data_3O6X # _model_server_result.job_id 7-x0Mhnfh4cmJv3v62nPIg _model_server_result.datetime_utc '2024-10-20 00:41:06' _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 3o6x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":4001}' # _entry.id 3O6X # _exptl.entry_id 3O6X _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 6 _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 3O6X _cell.length_a 198.25 _cell.length_b 203.96 _cell.length_c 234.59 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3O6X _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA _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 # 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 Q N N ? 4 W N N ? 4 CA N N ? 4 IA N N ? 4 OA 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 OE2 GLU 215 A GLU 215 1_555 G MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc2 A OE1 GLU 215 A GLU 215 1_555 G MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? metalc ? metalc3 A OE2 GLU 286 A GLU 286 1_555 H MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc4 A OE2 GLU 472 A GLU 472 1_555 G MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc5 G MG MG . A MG 1001 1_555 I O3A P3S . A P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc6 G MG MG . A MG 1001 1_555 J O1B ADP . A ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc7 B OE2 GLU 215 B GLU 215 1_555 N MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc8 B OE1 GLU 215 B GLU 215 1_555 N MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc9 B OE1 GLU 217 B GLU 217 1_555 O MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc10 B OE1 GLU 286 B GLU 286 1_555 O MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc11 B OE2 GLU 472 B GLU 472 1_555 N MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc12 N MG MG . B MG 1001 1_555 Q O1B ADP . B ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc13 O MG MG . B MG 2001 1_555 P O3A P3S . B P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc14 C OE2 GLU 215 C GLU 215 1_555 T MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc15 C OE1 GLU 215 C GLU 215 1_555 T MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc16 C OE1 GLU 217 C GLU 217 1_555 U MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc17 C OE1 GLU 286 C GLU 286 1_555 U MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc18 C OE2 GLU 472 C GLU 472 1_555 T MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc19 T MG MG . C MG 1001 1_555 W O1B ADP . C ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc20 U MG MG . C MG 2001 1_555 V O3A P3S . C P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc21 D OE2 GLU 215 D GLU 215 1_555 Z MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc22 D OE1 GLU 215 D GLU 215 1_555 Z MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc23 D OE1 GLU 217 D GLU 217 1_555 AA MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc24 D OE1 GLU 286 D GLU 286 1_555 AA MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc25 D OE2 GLU 472 D GLU 472 1_555 Z MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc26 Z MG MG . D MG 1001 1_555 CA O1B ADP . D ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc27 AA MG MG . D MG 2001 1_555 BA O3A P3S . D P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc28 E OE2 GLU 215 E GLU 215 1_555 FA MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc29 E OE1 GLU 215 E GLU 215 1_555 FA MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc30 E OE1 GLU 217 E GLU 217 1_555 GA MG MG . E MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc31 E OE1 GLU 286 E GLU 286 1_555 GA MG MG . E MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc32 E OE2 GLU 472 E GLU 472 1_555 FA MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc33 FA MG MG . E MG 1001 1_555 IA O1B ADP . E ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc34 GA MG MG . E MG 2001 1_555 HA O3A P3S . E P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? metalc ? metalc35 F OE2 GLU 215 F GLU 215 1_555 LA MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc36 F OE1 GLU 215 F GLU 215 1_555 LA MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc37 F OE1 GLU 217 F GLU 217 1_555 MA MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc38 F OE1 GLU 286 F GLU 286 1_555 MA MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc39 F OE2 GLU 472 F GLU 472 1_555 LA MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc40 LA MG MG . F MG 1001 1_555 OA O1B ADP . F ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc41 MA MG MG . F MG 2001 1_555 NA O3A P3S . F P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? # _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 3O6X _atom_sites.fract_transf_matrix[1][1] 0.005044 _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] 0.004903 _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] 0.004263 _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 2 MG A 1 1001 1001 MG MG . H 2 MG A 1 2001 2001 MG MG . I 3 P3S A 1 3001 3001 P3S P3S . J 4 ADP A 1 4001 4001 ADP ADP . K 5 CL A 1 5001 5001 CL CL . L 5 CL A 1 6001 6001 CL CL . M 5 CL A 1 730 5001 CL CL . N 2 MG B 1 1001 1001 MG MG . O 2 MG B 1 2001 2001 MG MG . P 3 P3S B 1 3001 3001 P3S P3S . Q 4 ADP B 1 4001 4001 ADP ADP . R 5 CL B 1 5001 5001 CL CL . S 5 CL B 1 6001 6001 CL CL . T 2 MG C 1 1001 1001 MG MG . U 2 MG C 1 2001 2001 MG MG . V 3 P3S C 1 3001 3001 P3S P3S . W 4 ADP C 1 4001 4001 ADP ADP . X 5 CL C 1 5001 5001 CL CL . Y 5 CL C 1 6001 6001 CL CL . Z 2 MG D 1 1001 1001 MG MG . AA 2 MG D 1 2001 2001 MG MG . BA 3 P3S D 1 3001 3001 P3S P3S . CA 4 ADP D 1 4001 4001 ADP ADP . DA 5 CL D 1 5001 5001 CL CL . EA 5 CL D 1 6001 6001 CL CL . FA 2 MG E 1 1001 1001 MG MG . GA 2 MG E 1 2001 2001 MG MG . HA 3 P3S E 1 3001 3001 P3S P3S . IA 4 ADP E 1 4001 4001 ADP ADP . JA 5 CL E 1 5001 5001 CL CL . KA 5 CL E 1 6001 6001 CL CL . LA 2 MG F 1 1001 1001 MG MG . MA 2 MG F 1 2001 2001 MG MG . NA 3 P3S F 1 3001 3001 P3S P3S . OA 4 ADP F 1 4001 4001 ADP ADP . PA 5 CL F 1 6001 6001 CL CL . # 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 . . . W 4 48.084 42.077 191.328 1 99.64 ? PB ADP 4001 C 1 HETATM 2 O O1B ADP . . . W 4 47.712 41.8 192.733 1 100.01 ? O1B ADP 4001 C 1 HETATM 3 O O2B ADP . . . W 4 47.782 41.019 190.149 1 100.45 ? O2B ADP 4001 C 1 HETATM 4 O O3B ADP . . . W 4 48.281 43.579 190.778 1 103.61 ? O3B ADP 4001 C 1 HETATM 5 P PA ADP . . . W 4 50.656 41.989 190.147 1 103.56 ? PA ADP 4001 C 1 HETATM 6 O O1A ADP . . . W 4 50.186 43.052 189.23 1 100.1 ? O1A ADP 4001 C 1 HETATM 7 O O2A ADP . . . W 4 52.086 42.358 190.792 1 107 ? O2A ADP 4001 C 1 HETATM 8 O O3A ADP . . . W 4 49.663 41.757 191.397 1 101.23 ? O3A ADP 4001 C 1 HETATM 9 O O5' ADP . . . W 4 50.834 40.557 189.428 1 108.8 ? O5' ADP 4001 C 1 HETATM 10 C C5' ADP . . . W 4 49.866 40.094 188.481 1 112.39 ? C5' ADP 4001 C 1 HETATM 11 C C4' ADP . . . W 4 50.113 38.631 188.102 1 113.73 ? C4' ADP 4001 C 1 HETATM 12 O O4' ADP . . . W 4 49.084 38.157 187.214 1 115.73 ? O4' ADP 4001 C 1 HETATM 13 C C3' ADP . . . W 4 51.438 38.439 187.358 1 113.98 ? C3' ADP 4001 C 1 HETATM 14 O O3' ADP . . . W 4 52.15 37.34 187.931 1 112.26 ? O3' ADP 4001 C 1 HETATM 15 C C2' ADP . . . W 4 50.966 38.056 185.956 1 114.61 ? C2' ADP 4001 C 1 HETATM 16 O O2' ADP . . . W 4 51.94 37.215 185.333 1 111.34 ? O2' ADP 4001 C 1 HETATM 17 C C1' ADP . . . W 4 49.76 37.216 186.368 1 120.03 ? C1' ADP 4001 C 1 HETATM 18 N N9 ADP . . . W 4 48.947 36.847 185.187 1 123.44 ? N9 ADP 4001 C 1 HETATM 19 C C8 ADP . . . W 4 48.423 37.692 184.303 1 122.88 ? C8 ADP 4001 C 1 HETATM 20 N N7 ADP . . . W 4 47.76 37.01 183.372 1 124.01 ? N7 ADP 4001 C 1 HETATM 21 C C5 ADP . . . W 4 47.86 35.718 183.665 1 125.45 ? C5 ADP 4001 C 1 HETATM 22 C C6 ADP . . . W 4 47.381 34.554 183.079 1 123.95 ? C6 ADP 4001 C 1 HETATM 23 N N6 ADP . . . W 4 46.658 34.607 181.964 1 122.97 ? N6 ADP 4001 C 1 HETATM 24 N N1 ADP . . . W 4 47.665 33.376 183.652 1 123.75 ? N1 ADP 4001 C 1 HETATM 25 C C2 ADP . . . W 4 48.389 33.314 184.755 1 122.65 ? C2 ADP 4001 C 1 HETATM 26 N N3 ADP . . . W 4 48.862 34.401 185.339 1 124.33 ? N3 ADP 4001 C 1 HETATM 27 C C4 ADP . . . W 4 48.617 35.611 184.823 1 125.49 ? C4 ADP 4001 C 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #