data_3JQP # _model_server_result.job_id ndALnUChYeT4UakwjNrOFg _model_server_result.datetime_utc '2024-11-25 11:40:49' _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 3jqp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":416}' # _entry.id 3JQP # _exptl.entry_id 3JQP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-2'-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 3JQP _cell.length_a 122.57 _cell.length_b 122.57 _cell.length_c 133.744 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JQP _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 PISA dimeric 2 software_defined_assembly 5 PISA dimeric 2 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,S,T 1 1 C,D,K,L,M,N,U,V 2 1 E,F,O,P,Q,R,W,X 3 1 A,G,H,S 4 1 B,I,J,T 4 2 C,K,L,U 5 1 D,M,N,V 5 3 E,O,P,W 6 1 F,Q,R,X 6 4 # 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_444 -x+y-1,-x-1,z-1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -61.285 -106.148734 -44.581333 3 'crystal symmetry operation' 2_555 -y,x-y,z+1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 44.581333 4 'crystal symmetry operation' 3_454 -x+y-1,-x,z-1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -122.57 0 -44.581333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R 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 disulf ? disulf1 A SG CYS 99 A CYS 99 1_555 B SG CYS 99 B CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? disulf ? disulf2 C SG CYS 99 C CYS 99 1_555 D SG CYS 99 D CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? disulf ? disulf3 E SG CYS 99 E CYS 99 1_555 F SG CYS 99 F CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A2P _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-2'-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 P1 O1P A2P doub 1 n n P1 O2P A2P sing 2 n n P1 O3P A2P sing 3 n n P1 O2' A2P sing 4 n n O2P HOP2 A2P sing 5 n n O3P HOP3 A2P sing 6 n n P2 O4P A2P doub 7 n n P2 O5P A2P sing 8 n n P2 O6P A2P sing 9 n n P2 O5' A2P sing 10 n n O5P HOP5 A2P sing 11 n n O6P HOP6 A2P sing 12 n n O5' C5' A2P sing 13 n n C5' C4' A2P sing 14 n n C5' "H5'1" A2P sing 15 n n C5' "H5'2" A2P sing 16 n n C4' O4' A2P sing 17 n n C4' C3' A2P sing 18 n n C4' H4' A2P sing 19 n n O4' C1' A2P sing 20 n n C3' O3' A2P sing 21 n n C3' C2' A2P sing 22 n n C3' H3' A2P sing 23 n n O3' HO3' A2P sing 24 n n C2' O2' A2P sing 25 n n C2' C1' A2P sing 26 n n C2' H2' A2P sing 27 n n C1' N9 A2P sing 28 n n C1' H1' A2P sing 29 n n N9 C8 A2P sing 30 n y N9 C4 A2P sing 31 n y C8 N7 A2P doub 32 n y C8 H8 A2P sing 33 n n N7 C5 A2P sing 34 n y C5 C6 A2P sing 35 n y C5 C4 A2P doub 36 n y C6 N6 A2P sing 37 n n C6 N1 A2P doub 38 n y N6 HN61 A2P sing 39 n n N6 HN62 A2P sing 40 n n N1 C2 A2P sing 41 n y C2 N3 A2P doub 42 n y C2 H2 A2P sing 43 n n N3 C4 A2P sing 44 n y # _atom_sites.entry_id 3JQP _atom_sites.fract_transf_matrix[1][1] 0.008159 _atom_sites.fract_transf_matrix[1][2] 0.00471 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009421 _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] 0.007477 _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 G 2 FAD A 1 415 415 FAD FAD . H 3 A2P A 1 416 416 A2P A2P . I 2 FAD B 1 415 415 FAD FAD . J 3 A2P B 1 416 416 A2P A2P . K 2 FAD C 1 415 415 FAD FAD . L 3 A2P C 1 416 416 A2P A2P . M 2 FAD D 1 415 415 FAD FAD . N 3 A2P D 1 416 416 A2P A2P . O 2 FAD E 1 415 415 FAD FAD . P 3 A2P E 1 416 416 A2P A2P . Q 2 FAD F 1 415 415 FAD FAD . R 3 A2P F 1 416 416 A2P A2P . S 4 HOH A 1 317 8 HOH HOH . S 4 HOH A 2 318 9 HOH HOH . S 4 HOH A 3 319 15 HOH HOH . S 4 HOH A 4 320 20 HOH HOH . S 4 HOH A 5 321 26 HOH HOH . S 4 HOH A 6 322 57 HOH HOH . S 4 HOH A 7 323 61 HOH HOH . S 4 HOH A 8 324 80 HOH HOH . S 4 HOH A 9 325 85 HOH HOH . S 4 HOH A 10 326 100 HOH HOH . S 4 HOH A 11 327 104 HOH HOH . S 4 HOH A 12 329 125 HOH HOH . S 4 HOH A 13 330 129 HOH HOH . S 4 HOH A 14 331 138 HOH HOH . S 4 HOH A 15 332 152 HOH HOH . S 4 HOH A 16 333 171 HOH HOH . S 4 HOH A 17 334 175 HOH HOH . S 4 HOH A 18 335 178 HOH HOH . S 4 HOH A 19 336 199 HOH HOH . S 4 HOH A 20 337 207 HOH HOH . S 4 HOH A 21 338 212 HOH HOH . S 4 HOH A 22 339 221 HOH HOH . S 4 HOH A 23 340 257 HOH HOH . S 4 HOH A 24 341 261 HOH HOH . S 4 HOH A 25 342 262 HOH HOH . S 4 HOH A 26 343 266 HOH HOH . S 4 HOH A 27 344 272 HOH HOH . S 4 HOH A 28 345 275 HOH HOH . S 4 HOH A 29 346 281 HOH HOH . T 4 HOH B 1 317 1 HOH HOH . T 4 HOH B 2 318 6 HOH HOH . T 4 HOH B 3 319 13 HOH HOH . T 4 HOH B 4 320 21 HOH HOH . T 4 HOH B 5 321 34 HOH HOH . T 4 HOH B 6 322 37 HOH HOH . T 4 HOH B 7 323 75 HOH HOH . T 4 HOH B 8 324 79 HOH HOH . T 4 HOH B 9 325 81 HOH HOH . T 4 HOH B 10 326 92 HOH HOH . T 4 HOH B 11 327 98 HOH HOH . T 4 HOH B 12 328 118 HOH HOH . T 4 HOH B 13 329 109 HOH HOH . T 4 HOH B 14 330 126 HOH HOH . T 4 HOH B 15 331 131 HOH HOH . T 4 HOH B 16 332 161 HOH HOH . T 4 HOH B 17 333 184 HOH HOH . T 4 HOH B 18 334 196 HOH HOH . T 4 HOH B 19 335 198 HOH HOH . T 4 HOH B 20 336 209 HOH HOH . T 4 HOH B 21 337 220 HOH HOH . T 4 HOH B 22 338 226 HOH HOH . T 4 HOH B 23 339 243 HOH HOH . T 4 HOH B 24 340 248 HOH HOH . T 4 HOH B 25 341 260 HOH HOH . T 4 HOH B 26 342 264 HOH HOH . T 4 HOH B 27 343 268 HOH HOH . T 4 HOH B 28 344 286 HOH HOH . T 4 HOH B 29 345 99 HOH HOH . U 4 HOH C 1 317 7 HOH HOH . U 4 HOH C 2 318 11 HOH HOH . U 4 HOH C 3 319 19 HOH HOH . U 4 HOH C 4 320 22 HOH HOH . U 4 HOH C 5 321 45 HOH HOH . U 4 HOH C 6 322 50 HOH HOH . U 4 HOH C 7 323 52 HOH HOH . U 4 HOH C 8 324 59 HOH HOH . U 4 HOH C 9 325 78 HOH HOH . U 4 HOH C 10 326 88 HOH HOH . U 4 HOH C 11 327 120 HOH HOH . U 4 HOH C 12 328 145 HOH HOH . U 4 HOH C 13 329 172 HOH HOH . U 4 HOH C 14 330 181 HOH HOH . U 4 HOH C 15 331 187 HOH HOH . U 4 HOH C 16 332 188 HOH HOH . U 4 HOH C 17 333 189 HOH HOH . U 4 HOH C 18 334 218 HOH HOH . U 4 HOH C 19 335 223 HOH HOH . U 4 HOH C 20 336 228 HOH HOH . U 4 HOH C 21 337 231 HOH HOH . U 4 HOH C 22 338 232 HOH HOH . U 4 HOH C 23 339 234 HOH HOH . U 4 HOH C 24 340 253 HOH HOH . U 4 HOH C 25 341 263 HOH HOH . U 4 HOH C 26 342 265 HOH HOH . U 4 HOH C 27 343 273 HOH HOH . U 4 HOH C 28 344 274 HOH HOH . U 4 HOH C 29 345 280 HOH HOH . V 4 HOH D 1 317 2 HOH HOH . V 4 HOH D 2 318 17 HOH HOH . V 4 HOH D 3 319 23 HOH HOH . V 4 HOH D 4 320 33 HOH HOH . V 4 HOH D 5 321 41 HOH HOH . V 4 HOH D 6 322 55 HOH HOH . V 4 HOH D 7 323 58 HOH HOH . V 4 HOH D 8 324 71 HOH HOH . V 4 HOH D 9 325 76 HOH HOH . V 4 HOH D 10 326 97 HOH HOH . V 4 HOH D 11 327 119 HOH HOH . V 4 HOH D 12 328 132 HOH HOH . V 4 HOH D 13 329 142 HOH HOH . V 4 HOH D 14 330 148 HOH HOH . V 4 HOH D 15 331 177 HOH HOH . V 4 HOH D 16 332 191 HOH HOH . V 4 HOH D 17 333 192 HOH HOH . V 4 HOH D 18 334 200 HOH HOH . V 4 HOH D 19 335 203 HOH HOH . V 4 HOH D 20 336 205 HOH HOH . V 4 HOH D 21 337 217 HOH HOH . V 4 HOH D 22 338 219 HOH HOH . V 4 HOH D 23 339 233 HOH HOH . V 4 HOH D 24 340 241 HOH HOH . V 4 HOH D 25 341 249 HOH HOH . V 4 HOH D 26 342 258 HOH HOH . V 4 HOH D 27 343 270 HOH HOH . V 4 HOH D 28 344 278 HOH HOH . V 4 HOH D 29 345 279 HOH HOH . V 4 HOH D 30 346 285 HOH HOH . W 4 HOH E 1 317 10 HOH HOH . W 4 HOH E 2 318 24 HOH HOH . W 4 HOH E 3 319 47 HOH HOH . W 4 HOH E 4 320 63 HOH HOH . W 4 HOH E 5 321 68 HOH HOH . W 4 HOH E 6 322 74 HOH HOH . W 4 HOH E 7 323 86 HOH HOH . W 4 HOH E 8 324 124 HOH HOH . W 4 HOH E 9 325 153 HOH HOH . W 4 HOH E 10 326 168 HOH HOH . W 4 HOH E 11 327 176 HOH HOH . W 4 HOH E 12 328 180 HOH HOH . W 4 HOH E 13 329 195 HOH HOH . W 4 HOH E 14 330 201 HOH HOH . W 4 HOH E 15 331 211 HOH HOH . W 4 HOH E 16 332 213 HOH HOH . W 4 HOH E 17 333 222 HOH HOH . W 4 HOH E 18 334 244 HOH HOH . W 4 HOH E 19 335 247 HOH HOH . W 4 HOH E 20 336 251 HOH HOH . W 4 HOH E 21 337 255 HOH HOH . W 4 HOH E 22 338 269 HOH HOH . X 4 HOH F 1 317 18 HOH HOH . X 4 HOH F 2 318 40 HOH HOH . X 4 HOH F 3 319 62 HOH HOH . X 4 HOH F 4 320 67 HOH HOH . X 4 HOH F 5 321 69 HOH HOH . X 4 HOH F 6 322 73 HOH HOH . X 4 HOH F 7 323 93 HOH HOH . X 4 HOH F 8 324 94 HOH HOH . X 4 HOH F 9 325 96 HOH HOH . X 4 HOH F 10 326 115 HOH HOH . X 4 HOH F 11 327 134 HOH HOH . X 4 HOH F 12 328 149 HOH HOH . X 4 HOH F 13 329 169 HOH HOH . X 4 HOH F 14 330 179 HOH HOH . X 4 HOH F 15 331 183 HOH HOH . X 4 HOH F 16 332 206 HOH HOH . X 4 HOH F 17 333 215 HOH HOH . X 4 HOH F 18 334 216 HOH HOH . X 4 HOH F 19 335 236 HOH HOH . X 4 HOH F 20 336 245 HOH HOH . X 4 HOH F 21 337 246 HOH HOH . X 4 HOH F 22 338 250 HOH HOH . X 4 HOH F 23 339 252 HOH HOH . X 4 HOH F 24 340 256 HOH HOH . X 4 HOH F 25 341 267 HOH HOH . X 4 HOH F 26 342 271 HOH HOH . X 4 HOH F 27 343 276 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 P1 A2P . . . P 3 -66.186 35.376 0.098 1 68.03 ? P1 A2P 416 E 1 HETATM 2 O O1P A2P . . . P 3 -67.453 35.961 0.673 1 67.97 ? O1P A2P 416 E 1 HETATM 3 O O2P A2P . . . P 3 -64.911 35.977 0.644 1 67.84 ? O2P A2P 416 E 1 HETATM 4 O O3P A2P . . . P 3 -66.201 35.191 -1.402 1 69.29 ? O3P A2P 416 E 1 HETATM 5 P P2 A2P . . . P 3 -60.232 33.521 0.784 1 59.81 ? P2 A2P 416 E 1 HETATM 6 O O4P A2P . . . P 3 -60.277 34.753 1.658 1 60.83 ? O4P A2P 416 E 1 HETATM 7 O O5P A2P . . . P 3 -60.229 33.815 -0.696 1 57.73 ? O5P A2P 416 E 1 HETATM 8 O O6P A2P . . . P 3 -59.232 32.478 1.224 1 61.1 ? O6P A2P 416 E 1 HETATM 9 O O5' A2P . . . P 3 -61.659 32.821 1.045 1 61.12 ? O5' A2P 416 E 1 HETATM 10 C C5' A2P . . . P 3 -62.077 31.664 0.322 1 62.24 ? C5' A2P 416 E 1 HETATM 11 C C4' A2P . . . P 3 -63.538 31.352 0.645 1 63.97 ? C4' A2P 416 E 1 HETATM 12 O O4' A2P . . . P 3 -63.814 31.549 2.04 1 63.77 ? O4' A2P 416 E 1 HETATM 13 C C3' A2P . . . P 3 -64.491 32.268 -0.115 1 64.31 ? C3' A2P 416 E 1 HETATM 14 O O3' A2P . . . P 3 -65.634 31.515 -0.548 1 64.44 ? O3' A2P 416 E 1 HETATM 15 C C2' A2P . . . P 3 -64.929 33.254 0.942 1 64.09 ? C2' A2P 416 E 1 HETATM 16 O O2' A2P . . . P 3 -66.178 33.866 0.649 1 65.63 ? O2' A2P 416 E 1 HETATM 17 C C1' A2P . . . P 3 -65.019 32.315 2.124 1 62.81 ? C1' A2P 416 E 1 HETATM 18 N N9 A2P . . . P 3 -65.217 33.045 3.397 1 60.98 ? N9 A2P 416 E 1 HETATM 19 C C8 A2P . . . P 3 -65.124 34.373 3.594 1 60.08 ? C8 A2P 416 E 1 HETATM 20 N N7 A2P . . . P 3 -65.394 34.686 4.889 1 59.67 ? N7 A2P 416 E 1 HETATM 21 C C5 A2P . . . P 3 -65.674 33.537 5.534 1 58.34 ? C5 A2P 416 E 1 HETATM 22 C C6 A2P . . . P 3 -66.042 33.143 6.913 1 57.19 ? C6 A2P 416 E 1 HETATM 23 N N6 A2P . . . P 3 -66.17 34.065 7.897 1 55.66 ? N6 A2P 416 E 1 HETATM 24 N N1 A2P . . . P 3 -66.245 31.828 7.157 1 57.62 ? N1 A2P 416 E 1 HETATM 25 C C2 A2P . . . P 3 -66.122 30.897 6.191 1 58.06 ? C2 A2P 416 E 1 HETATM 26 N N3 A2P . . . P 3 -65.794 31.183 4.92 1 57.75 ? N3 A2P 416 E 1 HETATM 27 C C4 A2P . . . P 3 -65.561 32.461 4.541 1 59.21 ? C4 A2P 416 E 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #