data_6S5G # _model_server_result.job_id itMn0dibz7-V4zyBEUUkWw _model_server_result.datetime_utc '2024-11-08 16:06:45' _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 6s5g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":601}' # _entry.id 6S5G # _exptl.entry_id 6S5G _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 6S5G _cell.length_a 85.335 _cell.length_b 132.925 _cell.length_c 203.263 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S5G _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 ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_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 85.335 0 0 3 'crystal symmetry operation' 2_455 -x-1/2,-y,z+1/2 -1 0 0 0 -1 0 0 0 1 -42.6675 0 101.6315 4 'crystal symmetry operation' 4_555 x+1/2,-y+1/2,-z 1 0 0 0 -1 0 0 0 -1 42.6675 66.4625 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 6S5G _atom_sites.fract_transf_matrix[1][1] 0.011719 _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] 0.007523 _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] 0.00492 _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 . . . J 2 -8.59 9.298 -1.115 1 149.94 ? PB ADP 601 B 1 HETATM 2 O O1B ADP . . . J 2 -8.123 8.244 -2.09 1 148.82 ? O1B ADP 601 B 1 HETATM 3 O O2B ADP . . . J 2 -10.076 9.3 -0.858 1 148.01 -1 O2B ADP 601 B 1 HETATM 4 O O3B ADP . . . J 2 -8 10.669 -1.332 1 151.42 ? O3B ADP 601 B 1 HETATM 5 P PA ADP . . . J 2 -6.378 8.615 0.467 1 153.38 ? PA ADP 601 B 1 HETATM 6 O O1A ADP . . . J 2 -5.643 9.097 -0.761 1 153.92 ? O1A ADP 601 B 1 HETATM 7 O O2A ADP . . . J 2 -6.144 7.217 0.986 1 155.45 -1 O2A ADP 601 B 1 HETATM 8 O O3A ADP . . . J 2 -7.961 8.844 0.293 1 152.36 ? O3A ADP 601 B 1 HETATM 9 O O5' ADP . . . J 2 -6.063 9.653 1.653 1 154.56 ? O5' ADP 601 B 1 HETATM 10 C C5' ADP . . . J 2 -6.125 9.238 3.013 1 155.44 ? C5' ADP 601 B 1 HETATM 11 C C4' ADP . . . J 2 -5.583 10.359 3.887 1 156.44 ? C4' ADP 601 B 1 HETATM 12 O O4' ADP . . . J 2 -6.281 10.403 5.132 1 157.07 ? O4' ADP 601 B 1 HETATM 13 C C3' ADP . . . J 2 -4.109 10.143 4.19 1 157.89 ? C3' ADP 601 B 1 HETATM 14 O O3' ADP . . . J 2 -3.334 11.186 3.594 1 158.62 ? O3' ADP 601 B 1 HETATM 15 C C2' ADP . . . J 2 -3.991 10.201 5.7 1 158.37 ? C2' ADP 601 B 1 HETATM 16 O O2' ADP . . . J 2 -2.98 11.135 6.084 1 158.85 ? O2' ADP 601 B 1 HETATM 17 C C1' ADP . . . J 2 -5.358 10.644 6.195 1 158.16 ? C1' ADP 601 B 1 HETATM 18 N N9 ADP . . . J 2 -5.742 9.86 7.394 1 161.52 ? N9 ADP 601 B 1 HETATM 19 C C8 ADP . . . J 2 -5.846 8.52 7.457 1 160.9 ? C8 ADP 601 B 1 HETATM 20 N N7 ADP . . . J 2 -6.213 8.117 8.7 1 161.49 ? N7 ADP 601 B 1 HETATM 21 C C5 ADP . . . J 2 -6.347 9.22 9.46 1 162.32 ? C5 ADP 601 B 1 HETATM 22 C C6 ADP . . . J 2 -6.712 9.512 10.867 1 161.89 ? C6 ADP 601 B 1 HETATM 23 N N6 ADP . . . J 2 -7.015 8.515 11.733 1 163 ? N6 ADP 601 B 1 HETATM 24 N N1 ADP . . . J 2 -6.732 10.806 11.256 1 162.44 ? N1 ADP 601 B 1 HETATM 25 C C2 ADP . . . J 2 -6.433 11.807 10.405 1 161.84 ? C2 ADP 601 B 1 HETATM 26 N N3 ADP . . . J 2 -6.093 11.615 9.117 1 162.43 ? N3 ADP 601 B 1 HETATM 27 C C4 ADP . . . J 2 -6.032 10.367 8.594 1 162.75 ? C4 ADP 601 B 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #