data_1Z29 # _model_server_result.job_id 28htI9D2ctvs7rHHp-BT7g _model_server_result.datetime_utc '2024-10-20 03:52:32' _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 1z29 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2001}' # _entry.id 1Z29 # _exptl.entry_id 1Z29 _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-3'-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 103.69 _cell.angle_gamma 90 _cell.entry_id 1Z29 _cell.length_a 58.398 _cell.length_b 65.399 _cell.length_c 86.517 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z29 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A NZ LYS 106 A LYS 106 1_555 B CA CA . A CA 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.281 ? metalc ? metalc2 A OH TYR 240 A TYR 240 1_555 B CA CA . A CA 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.292 ? metalc ? metalc3 D O ACY . A ACY 721 1_555 B CA CA . A CA 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? metalc ? metalc4 B CA CA . A CA 1010 1_555 E O HOH . A HOH 2057 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? # _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 1Z29 _atom_sites.fract_transf_matrix[1][1] 0.017124 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004171 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015291 _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] 0.011896 _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 CA A 1 1010 1010 CA CA . C 3 A3P A 1 2001 2001 A3P A3P . D 4 ACY A 1 721 721 ACY ACY . E 5 HOH A 1 2002 1 HOH WAT . E 5 HOH A 2 2003 2 HOH WAT . E 5 HOH A 3 2004 3 HOH WAT . E 5 HOH A 4 2005 4 HOH WAT . E 5 HOH A 5 2006 5 HOH WAT . E 5 HOH A 6 2007 6 HOH WAT . E 5 HOH A 7 2008 7 HOH WAT . E 5 HOH A 8 2009 8 HOH WAT . E 5 HOH A 9 2010 9 HOH WAT . E 5 HOH A 10 2011 10 HOH WAT . E 5 HOH A 11 2012 11 HOH WAT . E 5 HOH A 12 2013 12 HOH WAT . E 5 HOH A 13 2014 13 HOH WAT . E 5 HOH A 14 2015 14 HOH WAT . E 5 HOH A 15 2016 15 HOH WAT . E 5 HOH A 16 2017 16 HOH WAT . E 5 HOH A 17 2018 17 HOH WAT . E 5 HOH A 18 2019 18 HOH WAT . E 5 HOH A 19 2020 19 HOH WAT . E 5 HOH A 20 2021 20 HOH WAT . E 5 HOH A 21 2022 21 HOH WAT . E 5 HOH A 22 2023 22 HOH WAT . E 5 HOH A 23 2024 23 HOH WAT . E 5 HOH A 24 2025 24 HOH WAT . E 5 HOH A 25 2026 25 HOH WAT . E 5 HOH A 26 2027 26 HOH WAT . E 5 HOH A 27 2028 27 HOH WAT . E 5 HOH A 28 2029 28 HOH WAT . E 5 HOH A 29 2030 29 HOH WAT . E 5 HOH A 30 2031 30 HOH WAT . E 5 HOH A 31 2032 31 HOH WAT . E 5 HOH A 32 2033 32 HOH WAT . E 5 HOH A 33 2034 33 HOH WAT . E 5 HOH A 34 2035 34 HOH WAT . E 5 HOH A 35 2036 35 HOH WAT . E 5 HOH A 36 2037 36 HOH WAT . E 5 HOH A 37 2038 37 HOH WAT . E 5 HOH A 38 2039 38 HOH WAT . E 5 HOH A 39 2040 39 HOH WAT . E 5 HOH A 40 2041 40 HOH WAT . E 5 HOH A 41 2042 41 HOH WAT . E 5 HOH A 42 2043 42 HOH WAT . E 5 HOH A 43 2044 43 HOH WAT . E 5 HOH A 44 2045 44 HOH WAT . E 5 HOH A 45 2046 46 HOH WAT . E 5 HOH A 46 2047 47 HOH WAT . E 5 HOH A 47 2048 48 HOH WAT . E 5 HOH A 48 2049 49 HOH WAT . E 5 HOH A 49 2050 50 HOH WAT . E 5 HOH A 50 2051 51 HOH WAT . E 5 HOH A 51 2052 52 HOH WAT . E 5 HOH A 52 2053 53 HOH WAT . E 5 HOH A 53 2054 54 HOH WAT . E 5 HOH A 54 2055 55 HOH WAT . E 5 HOH A 55 2056 56 HOH WAT . E 5 HOH A 56 2057 57 HOH WAT . # 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 . . . C 3 11.416 2.652 26.28 1 29.14 ? P1 A3P 2001 A 1 HETATM 2 O O1P A3P . . . C 3 10.825 3.626 27.213 1 29.71 ? O1P A3P 2001 A 1 HETATM 3 O O2P A3P . . . C 3 12.505 3.105 25.385 1 28.77 ? O2P A3P 2001 A 1 HETATM 4 O O3P A3P . . . C 3 11.734 1.435 27.064 1 29.23 ? O3P A3P 2001 A 1 HETATM 5 P P2 A3P . . . C 3 4.457 2.725 23.125 1 31.32 ? P2 A3P 2001 A 1 HETATM 6 O O4P A3P . . . C 3 4.169 3.811 24.09 1 30.26 ? O4P A3P 2001 A 1 HETATM 7 O O5P A3P . . . C 3 4.515 3.083 21.688 1 31.99 ? O5P A3P 2001 A 1 HETATM 8 O O6P A3P . . . C 3 3.534 1.584 23.43 1 34.88 ? O6P A3P 2001 A 1 HETATM 9 O O5' A3P . . . C 3 5.893 2.156 23.505 1 31.84 ? O5' A3P 2001 A 1 HETATM 10 C C5' A3P . . . C 3 6.97 3.019 23.847 1 32.31 ? C5' A3P 2001 A 1 HETATM 11 C C4' A3P . . . C 3 8.201 2.189 24.109 1 33.53 ? C4' A3P 2001 A 1 HETATM 12 O O4' A3P . . . C 3 8.527 1.51 22.851 1 34.49 ? O4' A3P 2001 A 1 HETATM 13 C C3' A3P . . . C 3 9.482 2.979 24.473 1 33.69 ? C3' A3P 2001 A 1 HETATM 14 O O3' A3P . . . C 3 10.259 2.101 25.313 1 33.41 ? O3' A3P 2001 A 1 HETATM 15 C C2' A3P . . . C 3 10.097 3.216 23.099 1 34.32 ? C2' A3P 2001 A 1 HETATM 16 O O2' A3P . . . C 3 11.444 3.678 23.057 1 33.29 ? O2' A3P 2001 A 1 HETATM 17 C C1' A3P . . . C 3 9.851 1.845 22.44 1 33.52 ? C1' A3P 2001 A 1 HETATM 18 N N9 A3P . . . C 3 9.88 1.837 20.961 1 33.96 ? N9 A3P 2001 A 1 HETATM 19 C C8 A3P . . . C 3 9.207 2.655 20.07 1 32.58 ? C8 A3P 2001 A 1 HETATM 20 N N7 A3P . . . C 3 9.455 2.392 18.804 1 31.52 ? N7 A3P 2001 A 1 HETATM 21 C C5 A3P . . . C 3 10.341 1.336 18.854 1 32.29 ? C5 A3P 2001 A 1 HETATM 22 C C6 A3P . . . C 3 11.012 0.569 17.834 1 34.28 ? C6 A3P 2001 A 1 HETATM 23 N N6 A3P . . . C 3 10.855 0.789 16.523 1 34.67 ? N6 A3P 2001 A 1 HETATM 24 N N1 A3P . . . C 3 11.857 -0.454 18.226 1 35.11 ? N1 A3P 2001 A 1 HETATM 25 C C2 A3P . . . C 3 12.032 -0.697 19.573 1 36.86 ? C2 A3P 2001 A 1 HETATM 26 N N3 A3P . . . C 3 11.452 -0.034 20.623 1 34.94 ? N3 A3P 2001 A 1 HETATM 27 C C4 A3P . . . C 3 10.619 0.974 20.187 1 33.81 ? C4 A3P 2001 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #