data_8A3V # _model_server_result.job_id uPMi0K2LHIoigYCsIG3ijA _model_server_result.datetime_utc '2024-10-18 16:23:19' _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 8a3v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 8A3V # _exptl.entry_id 8A3V _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 2 _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 120 _cell.entry_id 8A3V _cell.length_a 186.515 _cell.length_b 186.515 _cell.length_c 252.839 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8A3V _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,C,E,F,G,H 1 1,2,3 D 1 4,5,6 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 186.515 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 93.2575 161.526728 0 4 'crystal symmetry operation' 10_555 y+2/3,x+1/3,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 93.2575 53.842243 84.279667 5 'crystal symmetry operation' 11_555 x-y+2/3,-y+1/3,-z+1/3 1 0 0 0 -1 0 0 0 -1 93.2575 53.842243 84.279667 6 'crystal symmetry operation' 12_555 -x+2/3,-x+y+1/3,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 93.2575 53.842243 84.279667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G 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 OG1 THR 235 A THR 235 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A OD1 ASP 340 A ASP 340 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc3 B OG1 THR 235 B THR 235 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc4 B OD1 ASP 340 B ASP 340 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? # _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 8A3V _atom_sites.fract_transf_matrix[1][1] 0.005361 _atom_sites.fract_transf_matrix[1][2] 0.003095 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006191 _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] 0.003955 _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 E 3 ADP A 1 501 504 ADP ADP . F 4 MG A 1 502 505 MG MG . G 3 ADP B 1 501 504 ADP ADP . H 4 MG B 1 502 505 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 . . . E 3 65.545 46.678 24.45 1 72.29 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . E 3 64.868 47.266 23.21 1 72.19 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . E 3 65.62 47.635 25.59 1 72.29 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . E 3 66.919 46.128 24.041 1 72.36 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . E 3 63.099 45.233 25.046 1 72.38 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . E 3 62.646 44.176 24.031 1 72.47 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . E 3 62.415 46.516 24.777 1 72.25 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . E 3 64.67 45.414 24.864 1 72.31 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . E 3 62.83 44.673 26.533 1 72.45 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . E 3 61.79 43.733 26.879 1 72.39 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . E 3 61.423 43.909 28.332 1 72.26 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . E 3 60.262 43.105 28.64 1 72.19 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . E 3 62.496 43.512 29.346 1 72.23 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . E 3 62.532 44.418 30.443 1 72.33 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . E 3 62.08 42.094 29.75 1 72.04 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . E 3 62.501 41.751 31.066 1 71.92 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . E 3 60.557 42.19 29.678 1 72.02 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . E 3 59.895 40.926 29.374 1 71.8 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . E 3 59.855 40.287 28.163 1 71.77 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . E 3 59.154 39.179 28.166 1 71.74 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . E 3 58.695 39.084 29.471 1 71.64 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . E 3 57.862 38.151 30.119 1 71.52 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . E 3 57.353 37.072 29.521 1 71.43 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . E 3 57.565 38.371 31.419 1 71.48 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . E 3 58.081 39.445 32.024 1 71.44 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . E 3 58.882 40.388 31.519 1 71.51 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . E 3 59.149 40.151 30.229 1 71.65 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #