data_5ZO9 # _model_server_result.job_id gxaDBIjgFaoE9z9bUInblw _model_server_result.datetime_utc '2024-10-22 03:37:05' _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 5zo9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":600}' # _entry.id 5ZO9 # _exptl.entry_id 5ZO9 _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 102.19 _cell.angle_gamma 90 _cell.entry_id 5ZO9 _cell.length_a 155.158 _cell.length_b 50.729 _cell.length_c 94.309 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZO9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E,F,G,H,O 1 1 B,I,J,K,L,M,N,P 2 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 # 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 I N 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 OG1 THR 103 A THR 112 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc2 A OE1 GLU 158 A GLU 167 1_555 H NA NA . A NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc3 C O1B ADP . A ADP 600 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc4 D MG MG . A MG 601 1_555 O O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc5 G O1 SO4 . A SO4 604 1_555 H NA NA . A NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.02 ? metalc ? metalc6 B OG1 THR 103 B THR 112 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc7 B OE1 GLU 158 B GLU 167 1_555 N NA NA . B NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc8 I O2B ADP . B ADP 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc9 J MG MG . B MG 601 1_555 P O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc10 M O4 SO4 . B SO4 604 1_555 N NA NA . B NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? # _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 54 n n PB O2B ADP sing 55 n n PB O3B ADP sing 56 n n PB O3A ADP sing 57 n n O2B HOB2 ADP sing 58 n n O3B HOB3 ADP sing 59 n n PA O1A ADP doub 60 n n PA O2A ADP sing 61 n n PA O3A ADP sing 62 n n PA O5' ADP sing 63 n n O2A HOA2 ADP sing 64 n n O5' C5' ADP sing 65 n n C5' C4' ADP sing 66 n n C5' "H5'1" ADP sing 67 n n C5' "H5'2" ADP sing 68 n n C4' O4' ADP sing 69 n n C4' C3' ADP sing 70 n n C4' H4' ADP sing 71 n n O4' C1' ADP sing 72 n n C3' O3' ADP sing 73 n n C3' C2' ADP sing 74 n n C3' H3' ADP sing 75 n n O3' HO3' ADP sing 76 n n C2' O2' ADP sing 77 n n C2' C1' ADP sing 78 n n C2' H2' ADP sing 79 n n O2' HO2' ADP sing 80 n n C1' N9 ADP sing 81 n n C1' H1' ADP sing 82 n n N9 C8 ADP sing 83 n y N9 C4 ADP sing 84 n y C8 N7 ADP doub 85 n y C8 H8 ADP sing 86 n n N7 C5 ADP sing 87 n y C5 C6 ADP sing 88 n y C5 C4 ADP doub 89 n y C6 N6 ADP sing 90 n n C6 N1 ADP doub 91 n y N6 HN61 ADP sing 92 n n N6 HN62 ADP sing 93 n n N1 C2 ADP sing 94 n y C2 N3 ADP doub 95 n y C2 H2 ADP sing 96 n n N3 C4 ADP sing 97 n y # _atom_sites.entry_id 5ZO9 _atom_sites.fract_transf_matrix[1][1] 0.006445 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001392 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019713 _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] 0.010848 _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 1 600 600 ADP ADP . D 3 MG A 1 601 601 MG MG . E 4 4C5 A 1 602 602 4C5 4C5 . F 5 SO4 A 1 603 603 SO4 SO4 . G 5 SO4 A 1 604 604 SO4 SO4 . H 6 NA A 1 605 605 NA NA . I 2 ADP B 1 600 600 ADP ADP . J 3 MG B 1 601 601 MG MG . K 4 4C5 B 1 602 602 4C5 4C5 . L 5 SO4 B 1 603 603 SO4 SO4 . M 5 SO4 B 1 604 604 SO4 SO4 . N 6 NA B 1 605 605 NA NA . O 7 HOH A 1 701 18 HOH HOH . O 7 HOH A 2 702 6 HOH HOH . O 7 HOH A 3 703 5 HOH HOH . O 7 HOH A 4 704 17 HOH HOH . O 7 HOH A 5 705 7 HOH HOH . O 7 HOH A 6 706 10 HOH HOH . O 7 HOH A 7 707 13 HOH HOH . O 7 HOH A 8 708 9 HOH HOH . O 7 HOH A 9 709 1 HOH HOH . P 7 HOH B 1 701 15 HOH HOH . P 7 HOH B 2 702 4 HOH HOH . P 7 HOH B 3 703 14 HOH HOH . P 7 HOH B 4 704 16 HOH HOH . P 7 HOH B 5 705 8 HOH HOH . P 7 HOH B 6 706 12 HOH HOH . P 7 HOH B 7 707 11 HOH HOH . P 7 HOH B 8 708 3 HOH HOH . P 7 HOH B 9 709 2 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 28.406 -8.37 -0.016 1 42.43 ? PB ADP 600 A 1 HETATM 2 O O1B ADP . . . C 2 28.005 -7.31 -1.022 1 30.09 ? O1B ADP 600 A 1 HETATM 3 O O2B ADP . . . C 2 27.615 -8.304 1.263 1 36.27 ? O2B ADP 600 A 1 HETATM 4 O O3B ADP . . . C 2 29.954 -8.512 0.165 1 36.11 ? O3B ADP 600 A 1 HETATM 5 P PA ADP . . . C 2 27.601 -10.255 -1.948 1 43.95 ? PA ADP 600 A 1 HETATM 6 O O1A ADP . . . C 2 28.861 -9.953 -2.74 1 32.66 ? O1A ADP 600 A 1 HETATM 7 O O2A ADP . . . C 2 26.265 -9.625 -2.323 1 40.86 ? O2A ADP 600 A 1 HETATM 8 O O3A ADP . . . C 2 27.885 -9.849 -0.417 1 37.64 ? O3A ADP 600 A 1 HETATM 9 O O5' ADP . . . C 2 27.226 -11.856 -1.873 1 41.8 ? O5' ADP 600 A 1 HETATM 10 C C5' ADP . . . C 2 28.069 -12.865 -1.311 1 41.92 ? C5' ADP 600 A 1 HETATM 11 C C4' ADP . . . C 2 28.016 -14.168 -2.098 1 41.34 ? C4' ADP 600 A 1 HETATM 12 O O4' ADP . . . C 2 27.091 -15.083 -1.48 1 42.71 ? O4' ADP 600 A 1 HETATM 13 C C3' ADP . . . C 2 27.517 -13.988 -3.511 1 42.03 ? C3' ADP 600 A 1 HETATM 14 O O3' ADP . . . C 2 28.026 -15.031 -4.302 1 40.44 ? O3' ADP 600 A 1 HETATM 15 C C2' ADP . . . C 2 26.024 -14.198 -3.414 1 45.52 ? C2' ADP 600 A 1 HETATM 16 O O2' ADP . . . C 2 25.426 -14.63 -4.637 1 44.98 ? O2' ADP 600 A 1 HETATM 17 C C1' ADP . . . C 2 25.893 -15.213 -2.275 1 45.95 ? C1' ADP 600 A 1 HETATM 18 N N9 ADP . . . C 2 24.675 -14.85 -1.515 1 48.77 ? N9 ADP 600 A 1 HETATM 19 C C8 ADP . . . C 2 24.565 -13.809 -0.633 1 51.97 ? C8 ADP 600 A 1 HETATM 20 N N7 ADP . . . C 2 23.319 -13.712 -0.105 1 46.28 ? N7 ADP 600 A 1 HETATM 21 C C5 ADP . . . C 2 22.621 -14.701 -0.672 1 47.61 ? C5 ADP 600 A 1 HETATM 22 C C6 ADP . . . C 2 21.238 -15.183 -0.55 1 47.91 ? C6 ADP 600 A 1 HETATM 23 N N6 ADP . . . C 2 20.407 -14.527 0.29 1 45.65 ? N6 ADP 600 A 1 HETATM 24 N N1 ADP . . . C 2 20.869 -16.263 -1.306 1 46.68 ? N1 ADP 600 A 1 HETATM 25 C C2 ADP . . . C 2 21.732 -16.895 -2.139 1 45.19 ? C2 ADP 600 A 1 HETATM 26 N N3 ADP . . . C 2 23.024 -16.494 -2.3 1 47.29 ? N3 ADP 600 A 1 HETATM 27 C C4 ADP . . . C 2 23.506 -15.444 -1.601 1 46.78 ? C4 ADP 600 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #