data_5JI2 # _model_server_result.job_id sySay5HhY6HgsELHwgmU5A _model_server_result.datetime_utc '2025-03-29 05:08:26' _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 5ji2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 5JI2 # _exptl.entry_id 5JI2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 120 _cell.entry_id 5JI2 _cell.length_a 170.005 _cell.length_b 170.005 _cell.length_c 163.385 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JI2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H 1 1 C,D,I 2 1 E,F,J,K 3 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 ? 4 J N N ? 4 K 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 O CYS 160 A CYS 159 1_555 G MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? metalc ? metalc2 A O THR 163 A THR 162 1_555 G MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc3 B O GLY 157 B GLY 156 1_555 H MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc4 B O THR 163 B THR 162 1_555 H MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? metalc ? metalc5 D O GLY 157 D GLY 156 1_555 I MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc6 D O THR 163 D THR 162 1_555 I MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? # _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 5JI2 _atom_sites.fract_transf_matrix[1][1] 0.005882 _atom_sites.fract_transf_matrix[1][2] 0.003396 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006792 _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] 0.006121 _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 G 3 MG A 1 201 1 MG MG . H 3 MG B 1 201 2 MG MG . I 3 MG D 1 201 3 MG MG . J 4 ADP E 1 501 450 ADP ADP . K 4 ADP F 1 501 450 ADP ADP . # 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 . . . J 4 16.715 69.644 38.457 1 73.3 ? PB ADP 501 E 1 HETATM 2 O O1B ADP . . . J 4 15.746 70.45 37.625 1 80.06 ? O1B ADP 501 E 1 HETATM 3 O O2B ADP . . . J 4 16.755 70.008 39.919 1 95.55 ? O2B ADP 501 E 1 HETATM 4 O O3B ADP . . . J 4 16.679 68.159 38.207 1 90.82 ? O3B ADP 501 E 1 HETATM 5 P PA ADP . . . J 4 18.521 69.942 36.353 1 74.91 ? PA ADP 501 E 1 HETATM 6 O O1A ADP . . . J 4 17.819 71.049 35.611 1 100.65 ? O1A ADP 501 E 1 HETATM 7 O O2A ADP . . . J 4 18.331 68.506 35.929 1 65.37 ? O2A ADP 501 E 1 HETATM 8 O O3A ADP . . . J 4 18.162 70.081 37.915 1 82.66 ? O3A ADP 501 E 1 HETATM 9 O O5' ADP . . . J 4 20.091 70.271 36.328 1 79.28 ? O5' ADP 501 E 1 HETATM 10 C C5' ADP . . . J 4 20.98 69.232 36.705 1 72.46 ? C5' ADP 501 E 1 HETATM 11 C C4' ADP . . . J 4 22.427 69.581 36.409 1 68.5 ? C4' ADP 501 E 1 HETATM 12 O O4' ADP . . . J 4 23.248 68.628 37.08 1 79.83 ? O4' ADP 501 E 1 HETATM 13 C C3' ADP . . . J 4 22.72 69.45 34.933 1 76.87 ? C3' ADP 501 E 1 HETATM 14 O O3' ADP . . . J 4 23.748 70.369 34.55 1 95.92 ? O3' ADP 501 E 1 HETATM 15 C C2' ADP . . . J 4 23.18 68.014 34.784 1 74.32 ? C2' ADP 501 E 1 HETATM 16 O O2' ADP . . . J 4 24.272 67.92 33.863 1 80.32 ? O2' ADP 501 E 1 HETATM 17 C C1' ADP . . . J 4 23.585 67.567 36.181 1 76.14 ? C1' ADP 501 E 1 HETATM 18 N N9 ADP . . . J 4 22.82 66.357 36.581 1 79.38 ? N9 ADP 501 E 1 HETATM 19 C C8 ADP . . . J 4 21.922 66.314 37.586 1 86.5 ? C8 ADP 501 E 1 HETATM 20 N N7 ADP . . . J 4 21.391 65.075 37.717 1 84.25 ? N7 ADP 501 E 1 HETATM 21 C C5 ADP . . . J 4 21.955 64.3 36.783 1 79.59 ? C5 ADP 501 E 1 HETATM 22 C C6 ADP . . . J 4 21.832 62.887 36.385 1 80.56 ? C6 ADP 501 E 1 HETATM 23 N N6 ADP . . . J 4 20.977 62.069 37.044 1 86.01 ? N6 ADP 501 E 1 HETATM 24 N N1 ADP . . . J 4 22.593 62.452 35.357 1 81.98 ? N1 ADP 501 E 1 HETATM 25 C C2 ADP . . . J 4 23.442 63.271 34.706 1 80.04 ? C2 ADP 501 E 1 HETATM 26 N N3 ADP . . . J 4 23.599 64.572 35.023 1 80.2 ? N3 ADP 501 E 1 HETATM 27 C C4 ADP . . . J 4 22.898 65.139 36.035 1 81.43 ? C4 ADP 501 E 1 HETATM 28 H "H5'1" ADP . . . J 4 20.713 68.319 36.17 1 86.95 ? "H5'1" ADP 501 E 1 HETATM 29 H "H5'2" ADP . . . J 4 20.869 69.035 37.774 1 86.95 ? "H5'2" ADP 501 E 1 HETATM 30 H H4' ADP . . . J 4 22.647 70.603 36.749 1 82.2 ? H4' ADP 501 E 1 HETATM 31 H H3' ADP . . . J 4 21.802 69.613 34.351 1 92.24 ? H3' ADP 501 E 1 HETATM 32 H HO3' ADP . . . J 4 23.927 70.277 33.605 1 115.1 ? HO3' ADP 501 E 1 HETATM 33 H H2' ADP . . . J 4 22.336 67.4 34.44 1 89.18 ? H2' ADP 501 E 1 HETATM 34 H HO2' ADP . . . J 4 23.986 68.226 32.991 1 96.39 ? HO2' ADP 501 E 1 HETATM 35 H H1' ADP . . . J 4 24.665 67.368 36.205 1 91.37 ? H1' ADP 501 E 1 HETATM 36 H H8 ADP . . . J 4 21.658 67.161 38.207 1 103.81 ? H8 ADP 501 E 1 HETATM 37 H HN61 ADP . . . J 4 20.423 62.428 37.808 1 103.21 ? HN61 ADP 501 E 1 HETATM 38 H HN62 ADP . . . J 4 20.893 61.101 36.77 1 103.21 ? HN62 ADP 501 E 1 HETATM 39 H H2 ADP . . . J 4 24.027 62.865 33.89 1 96.04 ? H2 ADP 501 E 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #