data_1Q3S # _model_server_result.job_id dHuEgZ5aKfCK8VuUV5UWZw _model_server_result.datetime_utc '2025-07-31 04:15:20' _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":"R","auth_seq_id":5528}' # _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 . . . R 3 55.801 37.285 75.004 1 33.53 ? PB ADP 5528 E 1 HETATM 2 O O1B ADP . . . R 3 56.519 36.031 75.365 1 31.21 ? O1B ADP 5528 E 1 HETATM 3 O O2B ADP . . . R 3 56.341 37.854 73.727 1 33.67 ? O2B ADP 5528 E 1 HETATM 4 O O3B ADP . . . R 3 54.151 37.053 74.874 1 33.09 ? O3B ADP 5528 E 1 HETATM 5 P PA ADP . . . R 3 54.992 39.213 77.116 1 36.06 ? PA ADP 5528 E 1 HETATM 6 O O1A ADP . . . R 3 53.771 39.604 76.373 1 35.42 ? O1A ADP 5528 E 1 HETATM 7 O O2A ADP . . . R 3 55.699 40.423 77.645 1 35.89 ? O2A ADP 5528 E 1 HETATM 8 O O3A ADP . . . R 3 55.972 38.376 76.153 1 33.87 ? O3A ADP 5528 E 1 HETATM 9 O O5' ADP . . . R 3 54.664 38.163 78.303 1 34.78 ? O5' ADP 5528 E 1 HETATM 10 C C5' ADP . . . R 3 53.989 36.874 78.051 1 34.41 ? C5' ADP 5528 E 1 HETATM 11 C C4' ADP . . . R 3 54.338 35.876 79.207 1 33.28 ? C4' ADP 5528 E 1 HETATM 12 O O4' ADP . . . R 3 53.846 36.41 80.452 1 32.69 ? O4' ADP 5528 E 1 HETATM 13 C C3' ADP . . . R 3 53.689 34.481 79.041 1 33.6 ? C3' ADP 5528 E 1 HETATM 14 O O3' ADP . . . R 3 54.624 33.384 79.344 1 32.93 ? O3' ADP 5528 E 1 HETATM 15 C C2' ADP . . . R 3 52.535 34.446 80.054 1 33.25 ? C2' ADP 5528 E 1 HETATM 16 O O2' ADP . . . R 3 52.228 33.15 80.604 1 32.93 ? O2' ADP 5528 E 1 HETATM 17 C C1' ADP . . . R 3 52.943 35.489 81.074 1 32.14 ? C1' ADP 5528 E 1 HETATM 18 N N9 ADP . . . R 3 51.794 36.213 81.649 1 30.99 ? N9 ADP 5528 E 1 HETATM 19 C C8 ADP . . . R 3 50.887 36.963 80.989 1 30.44 ? C8 ADP 5528 E 1 HETATM 20 N N7 ADP . . . R 3 50.011 37.459 81.877 1 30.94 ? N7 ADP 5528 E 1 HETATM 21 C C5 ADP . . . R 3 50.339 37.042 83.088 1 31.48 ? C5 ADP 5528 E 1 HETATM 22 C C6 ADP . . . R 3 49.845 37.201 84.431 1 32.42 ? C6 ADP 5528 E 1 HETATM 23 N N6 ADP . . . R 3 48.75 37.954 84.695 1 32.05 ? N6 ADP 5528 E 1 HETATM 24 N N1 ADP . . . R 3 50.501 36.573 85.493 1 33.5 ? N1 ADP 5528 E 1 HETATM 25 C C2 ADP . . . R 3 51.621 35.793 85.302 1 33 ? C2 ADP 5528 E 1 HETATM 26 N N3 ADP . . . R 3 52.102 35.634 84.027 1 32.23 ? N3 ADP 5528 E 1 HETATM 27 C C4 ADP . . . R 3 51.509 36.224 82.925 1 31.29 ? C4 ADP 5528 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #