data_3RGL # _model_server_result.job_id Rgj5Yk9oheN84VVERn8dvQ _model_server_result.datetime_utc '2024-11-15 02:19:56' _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 3rgl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 3RGL # _exptl.entry_id 3RGL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 3RGL _cell.length_a 112.74 _cell.length_b 112.74 _cell.length_c 157.753 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RGL _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N 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 24 A ALA 0 1_555 A N MSE 25 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C MSE 25 A MSE 1 1_555 A N THR 26 A THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C GLN 29 A GLN 5 1_555 A N MSE 30 A MSE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C MSE 30 A MSE 6 1_555 A N ILE 31 A ILE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale5 A C ILE 45 A ILE 21 1_555 A N MSE 46 A MSE 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C MSE 46 A MSE 22 1_555 A N GLN 47 A GLN 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C ASP 50 A ASP 26 1_555 A N MSE 51 A MSE 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C MSE 51 A MSE 27 1_555 A N PRO 52 A PRO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale9 A C GLY 157 A GLY 133 1_555 A N MSE 158 A MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 A C MSE 158 A MSE 134 1_555 A N GLU 159 A GLU 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 A C ALA 189 A ALA 165 1_555 A N MSE 190 A MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale12 A C MSE 190 A MSE 166 1_555 A N TYR 191 A TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 A C CYS 264 A CYS 240 1_555 A N MSE 265 A MSE 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 A C MSE 265 A MSE 241 1_555 A N LEU 266 A LEU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 A C TYR 288 A TYR 264 1_555 A N MSE 289 A MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale16 A C MSE 289 A MSE 265 1_555 A N LEU 290 A LEU 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale17 B C ALA 24 B ALA 0 1_555 B N MSE 25 B MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 B C MSE 25 B MSE 1 1_555 B N THR 26 B THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale19 B C GLN 29 B GLN 5 1_555 B N MSE 30 B MSE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale20 B C MSE 30 B MSE 6 1_555 B N ILE 31 B ILE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale21 B C ILE 45 B ILE 21 1_555 B N MSE 46 B MSE 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale22 B C MSE 46 B MSE 22 1_555 B N GLN 47 B GLN 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale23 B C ASP 50 B ASP 26 1_555 B N MSE 51 B MSE 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale24 B C MSE 51 B MSE 27 1_555 B N PRO 52 B PRO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale25 B C GLY 157 B GLY 133 1_555 B N MSE 158 B MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale26 B C MSE 158 B MSE 134 1_555 B N GLU 159 B GLU 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale27 B C ALA 189 B ALA 165 1_555 B N MSE 190 B MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale28 B C MSE 190 B MSE 166 1_555 B N TYR 191 B TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale29 B C CYS 264 B CYS 240 1_555 B N MSE 265 B MSE 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale30 B C MSE 265 B MSE 241 1_555 B N LEU 266 B LEU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale31 B C TYR 288 B TYR 264 1_555 B N MSE 289 B MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale32 B C MSE 289 B MSE 265 1_555 B N LEU 290 B LEU 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 3RGL _atom_sites.fract_transf_matrix[1][1] 0.00887 _atom_sites.fract_transf_matrix[1][2] 0.005121 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010242 _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] 0.006339 _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 C 2 GLY A 1 301 301 GLY GLY . D 3 ATP A 1 401 401 ATP ATP . E 3 ATP B 1 401 401 ATP ATP . F 4 LMR B 1 501 501 LMR LMR . G 5 HOH A 1 302 3 HOH HOH . G 5 HOH A 2 303 4 HOH HOH . G 5 HOH A 3 304 9 HOH HOH . G 5 HOH A 4 305 10 HOH HOH . G 5 HOH A 5 306 11 HOH HOH . G 5 HOH A 6 307 12 HOH HOH . G 5 HOH A 7 308 13 HOH HOH . H 5 HOH B 1 288 1 HOH HOH . H 5 HOH B 2 289 2 HOH HOH . H 5 HOH B 3 290 5 HOH HOH . H 5 HOH B 4 291 6 HOH HOH . H 5 HOH B 5 292 7 HOH HOH . H 5 HOH B 6 293 8 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 ATP . . . D 3 -29.134 -0.74 -5.88 0.81 114.18 ? PG ATP 401 A 1 HETATM 2 O O1G ATP . . . D 3 -29.937 -1.147 -4.664 0.81 110.59 ? O1G ATP 401 A 1 HETATM 3 O O2G ATP . . . D 3 -29.757 0.389 -6.669 0.81 115.27 ? O2G ATP 401 A 1 HETATM 4 O O3G ATP . . . D 3 -28.647 -1.908 -6.71 0.81 113.85 ? O3G ATP 401 A 1 HETATM 5 P PB ATP . . . D 3 -26.809 0.93 -6.036 0.81 134.27 ? PB ATP 401 A 1 HETATM 6 O O1B ATP . . . D 3 -27.44 1.362 -7.341 0.81 134.9 ? O1B ATP 401 A 1 HETATM 7 O O2B ATP . . . D 3 -25.409 0.351 -6.05 0.81 126.79 ? O2B ATP 401 A 1 HETATM 8 O O3B ATP . . . D 3 -27.788 -0.096 -5.255 0.81 384.85 ? O3B ATP 401 A 1 HETATM 9 P PA ATP . . . D 3 -26.799 3.709 -5.488 0.81 139.76 ? PA ATP 401 A 1 HETATM 10 O O1A ATP . . . D 3 -28.2 4.269 -5.57 0.81 134.59 ? O1A ATP 401 A 1 HETATM 11 O O2A ATP . . . D 3 -25.885 3.797 -6.692 0.81 141.22 ? O2A ATP 401 A 1 HETATM 12 O O3A ATP . . . D 3 -26.846 2.171 -4.993 0.81 72.94 ? O3A ATP 401 A 1 HETATM 13 O O5' ATP . . . D 3 -26.056 4.377 -4.222 0.81 85.29 ? O5' ATP 401 A 1 HETATM 14 C C5' ATP . . . D 3 -25.571 5.718 -4.245 0.81 84.41 ? C5' ATP 401 A 1 HETATM 15 C C4' ATP . . . D 3 -24.148 5.709 -3.7 0.81 83.15 ? C4' ATP 401 A 1 HETATM 16 O O4' ATP . . . D 3 -24.023 4.685 -2.713 0.81 76.15 ? O4' ATP 401 A 1 HETATM 17 C C3' ATP . . . D 3 -23.113 5.39 -4.782 0.81 88 ? C3' ATP 401 A 1 HETATM 18 O O3' ATP . . . D 3 -22.45 6.58 -5.24 0.81 88.59 ? O3' ATP 401 A 1 HETATM 19 C C2' ATP . . . D 3 -22.132 4.415 -4.145 0.81 83.95 ? C2' ATP 401 A 1 HETATM 20 O O2' ATP . . . D 3 -20.823 4.985 -3.994 0.81 78.79 ? O2' ATP 401 A 1 HETATM 21 C C1' ATP . . . D 3 -22.714 4.106 -2.774 0.81 80.76 ? C1' ATP 401 A 1 HETATM 22 N N9 ATP . . . D 3 -22.737 2.633 -2.566 0.81 78.71 ? N9 ATP 401 A 1 HETATM 23 C C8 ATP . . . D 3 -23.612 1.756 -3.099 0.81 68.31 ? C8 ATP 401 A 1 HETATM 24 N N7 ATP . . . D 3 -23.333 0.485 -2.704 0.81 64.58 ? N7 ATP 401 A 1 HETATM 25 C C5 ATP . . . D 3 -22.255 0.547 -1.895 0.81 68.94 ? C5 ATP 401 A 1 HETATM 26 C C6 ATP . . . D 3 -21.431 -0.416 -1.125 0.81 64.54 ? C6 ATP 401 A 1 HETATM 27 N N6 ATP . . . D 3 -21.722 -1.735 -1.148 0.81 68.06 ? N6 ATP 401 A 1 HETATM 28 N N1 ATP . . . D 3 -20.383 0.054 -0.413 0.81 55.13 ? N1 ATP 401 A 1 HETATM 29 C C2 ATP . . . D 3 -20.088 1.365 -0.38 0.81 60.56 ? C2 ATP 401 A 1 HETATM 30 N N3 ATP . . . D 3 -20.793 2.299 -1.046 0.81 72.71 ? N3 ATP 401 A 1 HETATM 31 C C4 ATP . . . D 3 -21.863 1.96 -1.811 0.81 76.71 ? C4 ATP 401 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #