data_8IGW # _model_server_result.job_id tYG6KcWD-D6OC3tzs7Xbow _model_server_result.datetime_utc '2024-11-14 19:12:14' _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 8igw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":601}' # _entry.id 8IGW # _exptl.entry_id 8IGW _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 9 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.826 _cell.angle_gamma 90 _cell.entry_id 8IGW _cell.length_a 179.407 _cell.length_b 125.077 _cell.length_c 180.914 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8IGW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 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,B,C,D,E,F,M,N,O,P,Q,R,S,T 1 1 G,H,I,J,K,L,U,V,W,X,Y,Z,AA,BA,CA,DA 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 ? 3 M N N ? 3 O N N ? 3 Q N N ? 3 S N N ? 3 U N N ? 3 W N N ? 3 Y N N ? 3 AA N N ? 3 CA 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 M O1B ADP . A ADP 601 1_555 N MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc2 M O3B ADP . A ADP 601 1_555 N MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc3 B OD1 ASP 332 B ASP 329 1_555 P MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc4 B OD2 ASP 332 B ASP 329 1_555 P MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc5 O O2B ADP . B ADP 601 1_555 P MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc6 C OG1 THR 242 C THR 239 1_555 R MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc7 Q O2B ADP . C ADP 601 1_555 R MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc8 D OG SER 158 D SER 158 1_555 T MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc9 G OE1 GLU 268 G GLU 265 1_555 V MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc10 U O1B ADP . G ADP 601 1_555 V MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc11 H OG1 THR 242 H THR 239 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc12 H OE1 GLU 268 H GLU 265 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc13 W O2B ADP . H ADP 601 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc14 I OG1 THR 242 I THR 239 1_555 Z MG MG . I MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc15 I OE1 GLU 268 I GLU 265 1_555 Z MG MG . I MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc16 Y O2B ADP . I ADP 601 1_555 Z MG MG . I MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc17 Y O3B ADP . I ADP 601 1_555 Z MG MG . I MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc18 J OG SER 158 J SER 158 1_555 BA MG MG . J MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc19 AA O3B ADP . J ADP 601 1_555 BA MG MG . J MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc20 AA O1A ADP . J ADP 601 1_555 BA MG MG . J MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc21 L OG SER 158 L SER 158 1_555 DA MG MG . L MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc22 L OE2 GLU 248 L GLU 248 1_555 DA MG MG . L MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc23 CA O2A ADP . L ADP 601 1_555 DA MG MG . L MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? # _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 8IGW _atom_sites.fract_transf_matrix[1][1] 0.005574 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000373 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007995 _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] 0.00554 _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 M 3 ADP A 1 601 601 ADP ADP . N 4 MG A 1 602 602 MG MG . O 3 ADP B 1 601 601 ADP ADP . P 4 MG B 1 602 602 MG MG . Q 3 ADP C 1 601 601 ADP ADP . R 4 MG C 1 602 602 MG MG . S 3 ADP D 1 601 601 ADP ADP . T 4 MG D 1 602 602 MG MG . U 3 ADP G 1 601 601 ADP ADP . V 4 MG G 1 602 602 MG MG . W 3 ADP H 1 601 601 ADP ADP . X 4 MG H 1 602 602 MG MG . Y 3 ADP I 1 601 601 ADP ADP . Z 4 MG I 1 602 602 MG MG . AA 3 ADP J 1 601 601 ADP ADP . BA 4 MG J 1 602 602 MG MG . CA 3 ADP L 1 601 601 ADP ADP . DA 4 MG L 1 602 602 MG MG . # 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 3 -32.273 71.494 46.854 1 170.79 ? PB ADP 601 H 1 HETATM 2 O O1B ADP . . . W 3 -32.74 71.051 45.489 1 162.71 ? O1B ADP 601 H 1 HETATM 3 O O2B ADP . . . W 3 -31.834 72.936 46.825 1 172.01 ? O2B ADP 601 H 1 HETATM 4 O O3B ADP . . . W 3 -31.35 70.515 47.549 1 176.17 ? O3B ADP 601 H 1 HETATM 5 P PA ADP . . . W 3 -34.933 72.195 47.364 1 175.85 ? PA ADP 601 H 1 HETATM 6 O O1A ADP . . . W 3 -34.856 72.546 45.899 1 175.59 ? O1A ADP 601 H 1 HETATM 7 O O2A ADP . . . W 3 -35.294 73.276 48.353 1 179.83 ? O2A ADP 601 H 1 HETATM 8 O O3A ADP . . . W 3 -33.545 71.54 47.838 1 161.71 ? O3A ADP 601 H 1 HETATM 9 O O5' ADP . . . W 3 -35.973 70.98 47.517 1 169.59 ? O5' ADP 601 H 1 HETATM 10 C C5' ADP . . . W 3 -37.363 71.273 47.612 1 179.37 ? C5' ADP 601 H 1 HETATM 11 C C4' ADP . . . W 3 -38.105 70.097 48.224 1 176.1 ? C4' ADP 601 H 1 HETATM 12 O O4' ADP . . . W 3 -37.707 69.944 49.588 1 175.25 ? O4' ADP 601 H 1 HETATM 13 C C3' ADP . . . W 3 -39.604 70.34 48.208 1 187.67 ? C3' ADP 601 H 1 HETATM 14 O O3' ADP . . . W 3 -40.258 69.279 47.506 1 193.05 ? O3' ADP 601 H 1 HETATM 15 C C2' ADP . . . W 3 -40.036 70.329 49.658 1 188.14 ? C2' ADP 601 H 1 HETATM 16 O O2' ADP . . . W 3 -41.181 69.491 49.833 1 195.11 ? O2' ADP 601 H 1 HETATM 17 C C1' ADP . . . W 3 -38.852 69.763 50.424 1 182.84 ? C1' ADP 601 H 1 HETATM 18 N N9 ADP . . . W 3 -38.665 70.47 51.717 1 187.24 ? N9 ADP 601 H 1 HETATM 19 C C8 ADP . . . W 3 -37.521 71.029 52.151 1 189.01 ? C8 ADP 601 H 1 HETATM 20 N N7 ADP . . . W 3 -37.679 71.585 53.38 1 192.48 ? N7 ADP 601 H 1 HETATM 21 C C5 ADP . . . W 3 -38.954 71.375 53.754 1 197.02 ? C5 ADP 601 H 1 HETATM 22 C C6 ADP . . . W 3 -39.787 71.699 54.936 1 203.22 ? C6 ADP 601 H 1 HETATM 23 N N6 ADP . . . W 3 -39.275 72.376 55.993 1 203.31 ? N6 ADP 601 H 1 HETATM 24 N N1 ADP . . . W 3 -41.077 71.296 54.926 1 204.98 ? N1 ADP 601 H 1 HETATM 25 C C2 ADP . . . W 3 -41.601 70.623 53.886 1 204.09 ? C2 ADP 601 H 1 HETATM 26 N N3 ADP . . . W 3 -40.904 70.295 52.785 1 200.48 ? N3 ADP 601 H 1 HETATM 27 C C4 ADP . . . W 3 -39.599 70.635 52.658 1 193.5 ? C4 ADP 601 H 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 234 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 27 #