data_6S5B # _model_server_result.job_id 0-uuVYDYZ7VgL44G7cPk8g _model_server_result.datetime_utc '2025-03-20 20:30:43' _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 6s5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":601}' # _entry.id 6S5B # _exptl.entry_id 6S5B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 6S5B _cell.length_a 85.818 _cell.length_b 137.429 _cell.length_c 202.617 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J 1 1 G,H,O,P 1 2 C,D,K,L 1 3 E,F,M,N 1 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' 1_655 x+1,y,z 1 0 0 0 1 0 0 0 1 85.818 0 0 3 'crystal symmetry operation' 2_454 -x-1/2,-y,z-1/2 -1 0 0 0 -1 0 0 0 1 -42.909 0 -101.3085 4 'crystal symmetry operation' 4_545 x+1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 42.909 -68.7145 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N # _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 6S5B _atom_sites.fract_transf_matrix[1][1] 0.011653 _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] 0.007276 _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] 0.004935 _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 ADP A 1 601 601 ADP ADP . J 2 ADP B 1 601 601 ADP ADP . K 2 ADP C 1 601 601 ADP ADP . L 2 ADP D 1 601 601 ADP ADP . M 2 ADP E 1 601 601 ADP ADP . N 2 ADP F 1 601 601 ADP ADP . O 2 ADP G 1 601 601 ADP ADP . P 2 ADP H 1 601 601 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 . . . L 2 -23.502 5.76 63.199 1 174.53 ? PB ADP 601 D 1 HETATM 2 O O1B ADP . . . L 2 -22.542 6.498 62.297 1 118.81 ? O1B ADP 601 D 1 HETATM 3 O O2B ADP . . . L 2 -22.871 4.67 64.031 1 124.71 -1 O2B ADP 601 D 1 HETATM 4 O O3B ADP . . . L 2 -24.784 5.344 62.52 1 181.2 ? O3B ADP 601 D 1 HETATM 5 P PA ADP . . . L 2 -25.059 7.988 63.988 1 152.9 ? PA ADP 601 D 1 HETATM 6 O O1A ADP . . . L 2 -26.318 7.311 63.497 1 112 ? O1A ADP 601 D 1 HETATM 7 O O2A ADP . . . L 2 -25.156 8.898 65.189 1 122.76 -1 O2A ADP 601 D 1 HETATM 8 O O3A ADP . . . L 2 -23.935 6.87 64.287 1 147.29 ? O3A ADP 601 D 1 HETATM 9 O O5' ADP . . . L 2 -24.44 8.828 62.763 1 70.74 ? O5' ADP 601 D 1 HETATM 10 C C5' ADP . . . L 2 -25.294 9.37 61.758 1 73.36 ? C5' ADP 601 D 1 HETATM 11 C C4' ADP . . . L 2 -24.785 10.745 61.349 1 72.63 ? C4' ADP 601 D 1 HETATM 12 O O4' ADP . . . L 2 -25.248 11.092 60.043 1 121.04 ? O4' ADP 601 D 1 HETATM 13 C C3' ADP . . . L 2 -25.29 11.815 62.304 1 117.03 ? C3' ADP 601 D 1 HETATM 14 O O3' ADP . . . L 2 -24.206 12.328 63.082 1 100.68 ? O3' ADP 601 D 1 HETATM 15 C C2' ADP . . . L 2 -25.868 12.91 61.43 1 101.09 ? C2' ADP 601 D 1 HETATM 16 O O2' ADP . . . L 2 -25.235 14.156 61.725 1 119.55 ? O2' ADP 601 D 1 HETATM 17 C C1' ADP . . . L 2 -25.584 12.48 59.998 1 105.37 ? C1' ADP 601 D 1 HETATM 18 N N9 ADP . . . L 2 -26.784 12.697 59.153 1 97.84 ? N9 ADP 601 D 1 HETATM 19 C C8 ADP . . . L 2 -28.024 12.252 59.426 1 114.37 ? C8 ADP 601 D 1 HETATM 20 N N7 ADP . . . L 2 -28.901 12.621 58.459 1 113.08 ? N7 ADP 601 D 1 HETATM 21 C C5 ADP . . . L 2 -28.216 13.325 57.539 1 80.63 ? C5 ADP 601 D 1 HETATM 22 C C6 ADP . . . L 2 -28.533 14.009 56.263 1 80.44 ? C6 ADP 601 D 1 HETATM 23 N N6 ADP . . . L 2 -29.793 14.011 55.766 1 120.78 ? N6 ADP 601 D 1 HETATM 24 N N1 ADP . . . L 2 -27.524 14.629 55.611 1 70.98 ? N1 ADP 601 D 1 HETATM 25 C C2 ADP . . . L 2 -26.269 14.633 56.096 1 77.31 ? C2 ADP 601 D 1 HETATM 26 N N3 ADP . . . L 2 -25.91 14.035 57.246 1 89.07 ? N3 ADP 601 D 1 HETATM 27 C C4 ADP . . . L 2 -26.821 13.377 58.003 1 91.85 ? C4 ADP 601 D 1 # _model_server_stats.io_time_ms 121 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #