data_3QVU # _model_server_result.job_id kh1jX7CxmENCBKsbDw6tnA _model_server_result.datetime_utc '2024-11-08 17:54:11' _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 3qvu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":2001}' # _entry.id 3QVU # _exptl.entry_id 3QVU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 90 _cell.entry_id 3QVU _cell.length_a 66.86 _cell.length_b 71.54 _cell.length_c 122.77 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QVU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E,I 1 1 B,F,G,H,J 2 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 ? 4 E N N ? 4 G N N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 3QVU _atom_sites.fract_transf_matrix[1][1] 0.014957 _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] 0.013978 _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] 0.008145 _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 NPO A 1 296 1 NPO NPO . D 3 EDO A 1 297 1 EDO EDO . E 4 A3P A 1 2001 2001 A3P A3P . F 3 EDO B 1 296 1 EDO EDO . G 4 A3P B 1 2001 2001 A3P A3P . H 2 NPO B 1 297 1 NPO NPO . I 5 HOH A 1 298 6 HOH HOH . I 5 HOH A 2 299 9 HOH HOH . I 5 HOH A 3 300 10 HOH HOH . I 5 HOH A 4 301 11 HOH HOH . I 5 HOH A 5 302 15 HOH HOH . I 5 HOH A 6 303 21 HOH HOH . I 5 HOH A 7 304 22 HOH HOH . I 5 HOH A 8 305 24 HOH HOH . I 5 HOH A 9 306 26 HOH HOH . I 5 HOH A 10 307 32 HOH HOH . I 5 HOH A 11 308 34 HOH HOH . I 5 HOH A 12 309 36 HOH HOH . I 5 HOH A 13 310 46 HOH HOH . I 5 HOH A 14 311 47 HOH HOH . I 5 HOH A 15 312 48 HOH HOH . I 5 HOH A 16 313 49 HOH HOH . I 5 HOH A 17 314 50 HOH HOH . I 5 HOH A 18 315 51 HOH HOH . I 5 HOH A 19 316 52 HOH HOH . I 5 HOH A 20 317 56 HOH HOH . I 5 HOH A 21 318 57 HOH HOH . I 5 HOH A 22 319 60 HOH HOH . I 5 HOH A 23 320 63 HOH HOH . I 5 HOH A 24 321 64 HOH HOH . I 5 HOH A 25 322 65 HOH HOH . I 5 HOH A 26 323 72 HOH HOH . I 5 HOH A 27 324 73 HOH HOH . I 5 HOH A 28 325 76 HOH HOH . I 5 HOH A 29 326 80 HOH HOH . I 5 HOH A 30 327 81 HOH HOH . I 5 HOH A 31 328 82 HOH HOH . I 5 HOH A 32 329 85 HOH HOH . I 5 HOH A 33 330 86 HOH HOH . I 5 HOH A 34 331 89 HOH HOH . I 5 HOH A 35 332 90 HOH HOH . I 5 HOH A 36 333 91 HOH HOH . I 5 HOH A 37 334 93 HOH HOH . I 5 HOH A 38 335 94 HOH HOH . I 5 HOH A 39 336 95 HOH HOH . I 5 HOH A 40 337 97 HOH HOH . J 5 HOH B 1 298 2 HOH HOH . J 5 HOH B 2 299 3 HOH HOH . J 5 HOH B 3 300 4 HOH HOH . J 5 HOH B 4 301 7 HOH HOH . J 5 HOH B 5 302 8 HOH HOH . J 5 HOH B 6 303 12 HOH HOH . J 5 HOH B 7 304 13 HOH HOH . J 5 HOH B 8 305 14 HOH HOH . J 5 HOH B 9 306 16 HOH HOH . J 5 HOH B 10 307 17 HOH HOH . J 5 HOH B 11 308 18 HOH HOH . J 5 HOH B 12 309 19 HOH HOH . J 5 HOH B 13 310 20 HOH HOH . J 5 HOH B 14 311 23 HOH HOH . J 5 HOH B 15 312 25 HOH HOH . J 5 HOH B 16 313 27 HOH HOH . J 5 HOH B 17 314 29 HOH HOH . J 5 HOH B 18 315 35 HOH HOH . J 5 HOH B 19 316 37 HOH HOH . J 5 HOH B 20 317 38 HOH HOH . J 5 HOH B 21 318 39 HOH HOH . J 5 HOH B 22 319 40 HOH HOH . J 5 HOH B 23 320 41 HOH HOH . J 5 HOH B 24 321 42 HOH HOH . J 5 HOH B 25 322 43 HOH HOH . J 5 HOH B 26 323 45 HOH HOH . J 5 HOH B 27 324 53 HOH HOH . J 5 HOH B 28 325 54 HOH HOH . J 5 HOH B 29 326 55 HOH HOH . J 5 HOH B 30 327 61 HOH HOH . J 5 HOH B 31 328 62 HOH HOH . J 5 HOH B 32 329 66 HOH HOH . J 5 HOH B 33 330 67 HOH HOH . J 5 HOH B 34 331 68 HOH HOH . J 5 HOH B 35 332 69 HOH HOH . J 5 HOH B 36 333 70 HOH HOH . J 5 HOH B 37 334 71 HOH HOH . J 5 HOH B 38 335 74 HOH HOH . J 5 HOH B 39 336 75 HOH HOH . J 5 HOH B 40 337 77 HOH HOH . J 5 HOH B 41 338 78 HOH HOH . J 5 HOH B 42 339 79 HOH HOH . J 5 HOH B 43 340 83 HOH HOH . J 5 HOH B 44 341 84 HOH HOH . J 5 HOH B 45 342 87 HOH HOH . J 5 HOH B 46 343 92 HOH HOH . J 5 HOH B 47 344 96 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 A3P . . . G 4 13.368 -1.667 -21.166 1 16.2 ? P1 A3P 2001 B 1 HETATM 2 O O1P A3P . . . G 4 12.355 -2.495 -21.856 1 16.66 ? O1P A3P 2001 B 1 HETATM 3 O O2P A3P . . . G 4 12.767 -0.824 -19.92 1 10.83 ? O2P A3P 2001 B 1 HETATM 4 O O3P A3P . . . G 4 14.607 -2.528 -20.583 1 10.21 ? O3P A3P 2001 B 1 HETATM 5 P P2 A3P . . . G 4 13.582 1.385 -27.935 1 9.3 ? P2 A3P 2001 B 1 HETATM 6 O O4P A3P . . . G 4 12.328 0.659 -28.267 1 13.11 ? O4P A3P 2001 B 1 HETATM 7 O O5P A3P . . . G 4 13.348 2.984 -27.836 1 4.45 ? O5P A3P 2001 B 1 HETATM 8 O O6P A3P . . . G 4 14.718 1.145 -29.059 1 12.36 ? O6P A3P 2001 B 1 HETATM 9 O O5' A3P . . . G 4 14.23 0.953 -26.55 1 13.12 ? O5' A3P 2001 B 1 HETATM 10 C C5' A3P . . . G 4 13.383 0.834 -25.411 1 13.75 ? C5' A3P 2001 B 1 HETATM 11 C C4' A3P . . . G 4 14.22 0.535 -24.182 1 9.62 ? C4' A3P 2001 B 1 HETATM 12 O O4' A3P . . . G 4 14.96 1.736 -23.824 1 5.74 ? O4' A3P 2001 B 1 HETATM 13 C C3' A3P . . . G 4 13.309 0.224 -23 1 10.47 ? C3' A3P 2001 B 1 HETATM 14 O O3' A3P . . . G 4 14.067 -0.578 -22.105 1 15.21 ? O3' A3P 2001 B 1 HETATM 15 C C2' A3P . . . G 4 13.129 1.595 -22.385 1 7.93 ? C2' A3P 2001 B 1 HETATM 16 O O2' A3P . . . G 4 12.734 1.454 -21.017 1 4.6 ? O2' A3P 2001 B 1 HETATM 17 C C1' A3P . . . G 4 14.57 2.084 -22.471 1 10.4 ? C1' A3P 2001 B 1 HETATM 18 N N9 A3P . . . G 4 14.706 3.548 -22.254 1 11.31 ? N9 A3P 2001 B 1 HETATM 19 C C8 A3P . . . G 4 13.911 4.503 -22.738 1 11.52 ? C8 A3P 2001 B 1 HETATM 20 N N7 A3P . . . G 4 14.351 5.694 -22.333 1 12.45 ? N7 A3P 2001 B 1 HETATM 21 C C5 A3P . . . G 4 15.432 5.497 -21.587 1 13.2 ? C5 A3P 2001 B 1 HETATM 22 C C6 A3P . . . G 4 16.296 6.344 -20.908 1 13.84 ? C6 A3P 2001 B 1 HETATM 23 N N6 A3P . . . G 4 16.106 7.661 -20.935 1 10.98 ? N6 A3P 2001 B 1 HETATM 24 N N1 A3P . . . G 4 17.325 5.815 -20.228 1 12.56 ? N1 A3P 2001 B 1 HETATM 25 C C2 A3P . . . G 4 17.515 4.503 -20.202 1 13.43 ? C2 A3P 2001 B 1 HETATM 26 N N3 A3P . . . G 4 16.706 3.669 -20.838 1 15.2 ? N3 A3P 2001 B 1 HETATM 27 C C4 A3P . . . G 4 15.66 4.135 -21.537 1 13.28 ? C4 A3P 2001 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #