data_3AR3 # _model_server_result.job_id UXGjzJNAmp6dCkAqm3Byrg _model_server_result.datetime_utc '2024-11-23 12:37:27' _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 3ar3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1002}' # _entry.id 3AR3 # _exptl.entry_id 3AR3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 3AR3 _cell.length_a 71.309 _cell.length_b 71.309 _cell.length_c 590.026 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AR3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 6 _struct_asym.id I _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 disulf ? disulf1 A SG CYS 877 A CYS 876 1_555 A SG CYS 889 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A C ACE 1 A ACE 1 1_555 A N MET 2 A MET 1 1_555 A ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OD1 ASP 704 A ASP 703 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc2 A O LEU 712 A LEU 711 1_555 B NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc3 A O LYS 713 A LYS 712 1_555 B NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc4 A O ALA 715 A ALA 714 1_555 B NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc5 A OE1 GLU 733 A GLU 732 1_555 B NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc6 C MG MG . A MG 997 1_555 I O1B ADP . A ADP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc7 C MG MG . A MG 997 1_555 I O1A ADP . A ADP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc8 B NA NA . A NA 1000 1_555 J O HOH . A HOH 2142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc9 B NA NA . A NA 1000 1_555 J O HOH . A HOH 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 7 n n PB O2B ADP sing 8 n n PB O3B ADP sing 9 n n PB O3A ADP sing 10 n n O2B HOB2 ADP sing 11 n n O3B HOB3 ADP sing 12 n n PA O1A ADP doub 13 n n PA O2A ADP sing 14 n n PA O3A ADP sing 15 n n PA O5' ADP sing 16 n n O2A HOA2 ADP sing 17 n n O5' C5' ADP sing 18 n n C5' C4' ADP sing 19 n n C5' "H5'1" ADP sing 20 n n C5' "H5'2" ADP sing 21 n n C4' O4' ADP sing 22 n n C4' C3' ADP sing 23 n n C4' H4' ADP sing 24 n n O4' C1' ADP sing 25 n n C3' O3' ADP sing 26 n n C3' C2' ADP sing 27 n n C3' H3' ADP sing 28 n n O3' HO3' ADP sing 29 n n C2' O2' ADP sing 30 n n C2' C1' ADP sing 31 n n C2' H2' ADP sing 32 n n O2' HO2' ADP sing 33 n n C1' N9 ADP sing 34 n n C1' H1' ADP sing 35 n n N9 C8 ADP sing 36 n y N9 C4 ADP sing 37 n y C8 N7 ADP doub 38 n y C8 H8 ADP sing 39 n n N7 C5 ADP sing 40 n y C5 C6 ADP sing 41 n y C5 C4 ADP doub 42 n y C6 N6 ADP sing 43 n n C6 N1 ADP doub 44 n y N6 HN61 ADP sing 45 n n N6 HN62 ADP sing 46 n n N1 C2 ADP sing 47 n y C2 N3 ADP doub 48 n y C2 H2 ADP sing 49 n n N3 C4 ADP sing 50 n y # _atom_sites.entry_id 3AR3 _atom_sites.fract_transf_matrix[1][1] 0.014023 _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] 0.014023 _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] 0.001695 _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 NA A 1 1000 1000 NA NA . C 3 MG A 1 997 997 MG MG . D 3 MG A 1 1001 1001 MG MG . E 4 TG1 A 1 1003 1003 TG1 TG1 . F 5 PTY A 1 1011 1011 PTY PTY . G 5 PTY A 1 1012 1012 PTY PTY . H 5 PTY A 1 1013 1013 PTY PTY . I 6 ADP A 1 1002 1002 ADP ADP . J 7 HOH A 1 2001 2001 HOH HOH . J 7 HOH A 2 2002 2002 HOH HOH . J 7 HOH A 3 2004 2004 HOH HOH . J 7 HOH A 4 2005 2005 HOH HOH . J 7 HOH A 5 2101 2101 HOH HOH . J 7 HOH A 6 2102 2102 HOH HOH . J 7 HOH A 7 2103 2103 HOH HOH . J 7 HOH A 8 2104 2104 HOH HOH . J 7 HOH A 9 2105 2105 HOH HOH . J 7 HOH A 10 2106 2106 HOH HOH . J 7 HOH A 11 2107 2107 HOH HOH . J 7 HOH A 12 2108 2108 HOH HOH . J 7 HOH A 13 2109 2109 HOH HOH . J 7 HOH A 14 2110 2110 HOH HOH . J 7 HOH A 15 2111 2111 HOH HOH . J 7 HOH A 16 2112 2112 HOH HOH . J 7 HOH A 17 2113 2113 HOH HOH . J 7 HOH A 18 2114 2114 HOH HOH . J 7 HOH A 19 2115 2115 HOH HOH . J 7 HOH A 20 2116 2116 HOH HOH . J 7 HOH A 21 2117 2117 HOH HOH . J 7 HOH A 22 2118 2118 HOH HOH . J 7 HOH A 23 2119 2119 HOH HOH . J 7 HOH A 24 2120 2120 HOH HOH . J 7 HOH A 25 2122 2122 HOH HOH . J 7 HOH A 26 2123 2123 HOH HOH . J 7 HOH A 27 2124 2124 HOH HOH . J 7 HOH A 28 2126 2126 HOH HOH . J 7 HOH A 29 2127 2127 HOH HOH . J 7 HOH A 30 2128 2128 HOH HOH . J 7 HOH A 31 2129 2129 HOH HOH . J 7 HOH A 32 2130 2130 HOH HOH . J 7 HOH A 33 2131 2131 HOH HOH . J 7 HOH A 34 2132 2132 HOH HOH . J 7 HOH A 35 2133 2133 HOH HOH . J 7 HOH A 36 2134 2134 HOH HOH . J 7 HOH A 37 2135 2135 HOH HOH . J 7 HOH A 38 2136 2136 HOH HOH . J 7 HOH A 39 2138 2138 HOH HOH . J 7 HOH A 40 2140 2140 HOH HOH . J 7 HOH A 41 2141 2141 HOH HOH . J 7 HOH A 42 2142 2142 HOH HOH . J 7 HOH A 43 2143 2143 HOH HOH . J 7 HOH A 44 2144 2144 HOH HOH . J 7 HOH A 45 2145 2145 HOH HOH . J 7 HOH A 46 2146 2146 HOH HOH . J 7 HOH A 47 2147 2147 HOH HOH . J 7 HOH A 48 2148 2148 HOH HOH . J 7 HOH A 49 2149 2149 HOH HOH . J 7 HOH A 50 2150 2150 HOH HOH . J 7 HOH A 51 2152 2152 HOH HOH . J 7 HOH A 52 2154 2154 HOH HOH . J 7 HOH A 53 2155 2155 HOH HOH . J 7 HOH A 54 2156 2156 HOH HOH . J 7 HOH A 55 2157 2157 HOH HOH . J 7 HOH A 56 2160 2160 HOH HOH . J 7 HOH A 57 2161 2161 HOH HOH . J 7 HOH A 58 2162 2162 HOH HOH . J 7 HOH A 59 2163 2163 HOH HOH . J 7 HOH A 60 2164 2164 HOH HOH . J 7 HOH A 61 2165 2165 HOH HOH . J 7 HOH A 62 2166 2166 HOH HOH . J 7 HOH A 63 2167 2167 HOH HOH . J 7 HOH A 64 2168 2168 HOH HOH . J 7 HOH A 65 2170 2170 HOH HOH . J 7 HOH A 66 2171 2171 HOH HOH . J 7 HOH A 67 2173 2173 HOH HOH . J 7 HOH A 68 2174 2174 HOH HOH . J 7 HOH A 69 2175 2175 HOH HOH . J 7 HOH A 70 2176 2176 HOH HOH . J 7 HOH A 71 2177 2177 HOH HOH . J 7 HOH A 72 2180 2180 HOH HOH . J 7 HOH A 73 2185 2185 HOH HOH . J 7 HOH A 74 2186 2186 HOH HOH . J 7 HOH A 75 2188 2188 HOH HOH . J 7 HOH A 76 2189 2189 HOH HOH . J 7 HOH A 77 2191 2191 HOH HOH . J 7 HOH A 78 2193 2193 HOH HOH . J 7 HOH A 79 2194 2194 HOH HOH . J 7 HOH A 80 2195 2195 HOH HOH . J 7 HOH A 81 2196 2196 HOH HOH . J 7 HOH A 82 2201 2201 HOH HOH . J 7 HOH A 83 2204 2204 HOH HOH . J 7 HOH A 84 2209 2209 HOH HOH . J 7 HOH A 85 2210 2210 HOH HOH . J 7 HOH A 86 2212 2212 HOH HOH . J 7 HOH A 87 2232 2232 HOH HOH . J 7 HOH A 88 2243 2243 HOH HOH . J 7 HOH A 89 2245 2245 HOH HOH . J 7 HOH A 90 2251 2251 HOH HOH . J 7 HOH A 91 2300 2300 HOH HOH . J 7 HOH A 92 2301 2301 HOH HOH . J 7 HOH A 93 2302 2302 HOH HOH . J 7 HOH A 94 2306 2306 HOH HOH . J 7 HOH A 95 2308 2308 HOH HOH . J 7 HOH A 96 2314 2314 HOH HOH . J 7 HOH A 97 2316 2316 HOH HOH . J 7 HOH A 98 2317 2317 HOH HOH . J 7 HOH A 99 2319 2319 HOH HOH . J 7 HOH A 100 2322 2322 HOH HOH . J 7 HOH A 101 2323 2323 HOH HOH . J 7 HOH A 102 2326 2326 HOH HOH . J 7 HOH A 103 2327 2327 HOH HOH . J 7 HOH A 104 2330 2330 HOH HOH . J 7 HOH A 105 2332 2332 HOH HOH . J 7 HOH A 106 2333 2333 HOH HOH . J 7 HOH A 107 2334 2334 HOH HOH . J 7 HOH A 108 2337 2337 HOH HOH . J 7 HOH A 109 2339 2339 HOH HOH . J 7 HOH A 110 2341 2341 HOH HOH . J 7 HOH A 111 2501 2501 HOH HOH . J 7 HOH A 112 2506 2506 HOH HOH . J 7 HOH A 113 2508 2508 HOH HOH . J 7 HOH A 114 2513 2513 HOH HOH . J 7 HOH A 115 2514 2514 HOH HOH . J 7 HOH A 116 2517 2517 HOH HOH . J 7 HOH A 117 2519 2519 HOH HOH . J 7 HOH A 118 2602 2602 HOH HOH . J 7 HOH A 119 2603 2603 HOH HOH . J 7 HOH A 120 2604 2604 HOH HOH . J 7 HOH A 121 2605 2605 HOH HOH . J 7 HOH A 122 2606 2606 HOH HOH . J 7 HOH A 123 2608 2608 HOH HOH . J 7 HOH A 124 2613 2613 HOH HOH . J 7 HOH A 125 2615 2615 HOH HOH . J 7 HOH A 126 2616 2616 HOH HOH . J 7 HOH A 127 2618 2618 HOH HOH . J 7 HOH A 128 2619 2619 HOH HOH . J 7 HOH A 129 2620 2620 HOH HOH . J 7 HOH A 130 2623 2623 HOH HOH . J 7 HOH A 131 2624 2624 HOH HOH . J 7 HOH A 132 2625 2625 HOH HOH . J 7 HOH A 133 2626 2626 HOH HOH . J 7 HOH A 134 2627 2627 HOH HOH . J 7 HOH A 135 2628 2628 HOH HOH . J 7 HOH A 136 2630 2630 HOH HOH . J 7 HOH A 137 2631 2631 HOH HOH . J 7 HOH A 138 2634 2634 HOH HOH . J 7 HOH A 139 2636 2636 HOH HOH . J 7 HOH A 140 2640 2640 HOH HOH . J 7 HOH A 141 2641 2641 HOH HOH . J 7 HOH A 142 2642 2642 HOH HOH . J 7 HOH A 143 2643 2643 HOH HOH . J 7 HOH A 144 2647 2647 HOH HOH . J 7 HOH A 145 2649 2649 HOH HOH . J 7 HOH A 146 2652 2652 HOH HOH . J 7 HOH A 147 2654 2654 HOH HOH . J 7 HOH A 148 2655 2655 HOH HOH . J 7 HOH A 149 2656 2656 HOH HOH . J 7 HOH A 150 2660 2660 HOH HOH . J 7 HOH A 151 2663 2663 HOH HOH . J 7 HOH A 152 2668 2668 HOH HOH . J 7 HOH A 153 2672 2672 HOH HOH . J 7 HOH A 154 2673 2673 HOH HOH . J 7 HOH A 155 2685 2685 HOH HOH . J 7 HOH A 156 2702 2702 HOH HOH . J 7 HOH A 157 2802 2802 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 PB ADP . . . I 6 36.925 -1.327 134.007 1 94.09 ? PB ADP 1002 A 1 HETATM 2 O O1B ADP . . . I 6 36.953 0.159 134.052 1 93.58 ? O1B ADP 1002 A 1 HETATM 3 O O2B ADP . . . I 6 35.387 -1.836 133.873 1 96.53 ? O2B ADP 1002 A 1 HETATM 4 O O3B ADP . . . I 6 37.71 -1.803 132.827 1 94.3 ? O3B ADP 1002 A 1 HETATM 5 P PA ADP . . . I 6 38.737 -1.551 136.155 1 91.87 ? PA ADP 1002 A 1 HETATM 6 O O1A ADP . . . I 6 39.391 -0.23 135.801 1 92.05 ? O1A ADP 1002 A 1 HETATM 7 O O2A ADP . . . I 6 39.808 -2.627 136.229 1 92.25 ? O2A ADP 1002 A 1 HETATM 8 O O3A ADP . . . I 6 37.553 -1.902 135.322 1 93.41 ? O3A ADP 1002 A 1 HETATM 9 O O5' ADP . . . I 6 38.168 -1.38 137.658 1 90.15 ? O5' ADP 1002 A 1 HETATM 10 C C5' ADP . . . I 6 37.545 -2.471 138.334 1 84.18 ? C5' ADP 1002 A 1 HETATM 11 C C4' ADP . . . I 6 36.691 -2.018 139.529 1 80.89 ? C4' ADP 1002 A 1 HETATM 12 O O4' ADP . . . I 6 37.333 -1.034 140.378 1 78.42 ? O4' ADP 1002 A 1 HETATM 13 C C3' ADP . . . I 6 35.369 -1.452 139.095 1 81.35 ? C3' ADP 1002 A 1 HETATM 14 O O3' ADP . . . I 6 34.281 -2.411 139.148 1 81.37 ? O3' ADP 1002 A 1 HETATM 15 C C2' ADP . . . I 6 35.098 -0.214 139.953 1 79.84 ? C2' ADP 1002 A 1 HETATM 16 O O2' ADP . . . I 6 34.024 -0.421 140.883 1 78.95 ? O2' ADP 1002 A 1 HETATM 17 C C1' ADP . . . I 6 36.459 0.08 140.468 1 77.37 ? C1' ADP 1002 A 1 HETATM 18 N N9 ADP . . . I 6 37.08 1.372 139.948 1 77.12 ? N9 ADP 1002 A 1 HETATM 19 C C8 ADP . . . I 6 37.138 1.674 138.621 1 79.01 ? C8 ADP 1002 A 1 HETATM 20 N N7 ADP . . . I 6 37.743 2.871 138.445 1 77.68 ? N7 ADP 1002 A 1 HETATM 21 C C5 ADP . . . I 6 38.081 3.351 139.627 1 75.71 ? C5 ADP 1002 A 1 HETATM 22 C C6 ADP . . . I 6 38.733 4.532 140.137 1 75.15 ? C6 ADP 1002 A 1 HETATM 23 N N6 ADP . . . I 6 39.179 5.507 139.305 1 70.16 ? N6 ADP 1002 A 1 HETATM 24 N N1 ADP . . . I 6 38.919 4.688 141.514 1 74.17 ? N1 ADP 1002 A 1 HETATM 25 C C2 ADP . . . I 6 38.497 3.748 142.42 1 74.19 ? C2 ADP 1002 A 1 HETATM 26 N N3 ADP . . . I 6 37.878 2.626 141.946 1 73.55 ? N3 ADP 1002 A 1 HETATM 27 C C4 ADP . . . I 6 37.653 2.386 140.6 1 75.05 ? C4 ADP 1002 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #