data_3RUQ # _model_server_result.job_id kOXvo9MDdFKW3cNk3r9tNQ _model_server_result.datetime_utc '2024-11-13 07:20:15' _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 3ruq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":545}' # _entry.id 3RUQ # _exptl.entry_id 3RUQ _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 4 _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 3RUQ _cell.length_a 162.164 _cell.length_b 185.002 _cell.length_c 184.769 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RUQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -162.164 0 0 3 'crystal symmetry operation' 3_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -162.164 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L 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 OD1 ASP 91 A ASP 91 1_555 E MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc2 A OD2 ASP 91 A ASP 91 1_555 E MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc3 E MG MG . A MG 544 1_555 F O2A ADP . A ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc4 E MG MG . A MG 544 1_555 F O3B ADP . A ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 E MG MG . A MG 544 1_555 M O HOH . A HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc6 E MG MG . A MG 544 1_555 M O HOH . A HOH 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc7 B OD1 ASP 91 B ASP 91 1_555 G MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc8 B OD2 ASP 91 B ASP 91 1_555 G MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? metalc ? metalc9 G MG MG . B MG 544 1_555 H O3B ADP . B ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc10 G MG MG . B MG 544 1_555 H O2A ADP . B ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc11 G MG MG . B MG 544 1_555 N O HOH . B HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc12 G MG MG . B MG 544 1_555 N O HOH . B HOH 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc13 G MG MG . B MG 544 1_555 N O HOH . B HOH 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc14 C OD1 ASP 91 C ASP 91 1_555 I MG MG . C MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc15 I MG MG . C MG 544 1_555 J O2A ADP . C ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc16 I MG MG . C MG 544 1_555 J O3B ADP . C ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc17 I MG MG . C MG 544 1_555 O O HOH . C HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc18 I MG MG . C MG 544 1_555 O O HOH . C HOH 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc19 I MG MG . C MG 544 1_555 O O HOH . C HOH 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc20 D OD1 ASP 91 D ASP 91 1_555 K MG MG . D MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc21 K MG MG . D MG 544 1_555 L O2A ADP . D ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc22 K MG MG . D MG 544 1_555 L O1B ADP . D ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc23 K MG MG . D MG 544 1_555 P O HOH . D HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc24 K MG MG . D MG 544 1_555 P O HOH . D HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc25 K MG MG . D MG 544 1_555 P O HOH . D HOH 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? # _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 3RUQ _atom_sites.fract_transf_matrix[1][1] 0.006167 _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] 0.005405 _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] 0.005412 _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 E 2 MG A 1 544 544 MG MG . F 3 ADP A 1 545 545 ADP ADP . G 2 MG B 1 544 544 MG MG . H 3 ADP B 1 545 545 ADP ADP . I 2 MG C 1 544 544 MG MG . J 3 ADP C 1 545 545 ADP ADP . K 2 MG D 1 544 544 MG MG . L 3 ADP D 1 545 545 ADP ADP . M 4 HOH A 1 546 1 HOH HOH . M 4 HOH A 2 547 12 HOH HOH . M 4 HOH A 3 548 13 HOH HOH . M 4 HOH A 4 549 14 HOH HOH . M 4 HOH A 5 550 17 HOH HOH . M 4 HOH A 6 551 19 HOH HOH . M 4 HOH A 7 552 22 HOH HOH . M 4 HOH A 8 553 26 HOH HOH . M 4 HOH A 9 554 30 HOH HOH . M 4 HOH A 10 555 31 HOH HOH . M 4 HOH A 11 556 37 HOH HOH . M 4 HOH A 12 557 38 HOH HOH . M 4 HOH A 13 558 39 HOH HOH . M 4 HOH A 14 559 43 HOH HOH . M 4 HOH A 15 560 44 HOH HOH . M 4 HOH A 16 561 50 HOH HOH . M 4 HOH A 17 562 59 HOH HOH . N 4 HOH B 1 546 2 HOH HOH . N 4 HOH B 2 547 8 HOH HOH . N 4 HOH B 3 548 11 HOH HOH . N 4 HOH B 4 549 20 HOH HOH . N 4 HOH B 5 550 28 HOH HOH . N 4 HOH B 6 551 29 HOH HOH . N 4 HOH B 7 552 32 HOH HOH . N 4 HOH B 8 553 34 HOH HOH . N 4 HOH B 9 554 45 HOH HOH . N 4 HOH B 10 555 46 HOH HOH . N 4 HOH B 11 556 60 HOH HOH . N 4 HOH B 12 557 61 HOH HOH . O 4 HOH C 1 546 3 HOH HOH . O 4 HOH C 2 547 7 HOH HOH . O 4 HOH C 3 548 10 HOH HOH . O 4 HOH C 4 549 16 HOH HOH . O 4 HOH C 5 550 18 HOH HOH . O 4 HOH C 6 551 21 HOH HOH . O 4 HOH C 7 552 23 HOH HOH . O 4 HOH C 8 553 24 HOH HOH . O 4 HOH C 9 554 25 HOH HOH . O 4 HOH C 10 555 35 HOH HOH . O 4 HOH C 11 556 40 HOH HOH . O 4 HOH C 12 557 41 HOH HOH . O 4 HOH C 13 558 51 HOH HOH . O 4 HOH C 14 559 52 HOH HOH . O 4 HOH C 15 560 53 HOH HOH . O 4 HOH C 16 561 62 HOH HOH . P 4 HOH D 1 546 5 HOH HOH . P 4 HOH D 2 547 6 HOH HOH . P 4 HOH D 3 548 9 HOH HOH . P 4 HOH D 4 549 27 HOH HOH . P 4 HOH D 5 550 33 HOH HOH . P 4 HOH D 6 551 36 HOH HOH . P 4 HOH D 7 552 42 HOH HOH . P 4 HOH D 8 553 48 HOH HOH . P 4 HOH D 9 554 54 HOH HOH . P 4 HOH D 10 555 55 HOH HOH . P 4 HOH D 11 556 56 HOH HOH . P 4 HOH D 12 557 57 HOH HOH . P 4 HOH D 13 558 58 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 . . . J 3 -34.442 20.39 26.304 1 36.16 ? PB ADP 545 C 1 HETATM 2 O O1B ADP . . . J 3 -35.574 20.53 25.298 1 41.75 ? O1B ADP 545 C 1 HETATM 3 O O2B ADP . . . J 3 -34.925 19.786 27.603 1 45.01 ? O2B ADP 545 C 1 HETATM 4 O O3B ADP . . . J 3 -33.555 21.611 26.512 1 39.06 ? O3B ADP 545 C 1 HETATM 5 P PA ADP . . . J 3 -32.142 19.387 24.767 1 37.42 ? PA ADP 545 C 1 HETATM 6 O O1A ADP . . . J 3 -32.121 18.3 23.721 1 48.93 ? O1A ADP 545 C 1 HETATM 7 O O2A ADP . . . J 3 -31.97 20.822 24.338 1 42.39 ? O2A ADP 545 C 1 HETATM 8 O O3A ADP . . . J 3 -33.476 19.236 25.683 1 49.82 ? O3A ADP 545 C 1 HETATM 9 O O5' ADP . . . J 3 -31.015 18.976 25.83 1 51.25 ? O5' ADP 545 C 1 HETATM 10 C C5' ADP . . . J 3 -30.897 19.633 27.089 1 48.97 ? C5' ADP 545 C 1 HETATM 11 C C4' ADP . . . J 3 -30.012 18.731 27.941 1 56.04 ? C4' ADP 545 C 1 HETATM 12 O O4' ADP . . . J 3 -28.825 18.4 27.214 1 47.63 ? O4' ADP 545 C 1 HETATM 13 C C3' ADP . . . J 3 -29.583 19.427 29.22 1 62.56 ? C3' ADP 545 C 1 HETATM 14 O O3' ADP . . . J 3 -29.663 18.491 30.302 1 65.67 ? O3' ADP 545 C 1 HETATM 15 C C2' ADP . . . J 3 -28.134 19.796 29.004 1 45.15 ? C2' ADP 545 C 1 HETATM 16 O O2' ADP . . . J 3 -27.434 19.688 30.245 1 49.05 ? O2' ADP 545 C 1 HETATM 17 C C1' ADP . . . J 3 -27.696 18.704 28.044 1 41.76 ? C1' ADP 545 C 1 HETATM 18 N N9 ADP . . . J 3 -26.472 19.112 27.313 1 39.32 ? N9 ADP 545 C 1 HETATM 19 C C8 ADP . . . J 3 -26.302 20.178 26.508 1 52.65 ? C8 ADP 545 C 1 HETATM 20 N N7 ADP . . . J 3 -25.025 20.228 26.032 1 46.88 ? N7 ADP 545 C 1 HETATM 21 C C5 ADP . . . J 3 -24.363 19.176 26.548 1 44.96 ? C5 ADP 545 C 1 HETATM 22 C C6 ADP . . . J 3 -22.993 18.625 26.464 1 39.86 ? C6 ADP 545 C 1 HETATM 23 N N6 ADP . . . J 3 -22.061 19.241 25.714 1 37.1 ? N6 ADP 545 C 1 HETATM 24 N N1 ADP . . . J 3 -22.704 17.5 27.158 1 43.3 ? N1 ADP 545 C 1 HETATM 25 C C2 ADP . . . J 3 -23.64 16.887 27.911 1 50.69 ? C2 ADP 545 C 1 HETATM 26 N N3 ADP . . . J 3 -24.91 17.329 28.037 1 47.2 ? N3 ADP 545 C 1 HETATM 27 C C4 ADP . . . J 3 -25.319 18.45 27.394 1 44.95 ? C4 ADP 545 C 1 # _model_server_stats.io_time_ms 202 _model_server_stats.parse_time_ms 80 _model_server_stats.create_model_time_ms 72 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #