data_2GNK # _model_server_result.job_id sXaz3e-nTHftFYqO16QvJA _model_server_result.datetime_utc '2024-11-27 01:17:08' _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 2gnk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":200}' # _entry.id 2GNK # _exptl.entry_id 2GNK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 2GNK _cell.length_a 57.45 _cell.length_b 57.45 _cell.length_c 54.79 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GNK _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PQS trimeric 3 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1,2 A,B,C 2 1,3,2 # 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' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -28.725 49.753159 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 28.725 49.753159 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 # _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 2GNK _atom_sites.fract_transf_matrix[1][1] 0.017406 _atom_sites.fract_transf_matrix[1][2] 0.01005 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020099 _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] 0.018251 _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 ATP A 1 200 200 ATP ATP . C 3 HOH A 1 201 201 HOH HOH . C 3 HOH A 2 202 202 HOH HOH . C 3 HOH A 3 203 203 HOH HOH . C 3 HOH A 4 204 204 HOH HOH . C 3 HOH A 5 205 205 HOH HOH . C 3 HOH A 6 206 206 HOH HOH . C 3 HOH A 7 207 207 HOH HOH . C 3 HOH A 8 208 208 HOH HOH . C 3 HOH A 9 209 209 HOH HOH . C 3 HOH A 10 210 210 HOH HOH . C 3 HOH A 11 211 211 HOH HOH . C 3 HOH A 12 212 212 HOH HOH . C 3 HOH A 13 213 213 HOH HOH . C 3 HOH A 14 214 214 HOH HOH . C 3 HOH A 15 215 215 HOH HOH . C 3 HOH A 16 216 216 HOH HOH . C 3 HOH A 17 217 217 HOH HOH . C 3 HOH A 18 218 218 HOH HOH . C 3 HOH A 19 219 219 HOH HOH . C 3 HOH A 20 220 220 HOH HOH . C 3 HOH A 21 221 221 HOH HOH . C 3 HOH A 22 222 222 HOH HOH . C 3 HOH A 23 223 223 HOH HOH . C 3 HOH A 24 224 224 HOH HOH . C 3 HOH A 25 225 225 HOH HOH . C 3 HOH A 26 226 226 HOH HOH . C 3 HOH A 27 227 227 HOH HOH . C 3 HOH A 28 228 228 HOH HOH . C 3 HOH A 29 229 229 HOH HOH . C 3 HOH A 30 230 230 HOH HOH . C 3 HOH A 31 231 231 HOH HOH . C 3 HOH A 32 232 232 HOH HOH . C 3 HOH A 33 233 233 HOH HOH . C 3 HOH A 34 234 234 HOH HOH . C 3 HOH A 35 235 235 HOH HOH . C 3 HOH A 36 236 236 HOH HOH . C 3 HOH A 37 237 237 HOH HOH . C 3 HOH A 38 238 238 HOH HOH . C 3 HOH A 39 239 239 HOH HOH . C 3 HOH A 40 240 240 HOH HOH . C 3 HOH A 41 241 241 HOH HOH . C 3 HOH A 42 242 242 HOH HOH . C 3 HOH A 43 243 243 HOH HOH . C 3 HOH A 44 244 244 HOH HOH . C 3 HOH A 45 245 245 HOH HOH . C 3 HOH A 46 246 246 HOH HOH . C 3 HOH A 47 247 247 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 . . . B 2 -20.338 34.607 1.218 1 22.69 ? PG ATP 200 A 1 HETATM 2 O O1G ATP . . . B 2 -21.202 35.529 0.456 1 23.85 ? O1G ATP 200 A 1 HETATM 3 O O2G ATP . . . B 2 -19.054 34.151 0.644 1 27.61 ? O2G ATP 200 A 1 HETATM 4 O O3G ATP . . . B 2 -21.136 33.306 1.646 1 19.35 ? O3G ATP 200 A 1 HETATM 5 P PB ATP . . . B 2 -18.907 36.423 2.991 1 23.61 ? PB ATP 200 A 1 HETATM 6 O O1B ATP . . . B 2 -18.96 37.558 2.035 1 21.05 ? O1B ATP 200 A 1 HETATM 7 O O2B ATP . . . B 2 -19.087 36.691 4.445 1 25.63 ? O2B ATP 200 A 1 HETATM 8 O O3B ATP . . . B 2 -19.974 35.318 2.587 1 19.43 ? O3B ATP 200 A 1 HETATM 9 P PA ATP . . . B 2 -16.875 34.282 3.245 1 23.04 ? PA ATP 200 A 1 HETATM 10 O O1A ATP . . . B 2 -17.434 33.216 2.376 1 19.78 ? O1A ATP 200 A 1 HETATM 11 O O2A ATP . . . B 2 -16.98 34.158 4.721 1 22.94 ? O2A ATP 200 A 1 HETATM 12 O O3A ATP . . . B 2 -17.515 35.669 2.797 1 25.18 ? O3A ATP 200 A 1 HETATM 13 O O5' ATP . . . B 2 -15.337 34.463 2.866 1 24.67 ? O5' ATP 200 A 1 HETATM 14 C C5' ATP . . . B 2 -14.334 33.648 3.482 1 24.84 ? C5' ATP 200 A 1 HETATM 15 C C4' ATP . . . B 2 -13.038 34.419 3.659 1 20.71 ? C4' ATP 200 A 1 HETATM 16 O O4' ATP . . . B 2 -12.397 34.609 2.367 1 20.27 ? O4' ATP 200 A 1 HETATM 17 C C3' ATP . . . B 2 -13.116 35.832 4.233 1 20.12 ? C3' ATP 200 A 1 HETATM 18 O O3' ATP . . . B 2 -13.201 35.86 5.654 1 17.12 ? O3' ATP 200 A 1 HETATM 19 C C2' ATP . . . B 2 -11.775 36.403 3.81 1 18.25 ? C2' ATP 200 A 1 HETATM 20 O O2' ATP . . . B 2 -10.748 35.962 4.667 1 19.19 ? O2' ATP 200 A 1 HETATM 21 C C1' ATP . . . B 2 -11.595 35.78 2.423 1 17.06 ? C1' ATP 200 A 1 HETATM 22 N N9 ATP . . . B 2 -12.027 36.667 1.356 1 12.8 ? N9 ATP 200 A 1 HETATM 23 C C8 ATP . . . B 2 -13.299 36.815 0.896 1 13.95 ? C8 ATP 200 A 1 HETATM 24 N N7 ATP . . . B 2 -13.391 37.617 -0.139 1 17.53 ? N7 ATP 200 A 1 HETATM 25 C C5 ATP . . . B 2 -12.1 38.036 -0.356 1 15.07 ? C5 ATP 200 A 1 HETATM 26 C C6 ATP . . . B 2 -11.514 38.881 -1.33 1 11.32 ? C6 ATP 200 A 1 HETATM 27 N N6 ATP . . . B 2 -12.231 39.461 -2.303 1 11.71 ? N6 ATP 200 A 1 HETATM 28 N N1 ATP . . . B 2 -10.188 39.096 -1.277 1 5.94 ? N1 ATP 200 A 1 HETATM 29 C C2 ATP . . . B 2 -9.49 38.518 -0.286 1 7.96 ? C2 ATP 200 A 1 HETATM 30 N N3 ATP . . . B 2 -9.918 37.707 0.691 1 11.48 ? N3 ATP 200 A 1 HETATM 31 C C4 ATP . . . B 2 -11.23 37.496 0.586 1 13.37 ? C4 ATP 200 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 4 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 228 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #