data_1Q3S # _model_server_result.job_id eH_VIJuyRsZib9P1HsGuyg _model_server_result.datetime_utc '2025-07-31 04:24:13' _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 1q3s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":8528}' # _entry.id 1Q3S # _exptl.entry_id 1Q3S _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 8 _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 1Q3S _cell.length_a 207.425 _cell.length_b 236.23 _cell.length_c 234.106 _cell.Z_PDB 64 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Q3S _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 ? _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _pdbx_struct_assembly.details author_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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 207.425 0 117.053 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R N N ? 3 S N N ? 3 U N N ? 3 W 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 95 A ASP 95 1_555 I MG MG . A MG 1527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.149 ? metalc ? metalc2 A OD2 ASP 95 A ASP 95 1_555 I MG MG . A MG 1527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc3 I MG MG . A MG 1527 1_555 J O3B ADP . A ADP 1528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc4 I MG MG . A MG 1527 1_555 J O1A ADP . A ADP 1528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc5 B OD2 ASP 95 B ASP 95 1_555 K MG MG . B MG 2527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc6 K MG MG . B MG 2527 1_555 L O1A ADP . B ADP 2528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc7 K MG MG . B MG 2527 1_555 L O3B ADP . B ADP 2528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc8 C OD1 ASP 95 C ASP 95 1_555 M MG MG . C MG 3527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc9 C OD2 ASP 95 C ASP 95 1_555 M MG MG . C MG 3527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc10 M MG MG . C MG 3527 1_555 N O3B ADP . C ADP 3528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc11 M MG MG . C MG 3527 1_555 N O1A ADP . C ADP 3528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc12 D OD2 ASP 95 D ASP 95 1_555 O MG MG . D MG 4527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc13 O MG MG . D MG 4527 1_555 P O1A ADP . D ADP 4528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc14 O MG MG . D MG 4527 1_555 P O3B ADP . D ADP 4528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc15 E OD2 ASP 95 E ASP 95 1_555 Q MG MG . E MG 5527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc16 Q MG MG . E MG 5527 1_555 R O3B ADP . E ADP 5528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc17 Q MG MG . E MG 5527 1_555 R O1A ADP . E ADP 5528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc18 G OD2 ASP 95 G ASP 95 1_555 T MG MG . G MG 6527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc19 G OD1 ASP 95 G ASP 95 1_555 T MG MG . G MG 6527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc20 T MG MG . G MG 6527 1_555 U O3B ADP . G ADP 7528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc21 T MG MG . G MG 6527 1_555 U O1A ADP . G ADP 7528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc22 H OD2 ASP 95 H ASP 95 1_555 V MG MG . H MG 8527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc23 V MG MG . H MG 8527 1_555 W O3B ADP . H ADP 8528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc24 V MG MG . H MG 8527 1_555 W O1A ADP . H ADP 8528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? # _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 1Q3S _atom_sites.fract_transf_matrix[1][1] 0.004821 _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] 0.004233 _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] 0.004272 _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 I 2 MG A 1 1527 1527 MG MG . J 3 ADP A 1 1528 1528 ADP ADP . K 2 MG B 1 2527 2527 MG MG . L 3 ADP B 1 2528 2528 ADP ADP . M 2 MG C 1 3527 3527 MG MG . N 3 ADP C 1 3528 3528 ADP ADP . O 2 MG D 1 4527 4527 MG MG . P 3 ADP D 1 4528 4528 ADP ADP . Q 2 MG E 1 5527 5527 MG MG . R 3 ADP E 1 5528 5528 ADP ADP . S 3 ADP F 1 6528 6528 ADP ADP . T 2 MG G 1 6527 6527 MG MG . U 3 ADP G 1 7528 7528 ADP ADP . V 2 MG H 1 8527 8527 MG MG . W 3 ADP H 1 8528 8528 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 . . . W 3 97.426 117.403 34.165 1 27.65 ? PB ADP 8528 H 1 HETATM 2 O O1B ADP . . . W 3 97.129 118.142 35.424 1 27.65 ? O1B ADP 8528 H 1 HETATM 3 O O2B ADP . . . W 3 96.66 116.125 34.122 1 29.72 ? O2B ADP 8528 H 1 HETATM 4 O O3B ADP . . . W 3 97.123 118.327 32.805 1 29.28 ? O3B ADP 8528 H 1 HETATM 5 P PA ADP . . . W 3 100.083 117.465 32.987 1 26.49 ? PA ADP 8528 H 1 HETATM 6 O O1A ADP . . . W 3 99.473 117.436 31.651 1 26.96 ? O1A ADP 8528 H 1 HETATM 7 O O2A ADP . . . W 3 101.239 116.534 33.061 1 28.89 ? O2A ADP 8528 H 1 HETATM 8 O O3A ADP . . . W 3 98.967 117.083 34.049 1 26.66 ? O3A ADP 8528 H 1 HETATM 9 O O5' ADP . . . W 3 100.534 118.95 33.399 1 27.36 ? O5' ADP 8528 H 1 HETATM 10 C C5' ADP . . . W 3 99.583 120.056 33.43 1 27.08 ? C5' ADP 8528 H 1 HETATM 11 C C4' ADP . . . W 3 100.181 121.174 34.309 1 27.18 ? C4' ADP 8528 H 1 HETATM 12 O O4' ADP . . . W 3 101.407 121.665 33.721 1 26.62 ? O4' ADP 8528 H 1 HETATM 13 C C3' ADP . . . W 3 99.267 122.403 34.47 1 27.73 ? C3' ADP 8528 H 1 HETATM 14 O O3' ADP . . . W 3 99.285 122.935 35.823 1 29.27 ? O3' ADP 8528 H 1 HETATM 15 C C2' ADP . . . W 3 99.848 123.448 33.549 1 26.81 ? C2' ADP 8528 H 1 HETATM 16 O O2' ADP . . . W 3 99.584 124.805 33.903 1 28.95 ? O2' ADP 8528 H 1 HETATM 17 C C1' ADP . . . W 3 101.306 123.092 33.545 1 28.06 ? C1' ADP 8528 H 1 HETATM 18 N N9 ADP . . . W 3 102.01 123.608 32.351 1 29.02 ? N9 ADP 8528 H 1 HETATM 19 C C8 ADP . . . W 3 101.613 123.512 31.067 1 30.97 ? C8 ADP 8528 H 1 HETATM 20 N N7 ADP . . . W 3 102.528 124.101 30.287 1 31.54 ? N7 ADP 8528 H 1 HETATM 21 C C5 ADP . . . W 3 103.498 124.57 31.034 1 30.32 ? C5 ADP 8528 H 1 HETATM 22 C C6 ADP . . . W 3 104.721 125.273 30.826 1 30.96 ? C6 ADP 8528 H 1 HETATM 23 N N6 ADP . . . W 3 105.111 125.611 29.583 1 32.73 ? N6 ADP 8528 H 1 HETATM 24 N N1 ADP . . . W 3 105.529 125.617 31.911 1 31.98 ? N1 ADP 8528 H 1 HETATM 25 C C2 ADP . . . W 3 105.182 125.297 33.205 1 32.33 ? C2 ADP 8528 H 1 HETATM 26 N N3 ADP . . . W 3 104.003 124.619 33.417 1 31.97 ? N3 ADP 8528 H 1 HETATM 27 C C4 ADP . . . W 3 103.157 124.247 32.388 1 30.07 ? C4 ADP 8528 H 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #