data_3KIN # _model_server_result.job_id gYTbDr9d5kbCKsd3PvyThg _model_server_result.datetime_utc '2025-04-01 16:13:13' _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 3kin # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":400}' # _entry.id 3KIN # _exptl.entry_id 3KIN _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-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 3KIN _cell.length_a 72.15 _cell.length_b 91.85 _cell.length_c 141.68 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KIN _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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,D,E,F,G,H,I,J 1 1 A,B,E,G,H 2 1 C,D,F,I,J 2 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' 2_464 -x-1/2,-y+1,z-1/2 -1 0 0 0 -1 0 0 0 1 -36.075 91.85 -70.84 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F 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 3KIN _atom_sites.fract_transf_matrix[1][1] 0.01386 _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] 0.010887 _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] 0.007058 _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 E 3 ADP A 1 401 401 ADP ADP . F 3 ADP C 1 400 400 ADP ADP . G 4 HOH A 1 402 2 HOH HOH . G 4 HOH A 2 403 3 HOH HOH . G 4 HOH A 3 404 4 HOH HOH . G 4 HOH A 4 405 5 HOH HOH . G 4 HOH A 5 406 6 HOH HOH . G 4 HOH A 6 407 9 HOH HOH . G 4 HOH A 7 408 13 HOH HOH . G 4 HOH A 8 409 18 HOH HOH . G 4 HOH A 9 410 19 HOH HOH . G 4 HOH A 10 411 22 HOH HOH . G 4 HOH A 11 412 23 HOH HOH . G 4 HOH A 12 413 24 HOH HOH . G 4 HOH A 13 414 25 HOH HOH . G 4 HOH A 14 415 28 HOH HOH . G 4 HOH A 15 416 29 HOH HOH . G 4 HOH A 16 417 33 HOH HOH . G 4 HOH A 17 418 38 HOH HOH . G 4 HOH A 18 419 39 HOH HOH . G 4 HOH A 19 420 42 HOH HOH . G 4 HOH A 20 421 44 HOH HOH . G 4 HOH A 21 422 46 HOH HOH . G 4 HOH A 22 423 53 HOH HOH . G 4 HOH A 23 424 89 HOH HOH . H 4 HOH B 1 7 7 HOH HOH . H 4 HOH B 2 8 8 HOH HOH . H 4 HOH B 3 14 14 HOH HOH . H 4 HOH B 4 15 15 HOH HOH . H 4 HOH B 5 16 16 HOH HOH . H 4 HOH B 6 17 17 HOH HOH . H 4 HOH B 7 31 31 HOH HOH . H 4 HOH B 8 45 45 HOH HOH . H 4 HOH B 9 47 47 HOH HOH . H 4 HOH B 10 50 50 HOH HOH . H 4 HOH B 11 52 52 HOH HOH . I 4 HOH C 1 401 55 HOH HOH . I 4 HOH C 2 402 58 HOH HOH . I 4 HOH C 3 403 60 HOH HOH . I 4 HOH C 4 404 61 HOH HOH . I 4 HOH C 5 405 62 HOH HOH . I 4 HOH C 6 406 63 HOH HOH . I 4 HOH C 7 407 64 HOH HOH . I 4 HOH C 8 408 69 HOH HOH . I 4 HOH C 9 409 70 HOH HOH . I 4 HOH C 10 410 71 HOH HOH . I 4 HOH C 11 411 74 HOH HOH . I 4 HOH C 12 412 77 HOH HOH . I 4 HOH C 13 413 80 HOH HOH . I 4 HOH C 14 414 83 HOH HOH . I 4 HOH C 15 415 84 HOH HOH . I 4 HOH C 16 416 85 HOH HOH . I 4 HOH C 17 417 86 HOH HOH . I 4 HOH C 18 418 88 HOH HOH . J 4 HOH D 1 32 32 HOH HOH . J 4 HOH D 2 56 56 HOH HOH . J 4 HOH D 3 59 59 HOH HOH . J 4 HOH D 4 67 67 HOH HOH . J 4 HOH D 5 73 73 HOH HOH . J 4 HOH D 6 76 76 HOH HOH . J 4 HOH D 7 82 82 HOH HOH . J 4 HOH D 8 87 87 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 . . . F 3 -56.783 33.839 139.559 1 42.36 ? PB ADP 400 C 1 HETATM 2 O O1B ADP . . . F 3 -55.836 33.332 138.535 1 42.36 ? O1B ADP 400 C 1 HETATM 3 O O2B ADP . . . F 3 -56.39 33.34 140.894 1 42.36 ? O2B ADP 400 C 1 HETATM 4 O O3B ADP . . . F 3 -58.274 33.792 139.347 1 42.36 ? O3B ADP 400 C 1 HETATM 5 P PA ADP . . . F 3 -56.995 36.753 140.018 1 42.36 ? PA ADP 400 C 1 HETATM 6 O O1A ADP . . . F 3 -58.342 36.881 139.392 1 42.36 ? O1A ADP 400 C 1 HETATM 7 O O2A ADP . . . F 3 -56.142 37.585 139.042 1 42.36 ? O2A ADP 400 C 1 HETATM 8 O O3A ADP . . . F 3 -56.263 35.366 139.951 1 42.36 ? O3A ADP 400 C 1 HETATM 9 O O5' ADP . . . F 3 -57.168 37.306 141.486 1 42.36 ? O5' ADP 400 C 1 HETATM 10 C C5' ADP . . . F 3 -56.182 38.146 142.122 1 42.36 ? C5' ADP 400 C 1 HETATM 11 C C4' ADP . . . F 3 -56.469 39.496 141.405 1 42.36 ? C4' ADP 400 C 1 HETATM 12 O O4' ADP . . . F 3 -55.295 39.999 140.761 1 42.36 ? O4' ADP 400 C 1 HETATM 13 C C3' ADP . . . F 3 -56.939 40.457 142.503 1 42.36 ? C3' ADP 400 C 1 HETATM 14 O O3' ADP . . . F 3 -58.37 40.621 142.354 1 42.36 ? O3' ADP 400 C 1 HETATM 15 C C2' ADP . . . F 3 -56.221 41.818 142.044 1 42.36 ? C2' ADP 400 C 1 HETATM 16 O O2' ADP . . . F 3 -56.811 42.857 141.254 1 42.36 ? O2' ADP 400 C 1 HETATM 17 C C1' ADP . . . F 3 -54.952 41.258 141.361 1 42.36 ? C1' ADP 400 C 1 HETATM 18 N N9 ADP . . . F 3 -53.722 41.079 142.202 1 42.36 ? N9 ADP 400 C 1 HETATM 19 C C8 ADP . . . F 3 -52.741 40.129 142.187 1 42.36 ? C8 ADP 400 C 1 HETATM 20 N N7 ADP . . . F 3 -51.557 40.552 142.605 1 42.36 ? N7 ADP 400 C 1 HETATM 21 C C5 ADP . . . F 3 -51.81 41.893 142.917 1 42.36 ? C5 ADP 400 C 1 HETATM 22 C C6 ADP . . . F 3 -50.981 42.965 143.424 1 42.36 ? C6 ADP 400 C 1 HETATM 23 N N6 ADP . . . F 3 -49.689 42.761 143.692 1 42.36 ? N6 ADP 400 C 1 HETATM 24 N N1 ADP . . . F 3 -51.608 44.135 143.595 1 42.36 ? N1 ADP 400 C 1 HETATM 25 C C2 ADP . . . F 3 -52.906 44.36 143.321 1 42.36 ? C2 ADP 400 C 1 HETATM 26 N N3 ADP . . . F 3 -53.747 43.433 142.847 1 42.36 ? N3 ADP 400 C 1 HETATM 27 C C4 ADP . . . F 3 -53.108 42.233 142.687 1 42.36 ? C4 ADP 400 C 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #