data_2ZFM # _model_server_result.job_id s4ptLNL4nYF14UMDlMiKTg _model_server_result.datetime_utc '2024-12-06 07:45:35' _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 2zfm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2000}' # _entry.id 2ZFM # _exptl.entry_id 2ZFM _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 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 90 _cell.entry_id 2ZFM _cell.length_a 41.767 _cell.length_b 55.784 _cell.length_c 155.956 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZFM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _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 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 2ZFM _atom_sites.fract_transf_matrix[1][1] 0.023942 _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] 0.017926 _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] 0.006412 _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 ADP A 1 2000 2000 ADP ADP . C 3 HOH A 1 2001 1 HOH HOH . C 3 HOH A 2 2002 2 HOH HOH . C 3 HOH A 3 2003 3 HOH HOH . C 3 HOH A 4 2004 4 HOH HOH . C 3 HOH A 5 2005 5 HOH HOH . C 3 HOH A 6 2006 6 HOH HOH . C 3 HOH A 7 2007 7 HOH HOH . C 3 HOH A 8 2008 8 HOH HOH . C 3 HOH A 9 2009 9 HOH HOH . C 3 HOH A 10 2010 10 HOH HOH . C 3 HOH A 11 2011 11 HOH HOH . C 3 HOH A 12 2012 12 HOH HOH . C 3 HOH A 13 2013 13 HOH HOH . C 3 HOH A 14 2014 14 HOH HOH . C 3 HOH A 15 2015 15 HOH HOH . C 3 HOH A 16 2016 16 HOH HOH . C 3 HOH A 17 2017 17 HOH HOH . C 3 HOH A 18 2018 18 HOH HOH . C 3 HOH A 19 2019 19 HOH HOH . C 3 HOH A 20 2020 20 HOH HOH . C 3 HOH A 21 2021 21 HOH HOH . C 3 HOH A 22 2022 22 HOH HOH . C 3 HOH A 23 2023 23 HOH HOH . C 3 HOH A 24 2024 24 HOH HOH . C 3 HOH A 25 2025 25 HOH HOH . C 3 HOH A 26 2026 26 HOH HOH . C 3 HOH A 27 2027 27 HOH HOH . C 3 HOH A 28 2028 28 HOH HOH . C 3 HOH A 29 2029 29 HOH HOH . C 3 HOH A 30 2030 30 HOH HOH . C 3 HOH A 31 2031 31 HOH HOH . C 3 HOH A 32 2032 32 HOH HOH . C 3 HOH A 33 2033 33 HOH HOH . C 3 HOH A 34 2034 34 HOH HOH . C 3 HOH A 35 2035 35 HOH HOH . C 3 HOH A 36 2036 36 HOH HOH . C 3 HOH A 37 2037 37 HOH HOH . C 3 HOH A 38 2038 38 HOH HOH . C 3 HOH A 39 2039 39 HOH HOH . C 3 HOH A 40 2040 40 HOH HOH . C 3 HOH A 41 2041 41 HOH HOH . C 3 HOH A 42 2042 42 HOH HOH . C 3 HOH A 43 2043 43 HOH HOH . C 3 HOH A 44 2044 44 HOH HOH . C 3 HOH A 45 2045 45 HOH HOH . C 3 HOH A 46 2046 46 HOH HOH . C 3 HOH A 47 2047 47 HOH HOH . C 3 HOH A 48 2048 48 HOH HOH . C 3 HOH A 49 2049 49 HOH HOH . C 3 HOH A 50 2050 50 HOH HOH . C 3 HOH A 51 2051 51 HOH HOH . C 3 HOH A 52 2052 52 HOH HOH . C 3 HOH A 53 2053 53 HOH HOH . C 3 HOH A 54 2054 54 HOH HOH . C 3 HOH A 55 2055 55 HOH HOH . C 3 HOH A 56 2056 56 HOH HOH . C 3 HOH A 57 2057 57 HOH HOH . C 3 HOH A 58 2058 58 HOH HOH . C 3 HOH A 59 2059 59 HOH HOH . C 3 HOH A 60 2060 60 HOH HOH . C 3 HOH A 61 2061 61 HOH HOH . C 3 HOH A 62 2062 62 HOH HOH . C 3 HOH A 63 2063 63 HOH HOH . C 3 HOH A 64 2064 64 HOH HOH . C 3 HOH A 65 2065 65 HOH HOH . C 3 HOH A 66 2066 66 HOH HOH . C 3 HOH A 67 2067 67 HOH HOH . C 3 HOH A 68 2068 68 HOH HOH . C 3 HOH A 69 2069 69 HOH HOH . C 3 HOH A 70 2070 70 HOH HOH . C 3 HOH A 71 2071 71 HOH HOH . C 3 HOH A 72 2072 72 HOH HOH . C 3 HOH A 73 2073 73 HOH HOH . C 3 HOH A 74 2074 74 HOH HOH . C 3 HOH A 75 2075 75 HOH HOH . C 3 HOH A 76 2076 76 HOH HOH . C 3 HOH A 77 2077 77 HOH HOH . C 3 HOH A 78 2078 78 HOH HOH . C 3 HOH A 79 2079 79 HOH HOH . C 3 HOH A 80 2080 80 HOH HOH . C 3 HOH A 81 2081 81 HOH HOH . C 3 HOH A 82 2082 82 HOH HOH . C 3 HOH A 83 2083 83 HOH HOH . C 3 HOH A 84 2084 84 HOH HOH . C 3 HOH A 85 2085 85 HOH HOH . C 3 HOH A 86 2086 86 HOH HOH . C 3 HOH A 87 2087 87 HOH HOH . C 3 HOH A 88 2088 88 HOH HOH . C 3 HOH A 89 2089 89 HOH HOH . C 3 HOH A 90 2090 90 HOH HOH . C 3 HOH A 91 2091 91 HOH HOH . C 3 HOH A 92 2092 92 HOH HOH . C 3 HOH A 93 2093 93 HOH HOH . C 3 HOH A 94 2094 94 HOH HOH . C 3 HOH A 95 2095 95 HOH HOH . C 3 HOH A 96 2096 96 HOH HOH . C 3 HOH A 97 2097 97 HOH HOH . C 3 HOH A 98 2098 98 HOH HOH . C 3 HOH A 99 2099 99 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 . . . B 2 -4.122 20.982 7.276 1 29.26 ? PB ADP 2000 A 1 HETATM 2 O O1B ADP . . . B 2 -5.46 21.447 6.809 1 32.29 ? O1B ADP 2000 A 1 HETATM 3 O O2B ADP . . . B 2 -3.059 22.041 7.115 1 33.25 ? O2B ADP 2000 A 1 HETATM 4 O O3B ADP . . . B 2 -4.166 20.559 8.715 1 28.88 ? O3B ADP 2000 A 1 HETATM 5 P PA ADP . . . B 2 -2.839 18.464 6.517 1 33.94 ? PA ADP 2000 A 1 HETATM 6 O O1A ADP . . . B 2 -2.022 18.488 7.786 1 39.62 ? O1A ADP 2000 A 1 HETATM 7 O O2A ADP . . . B 2 -3.762 17.286 6.529 1 38.02 ? O2A ADP 2000 A 1 HETATM 8 O O3A ADP . . . B 2 -3.76 19.743 6.354 1 36.37 ? O3A ADP 2000 A 1 HETATM 9 O O5' ADP . . . B 2 -1.898 18.356 5.288 1 44.57 ? O5' ADP 2000 A 1 HETATM 10 C C5' ADP . . . B 2 -2.638 17.877 4.174 1 44.57 ? C5' ADP 2000 A 1 HETATM 11 C C4' ADP . . . B 2 -2.035 16.71 3.44 1 44.57 ? C4' ADP 2000 A 1 HETATM 12 O O4' ADP . . . B 2 -0.789 17.044 2.87 1 44.57 ? O4' ADP 2000 A 1 HETATM 13 C C3' ADP . . . B 2 -1.87 15.39 4.206 1 44.57 ? C3' ADP 2000 A 1 HETATM 14 O O3' ADP . . . B 2 -2.963 14.503 3.847 1 44.57 ? O3' ADP 2000 A 1 HETATM 15 C C2' ADP . . . B 2 -0.406 14.944 3.852 1 44.57 ? C2' ADP 2000 A 1 HETATM 16 O O2' ADP . . . B 2 -0.358 13.68 3.119 1 44.57 ? O2' ADP 2000 A 1 HETATM 17 C C1' ADP . . . B 2 0.212 16.12 3.034 1 44.57 ? C1' ADP 2000 A 1 HETATM 18 N N9 ADP . . . B 2 1.395 16.791 3.659 1 37.62 ? N9 ADP 2000 A 1 HETATM 19 C C8 ADP . . . B 2 1.492 18.015 4.271 1 37.94 ? C8 ADP 2000 A 1 HETATM 20 N N7 ADP . . . B 2 2.747 18.301 4.747 1 35.77 ? N7 ADP 2000 A 1 HETATM 21 C C5 ADP . . . B 2 3.492 17.17 4.413 1 30.79 ? C5 ADP 2000 A 1 HETATM 22 C C6 ADP . . . B 2 4.885 16.833 4.607 1 23.88 ? C6 ADP 2000 A 1 HETATM 23 N N6 ADP . . . B 2 5.797 17.622 5.201 1 27.01 ? N6 ADP 2000 A 1 HETATM 24 N N1 ADP . . . B 2 5.289 15.595 4.126 1 30.43 ? N1 ADP 2000 A 1 HETATM 25 C C2 ADP . . . B 2 4.367 14.771 3.512 1 26.76 ? C2 ADP 2000 A 1 HETATM 26 N N3 ADP . . . B 2 3.078 14.992 3.292 1 35.02 ? N3 ADP 2000 A 1 HETATM 27 C C4 ADP . . . B 2 2.677 16.217 3.762 1 31.07 ? C4 ADP 2000 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #