data_4BV3 # _model_server_result.job_id F9cnMYz5Ku8pmjW-CDpybQ _model_server_result.datetime_utc '2024-12-02 22:22:32' _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 4bv3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1393}' # _entry.id 4BV3 # _exptl.entry_id 4BV3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _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 90 _cell.entry_id 4BV3 _cell.length_a 60.94 _cell.length_b 63.38 _cell.length_c 66.35 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BV3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,J,K _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 3 _struct_asym.id C _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 SG CYS 141 A CYS 256 1_555 E ZN ZN . A ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc2 A SG CYS 144 A CYS 259 1_555 E ZN ZN . A ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc3 A SG CYS 165 A CYS 280 1_555 E ZN ZN . A ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 A SG CYS 168 A CYS 283 1_555 E ZN ZN . A ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc5 A OE2 GLU 210 A GLU 325 1_555 I NA NA . A NA 1399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc6 A OE2 GLU 217 A GLU 332 1_555 I NA NA . A NA 1399 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.951 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _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 N1 C2 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 4BV3 _atom_sites.fract_transf_matrix[1][1] 0.01641 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015778 _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] 0.015072 _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 NAD A 1 1392 1392 NAD NAD . C 3 APR A 1 1393 1393 APR APR . D 4 OCZ A 1 1394 1394 OCZ OCZ . E 5 ZN A 1 1395 1395 ZN ZN . F 6 NO3 A 1 1396 1396 NO3 NO3 . G 7 GOL A 1 1397 1397 GOL GOL . H 7 GOL A 1 1398 1398 GOL GOL . I 8 NA A 1 1399 1399 NA NA . J 9 CL A 1 1400 1400 CL CL . K 10 HOH A 1 2001 2001 HOH HOH . K 10 HOH A 2 2002 2002 HOH HOH . K 10 HOH A 3 2003 2003 HOH HOH . K 10 HOH A 4 2004 2004 HOH HOH . K 10 HOH A 5 2005 2005 HOH HOH . K 10 HOH A 6 2006 2006 HOH HOH . K 10 HOH A 7 2007 2007 HOH HOH . K 10 HOH A 8 2008 2008 HOH HOH . K 10 HOH A 9 2009 2009 HOH HOH . K 10 HOH A 10 2010 2010 HOH HOH . K 10 HOH A 11 2011 2011 HOH HOH . K 10 HOH A 12 2012 2012 HOH HOH . K 10 HOH A 13 2013 2013 HOH HOH . K 10 HOH A 14 2014 2014 HOH HOH . K 10 HOH A 15 2015 2015 HOH HOH . K 10 HOH A 16 2016 2016 HOH HOH . K 10 HOH A 17 2017 2017 HOH HOH . K 10 HOH A 18 2018 2018 HOH HOH . K 10 HOH A 19 2019 2019 HOH HOH . K 10 HOH A 20 2020 2020 HOH HOH . K 10 HOH A 21 2021 2021 HOH HOH . K 10 HOH A 22 2022 2022 HOH HOH . K 10 HOH A 23 2023 2023 HOH HOH . K 10 HOH A 24 2024 2024 HOH HOH . K 10 HOH A 25 2025 2025 HOH HOH . K 10 HOH A 26 2026 2026 HOH HOH . K 10 HOH A 27 2027 2027 HOH HOH . K 10 HOH A 28 2028 2028 HOH HOH . K 10 HOH A 29 2029 2029 HOH HOH . K 10 HOH A 30 2030 2030 HOH HOH . K 10 HOH A 31 2031 2031 HOH HOH . K 10 HOH A 32 2032 2032 HOH HOH . K 10 HOH A 33 2033 2033 HOH HOH . K 10 HOH A 34 2034 2034 HOH HOH . K 10 HOH A 35 2035 2035 HOH HOH . K 10 HOH A 36 2036 2036 HOH HOH . K 10 HOH A 37 2037 2037 HOH HOH . K 10 HOH A 38 2038 2038 HOH HOH . K 10 HOH A 39 2039 2039 HOH HOH . K 10 HOH A 40 2040 2040 HOH HOH . K 10 HOH A 41 2041 2041 HOH HOH . K 10 HOH A 42 2042 2042 HOH HOH . K 10 HOH A 43 2043 2043 HOH HOH . K 10 HOH A 44 2044 2044 HOH HOH . K 10 HOH A 45 2045 2045 HOH HOH . K 10 HOH A 46 2046 2046 HOH HOH . K 10 HOH A 47 2047 2047 HOH HOH . K 10 HOH A 48 2048 2048 HOH HOH . K 10 HOH A 49 2049 2049 HOH HOH . K 10 HOH A 50 2050 2050 HOH HOH . K 10 HOH A 51 2051 2051 HOH HOH . K 10 HOH A 52 2052 2052 HOH HOH . K 10 HOH A 53 2053 2053 HOH HOH . K 10 HOH A 54 2054 2054 HOH HOH . K 10 HOH A 55 2055 2055 HOH HOH . K 10 HOH A 56 2056 2056 HOH HOH . K 10 HOH A 57 2057 2057 HOH HOH . K 10 HOH A 58 2058 2058 HOH HOH . K 10 HOH A 59 2059 2059 HOH HOH . K 10 HOH A 60 2060 2060 HOH HOH . K 10 HOH A 61 2061 2061 HOH HOH . K 10 HOH A 62 2062 2062 HOH HOH . K 10 HOH A 63 2063 2063 HOH HOH . K 10 HOH A 64 2064 2064 HOH HOH . K 10 HOH A 65 2065 2065 HOH HOH . K 10 HOH A 66 2066 2066 HOH HOH . K 10 HOH A 67 2067 2067 HOH HOH . K 10 HOH A 68 2068 2068 HOH HOH . K 10 HOH A 69 2069 2069 HOH HOH . K 10 HOH A 70 2070 2070 HOH HOH . K 10 HOH A 71 2071 2071 HOH HOH . K 10 HOH A 72 2072 2072 HOH HOH . K 10 HOH A 73 2073 2073 HOH HOH . K 10 HOH A 74 2074 2074 HOH HOH . K 10 HOH A 75 2075 2075 HOH HOH . K 10 HOH A 76 2076 2076 HOH HOH . K 10 HOH A 77 2077 2077 HOH HOH . K 10 HOH A 78 2078 2078 HOH HOH . K 10 HOH A 79 2079 2079 HOH HOH . K 10 HOH A 80 2080 2080 HOH HOH . K 10 HOH A 81 2081 2081 HOH HOH . K 10 HOH A 82 2082 2082 HOH HOH . K 10 HOH A 83 2083 2083 HOH HOH . K 10 HOH A 84 2085 2085 HOH HOH . K 10 HOH A 85 2086 2086 HOH HOH . K 10 HOH A 86 2087 2087 HOH HOH . K 10 HOH A 87 2088 2088 HOH HOH . K 10 HOH A 88 2089 2089 HOH HOH . K 10 HOH A 89 2090 2090 HOH HOH . K 10 HOH A 90 2091 2091 HOH HOH . K 10 HOH A 91 2092 2092 HOH HOH . K 10 HOH A 92 2093 2093 HOH HOH . K 10 HOH A 93 2094 2094 HOH HOH . K 10 HOH A 94 2095 2095 HOH HOH . K 10 HOH A 95 2096 2096 HOH HOH . K 10 HOH A 96 2097 2097 HOH HOH . K 10 HOH A 97 2098 2098 HOH HOH . K 10 HOH A 98 2099 2099 HOH HOH . K 10 HOH A 99 2100 2100 HOH HOH . K 10 HOH A 100 2101 2101 HOH HOH . K 10 HOH A 101 2102 2102 HOH HOH . K 10 HOH A 102 2103 2103 HOH HOH . K 10 HOH A 103 2104 2104 HOH HOH . K 10 HOH A 104 2105 2105 HOH HOH . K 10 HOH A 105 2106 2106 HOH HOH . K 10 HOH A 106 2107 2107 HOH HOH . K 10 HOH A 107 2108 2108 HOH HOH . K 10 HOH A 108 2109 2109 HOH HOH . K 10 HOH A 109 2110 2110 HOH HOH . K 10 HOH A 110 2111 2111 HOH HOH . K 10 HOH A 111 2112 2112 HOH HOH . K 10 HOH A 112 2113 2113 HOH HOH . K 10 HOH A 113 2114 2114 HOH HOH . K 10 HOH A 114 2115 2115 HOH HOH . K 10 HOH A 115 2116 2116 HOH HOH . K 10 HOH A 116 2117 2117 HOH HOH . K 10 HOH A 117 2118 2118 HOH HOH . K 10 HOH A 118 2119 2119 HOH HOH . K 10 HOH A 119 2120 2120 HOH HOH . K 10 HOH A 120 2121 2121 HOH HOH . K 10 HOH A 121 2122 2122 HOH HOH . K 10 HOH A 122 2123 2123 HOH HOH . K 10 HOH A 123 2124 2124 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 N N1 APR . B . C 3 0.404 -13.442 -10.957 0.2 19.54 ? N1 APR 1393 A 1 HETATM 2 C C2 APR . B . C 3 1.564 -13.089 -11.533 0.2 19.66 ? C2 APR 1393 A 1 HETATM 3 N N3 APR . B . C 3 2.458 -12.292 -10.942 0.2 19.37 ? N3 APR 1393 A 1 HETATM 4 C C4 APR . B . C 3 2.229 -11.793 -9.709 0.2 19.01 ? C4 APR 1393 A 1 HETATM 5 C C5 APR . B . C 3 0.988 -12.122 -9.008 0.2 19.23 ? C5 APR 1393 A 1 HETATM 6 C C6 APR . B . C 3 0.05 -13.004 -9.728 0.2 19.61 ? C6 APR 1393 A 1 HETATM 7 N N6 APR . B . C 3 -1.12 -13.374 -9.172 0.2 19.41 ? N6 APR 1393 A 1 HETATM 8 N N7 APR . B . C 3 1.036 -11.487 -7.823 0.2 19.56 ? N7 APR 1393 A 1 HETATM 9 C C8 APR . B . C 3 2.207 -10.8 -7.769 0.2 18.84 ? C8 APR 1393 A 1 HETATM 10 N N9 APR . B . C 3 2.912 -11.001 -8.898 0.2 18.71 ? N9 APR 1393 A 1 HETATM 11 C C1' APR . B . C 3 4.235 -10.449 -9.233 0.2 18.27 ? C1' APR 1393 A 1 HETATM 12 C C2' APR . B . C 3 4.243 -8.965 -8.977 0.2 18.18 ? C2' APR 1393 A 1 HETATM 13 O O2' APR . B . C 3 3.624 -8.296 -10.08 0.2 17.87 ? O2' APR 1393 A 1 HETATM 14 C C3' APR . B . C 3 5.724 -8.718 -8.773 0.2 18.03 ? C3' APR 1393 A 1 HETATM 15 O O3' APR . B . C 3 6.384 -8.557 -10.022 0.2 18.01 ? O3' APR 1393 A 1 HETATM 16 O O4' APR . B . C 3 5.272 -11.003 -8.415 0.2 18.19 ? O4' APR 1393 A 1 HETATM 17 C C4' APR . B . C 3 6.231 -9.988 -8.11 0.2 17.86 ? C4' APR 1393 A 1 HETATM 18 C C5' APR . B . C 3 6.358 -9.854 -6.596 0.2 17.92 ? C5' APR 1393 A 1 HETATM 19 O O5' APR . B . C 3 7.706 -9.574 -6.212 0.2 17.9 ? O5' APR 1393 A 1 HETATM 20 P PA APR . B . C 3 8.025 -8.82 -4.819 0.2 17.31 ? PA APR 1393 A 1 HETATM 21 O O1A APR . B . C 3 6.746 -8.267 -4.254 0.2 17.52 ? O1A APR 1393 A 1 HETATM 22 O O2A APR . B . C 3 9.233 -7.945 -5.043 0.2 16.87 ? O2A APR 1393 A 1 HETATM 23 O O3A APR . B . C 3 8.487 -10.029 -3.854 0.2 16.85 ? O3A APR 1393 A 1 HETATM 24 P PB APR . B . C 3 9.637 -11.076 -4.275 0.2 16.81 ? PB APR 1393 A 1 HETATM 25 O O1B APR . B . C 3 9.977 -10.861 -5.728 0.2 16.78 ? O1B APR 1393 A 1 HETATM 26 O O2B APR . B . C 3 9.18 -12.428 -3.793 0.2 16.56 ? O2B APR 1393 A 1 HETATM 27 O O5D APR . B . C 3 10.942 -10.719 -3.413 0.2 17.02 ? O5D APR 1393 A 1 HETATM 28 C C5D APR . B . C 3 10.893 -9.785 -2.342 0.2 18.25 ? C5D APR 1393 A 1 HETATM 29 O O4D APR . B . C 3 12.795 -8.637 -1.444 0.2 19.58 ? O4D APR 1393 A 1 HETATM 30 O O1D APR . B . C 3 12.656 -6.588 -0.243 0.2 19.41 ? O1D APR 1393 A 1 HETATM 31 C C1D APR . B . C 3 12.861 -8.011 -0.152 0.2 19.72 ? C1D APR 1393 A 1 HETATM 32 O O2D APR . B . C 3 12.186 -8.863 2.037 0.2 20.66 ? O2D APR 1393 A 1 HETATM 33 C C2D APR . B . C 3 11.8 -8.721 0.669 0.2 19.55 ? C2D APR 1393 A 1 HETATM 34 O O3D APR . B . C 3 12.703 -10.842 0.772 0.2 18.39 ? O3D APR 1393 A 1 HETATM 35 C C3D APR . B . C 3 11.737 -10.089 0.049 0.2 19.23 ? C3D APR 1393 A 1 HETATM 36 C C4D APR . B . C 3 12.103 -9.886 -1.414 0.2 18.72 ? C4D APR 1393 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 424 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 36 #