data_2ZFK # _model_server_result.job_id 7oT-sFH9PL-BGHxVpcK7cA _model_server_result.datetime_utc '2025-03-06 23:07:37' _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 2zfk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2000}' # _entry.id 2ZFK # _exptl.entry_id 2ZFK _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 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 2ZFK _cell.length_a 39.477 _cell.length_b 50.162 _cell.length_c 157.06 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZFK _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,D,E,F _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OG _struct_conn.ptnr1_label_comp_id SER _struct_conn.ptnr1_label_seq_id 104 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id SER _struct_conn.ptnr1_auth_seq_id 104 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id MG _struct_conn.ptnr2_label_comp_id MG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id MG _struct_conn.ptnr2_auth_seq_id 2001 _struct_conn.ptnr2_symmetry 1_555 _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 2.687 _struct_conn.pdbx_value_order ? # _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 2ZFK _atom_sites.fract_transf_matrix[1][1] 0.025331 _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] 0.019935 _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] 0.006367 _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 MG A 1 2001 2001 MG MG . C 3 ADP A 1 2000 2000 ADP ADP . D 4 TRS A 1 2002 2002 TRS TRS . E 4 TRS A 1 2003 2003 TRS TRS . F 5 HOH A 1 2004 1 HOH HOH . F 5 HOH A 2 2005 2 HOH HOH . F 5 HOH A 3 2006 3 HOH HOH . F 5 HOH A 4 2007 4 HOH HOH . F 5 HOH A 5 2008 5 HOH HOH . F 5 HOH A 6 2009 6 HOH HOH . F 5 HOH A 7 2010 7 HOH HOH . F 5 HOH A 8 2011 8 HOH HOH . F 5 HOH A 9 2012 9 HOH HOH . F 5 HOH A 10 2013 10 HOH HOH . F 5 HOH A 11 2014 11 HOH HOH . F 5 HOH A 12 2015 12 HOH HOH . F 5 HOH A 13 2016 13 HOH HOH . F 5 HOH A 14 2017 14 HOH HOH . F 5 HOH A 15 2018 15 HOH HOH . F 5 HOH A 16 2019 16 HOH HOH . F 5 HOH A 17 2020 17 HOH HOH . F 5 HOH A 18 2021 18 HOH HOH . F 5 HOH A 19 2022 19 HOH HOH . F 5 HOH A 20 2023 20 HOH HOH . F 5 HOH A 21 2024 21 HOH HOH . F 5 HOH A 22 2025 22 HOH HOH . F 5 HOH A 23 2026 23 HOH HOH . F 5 HOH A 24 2027 24 HOH HOH . F 5 HOH A 25 2028 25 HOH HOH . F 5 HOH A 26 2029 26 HOH HOH . F 5 HOH A 27 2030 27 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 3 24.71 -19.943 7.39 1 94.53 ? PB ADP 2000 A 1 HETATM 2 O O1B ADP . . . C 3 26.199 -19.935 7.239 1 96.67 ? O1B ADP 2000 A 1 HETATM 3 O O2B ADP . . . C 3 24.173 -21.263 6.971 1 91.89 ? O2B ADP 2000 A 1 HETATM 4 O O3B ADP . . . C 3 24.307 -19.672 8.801 1 83.44 ? O3B ADP 2000 A 1 HETATM 5 P PA ADP . . . C 3 23.466 -17.379 6.874 1 86.84 ? PA ADP 2000 A 1 HETATM 6 O O1A ADP . . . C 3 22.518 -17.568 8.002 1 85.33 ? O1A ADP 2000 A 1 HETATM 7 O O2A ADP . . . C 3 24.514 -16.373 7.24 1 86.36 ? O2A ADP 2000 A 1 HETATM 8 O O3A ADP . . . C 3 24.165 -18.75 6.512 1 91.04 ? O3A ADP 2000 A 1 HETATM 9 O O5' ADP . . . C 3 22.679 -16.791 5.644 1 74.63 ? O5' ADP 2000 A 1 HETATM 10 C C5' ADP . . . C 3 22.555 -15.367 5.765 1 74.63 ? C5' ADP 2000 A 1 HETATM 11 C C4' ADP . . . C 3 22.135 -14.604 4.54 1 74.63 ? C4' ADP 2000 A 1 HETATM 12 O O4' ADP . . . C 3 21.135 -15.294 3.774 1 74.63 ? O4' ADP 2000 A 1 HETATM 13 C C3' ADP . . . C 3 21.643 -13.235 4.909 1 74.63 ? C3' ADP 2000 A 1 HETATM 14 O O3' ADP . . . C 3 22.607 -12.26 4.462 1 74.63 ? O3' ADP 2000 A 1 HETATM 15 C C2' ADP . . . C 3 20.209 -13.194 4.322 1 74.63 ? C2' ADP 2000 A 1 HETATM 16 O O2' ADP . . . C 3 19.927 -12.098 3.455 1 74.63 ? O2' ADP 2000 A 1 HETATM 17 C C1' ADP . . . C 3 20.012 -14.519 3.608 1 74.63 ? C1' ADP 2000 A 1 HETATM 18 N N9 ADP . . . C 3 18.826 -15.317 4.047 1 38.27 ? N9 ADP 2000 A 1 HETATM 19 C C8 ADP . . . C 3 18.773 -16.609 4.448 1 38.27 ? C8 ADP 2000 A 1 HETATM 20 N N7 ADP . . . C 3 17.53 -17.053 4.678 1 38.27 ? N7 ADP 2000 A 1 HETATM 21 C C5 ADP . . . C 3 16.739 -15.958 4.412 1 38.27 ? C5 ADP 2000 A 1 HETATM 22 C C6 ADP . . . C 3 15.33 -15.777 4.467 1 38.27 ? C6 ADP 2000 A 1 HETATM 23 N N6 ADP . . . C 3 14.478 -16.727 4.831 1 38.27 ? N6 ADP 2000 A 1 HETATM 24 N N1 ADP . . . C 3 14.843 -14.532 4.128 1 42.16 ? N1 ADP 2000 A 1 HETATM 25 C C2 ADP . . . C 3 15.728 -13.538 3.755 1 47.82 ? C2 ADP 2000 A 1 HETATM 26 N N3 ADP . . . C 3 17.052 -13.611 3.673 1 38.27 ? N3 ADP 2000 A 1 HETATM 27 C C4 ADP . . . C 3 17.51 -14.874 4.018 1 38.27 ? C4 ADP 2000 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #