data_3L8K # _model_server_result.job_id VyiypX4twz3CDs3QxU_JEA _model_server_result.datetime_utc '2024-11-27 16:23:24' _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 3l8k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":465}' # _entry.id 3L8K # _exptl.entry_id 3L8K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 3L8K _cell.length_a 114.186 _cell.length_b 126.737 _cell.length_c 165.993 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L8K _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # 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' 6_655 -x+1,-y+1/2,z -1 0 0 0 -1 0 0 0 1 114.186 63.3685 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _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 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3L8K _atom_sites.fract_transf_matrix[1][1] 0.008758 _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] 0.00789 _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] 0.006024 _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 ADP A 1 465 1 ADP ADP . D 3 PO4 A 1 466 2 PO4 PO4 . E 2 ADP B 1 465 1 ADP ADP . F 3 PO4 B 1 466 1 PO4 PO4 . G 4 HOH A 1 467 1 HOH HOH . G 4 HOH A 2 468 4 HOH HOH . G 4 HOH A 3 469 13 HOH HOH . G 4 HOH A 4 470 14 HOH HOH . G 4 HOH A 5 471 30 HOH HOH . G 4 HOH A 6 472 35 HOH HOH . G 4 HOH A 7 473 48 HOH HOH . G 4 HOH A 8 474 60 HOH HOH . G 4 HOH A 9 475 62 HOH HOH . G 4 HOH A 10 476 67 HOH HOH . G 4 HOH A 11 477 86 HOH HOH . G 4 HOH A 12 478 110 HOH HOH . G 4 HOH A 13 479 113 HOH HOH . G 4 HOH A 14 480 114 HOH HOH . G 4 HOH A 15 481 122 HOH HOH . G 4 HOH A 16 482 128 HOH HOH . G 4 HOH A 17 483 429 HOH HOH . G 4 HOH A 18 484 431 HOH HOH . G 4 HOH A 19 485 433 HOH HOH . G 4 HOH A 20 486 434 HOH HOH . G 4 HOH A 21 487 436 HOH HOH . G 4 HOH A 22 488 438 HOH HOH . G 4 HOH A 23 489 439 HOH HOH . H 4 HOH B 1 467 2 HOH HOH . H 4 HOH B 2 468 3 HOH HOH . H 4 HOH B 3 469 5 HOH HOH . H 4 HOH B 4 470 6 HOH HOH . H 4 HOH B 5 471 7 HOH HOH . H 4 HOH B 6 472 8 HOH HOH . H 4 HOH B 7 473 10 HOH HOH . H 4 HOH B 8 474 11 HOH HOH . H 4 HOH B 9 475 16 HOH HOH . H 4 HOH B 10 476 19 HOH HOH . H 4 HOH B 11 477 33 HOH HOH . H 4 HOH B 12 478 40 HOH HOH . H 4 HOH B 13 479 43 HOH HOH . H 4 HOH B 14 480 46 HOH HOH . H 4 HOH B 15 481 47 HOH HOH . H 4 HOH B 16 482 52 HOH HOH . H 4 HOH B 17 483 65 HOH HOH . H 4 HOH B 18 484 75 HOH HOH . H 4 HOH B 19 485 78 HOH HOH . H 4 HOH B 20 486 88 HOH HOH . H 4 HOH B 21 487 123 HOH HOH . H 4 HOH B 22 488 144 HOH HOH . H 4 HOH B 23 489 159 HOH HOH . H 4 HOH B 24 490 194 HOH HOH . H 4 HOH B 25 491 264 HOH HOH . H 4 HOH B 26 492 427 HOH HOH . H 4 HOH B 27 493 428 HOH HOH . H 4 HOH B 28 494 430 HOH HOH . H 4 HOH B 29 495 432 HOH HOH . H 4 HOH B 30 496 435 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 . . . C 2 -0.65 57.257 19.188 1 53.1 ? PB ADP 465 A 1 HETATM 2 O O1B ADP . . . C 2 -1.524 56.417 20.104 1 51.01 ? O1B ADP 465 A 1 HETATM 3 O O2B ADP . . . C 2 -0.702 58.735 19.342 1 52.34 ? O2B ADP 465 A 1 HETATM 4 O O3B ADP . . . C 2 0.778 56.735 19.049 1 55.69 ? O3B ADP 465 A 1 HETATM 5 P PA ADP . . . C 2 -1.706 55.93 16.824 1 52.64 ? PA ADP 465 A 1 HETATM 6 O O1A ADP . . . C 2 -0.801 54.763 17.152 1 54.09 ? O1A ADP 465 A 1 HETATM 7 O O2A ADP . . . C 2 -1.799 56.482 15.407 1 55.5 ? O2A ADP 465 A 1 HETATM 8 O O3A ADP . . . C 2 -1.336 57.226 17.735 1 53.84 ? O3A ADP 465 A 1 HETATM 9 O O5' ADP . . . C 2 -3.204 55.512 17.241 1 50.4 ? O5' ADP 465 A 1 HETATM 10 C C5' ADP . . . C 2 -4.283 56.429 17.215 1 47.94 ? C5' ADP 465 A 1 HETATM 11 C C4' ADP . . . C 2 -5.599 55.674 17.169 1 47.37 ? C4' ADP 465 A 1 HETATM 12 O O4' ADP . . . C 2 -6.673 56.618 17.196 1 46.69 ? O4' ADP 465 A 1 HETATM 13 C C3' ADP . . . C 2 -5.75 54.869 15.885 1 47.41 ? C3' ADP 465 A 1 HETATM 14 O O3' ADP . . . C 2 -5.857 53.496 16.259 1 48.43 ? O3' ADP 465 A 1 HETATM 15 C C2' ADP . . . C 2 -7.001 55.428 15.182 1 46.62 ? C2' ADP 465 A 1 HETATM 16 O O2' ADP . . . C 2 -7.876 54.432 14.631 1 43.5 ? O2' ADP 465 A 1 HETATM 17 C C1' ADP . . . C 2 -7.698 56.153 16.317 1 46.83 ? C1' ADP 465 A 1 HETATM 18 N N9 ADP . . . C 2 -8.579 57.281 15.949 1 48.14 ? N9 ADP 465 A 1 HETATM 19 C C8 ADP . . . C 2 -8.367 58.278 15.046 1 47.25 ? C8 ADP 465 A 1 HETATM 20 N N7 ADP . . . C 2 -9.427 59.125 15.037 1 45.28 ? N7 ADP 465 A 1 HETATM 21 C C5 ADP . . . C 2 -10.334 58.661 15.951 1 46.37 ? C5 ADP 465 A 1 HETATM 22 C C6 ADP . . . C 2 -11.694 59.028 16.455 1 44.3 ? C6 ADP 465 A 1 HETATM 23 N N6 ADP . . . C 2 -12.355 60.114 16.018 1 40.89 ? N6 ADP 465 A 1 HETATM 24 N N1 ADP . . . C 2 -12.266 58.238 17.395 1 47.64 ? N1 ADP 465 A 1 HETATM 25 C C2 ADP . . . C 2 -11.665 57.145 17.897 1 47.5 ? C2 ADP 465 A 1 HETATM 26 N N3 ADP . . . C 2 -10.448 56.753 17.469 1 47.41 ? N3 ADP 465 A 1 HETATM 27 C C4 ADP . . . C 2 -9.765 57.443 16.532 1 45.71 ? C4 ADP 465 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #