 1467 A 1 HETATM 26 C C6 APC . . . B 2 15.06 33.584 4.003 1 47.22 ? C6 APC 1467 A 1 HETATM 27 N N6 APC . . . B 2 14.637 34.85 4.173 1 42.6 ? N6 APC 1467 A 1 HETATM 28 N N1 APC . . . B 2 14.201 32.594 3.68 1 58.99 ? N1 APC 1467 A 1 HETATM 29 C C2 APC . . . B 2 14.602 31.29 3.545 1 60.84 ? C2 APC 1467 A 1 HETATM 30 N N3 APC . . . B 2 15.871 30.866 3.731 1 54.4 ? N3 APC 1467 A 1 HETATM 31 C C4 APC . . . B 2 16.831 31.775 4.076 1 58.36 ? C4 APC 1467 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #