data_8DAV # _model_server_result.job_id 0thrXC1lDW9SjO1K2VsrkA _model_server_result.datetime_utc '2024-12-27 00:53:30' _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 8dav # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":902}' # _entry.id 8DAV # _exptl.entry_id 8DAV _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 7 _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 8DAV _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DAV _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details undecameric _pdbx_struct_assembly.oligomeric_count 11 _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,X,Y _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 M N N ? 6 O N N ? 6 Q N N ? 6 S N N ? 6 T N N ? 6 U N N ? 6 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 covale ? covale1 I NZ LYS 48 I LYS 48 1_555 J C GLY 76 J GLY 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale2 J NZ LYS 48 J LYS 148 1_555 K C GLY 76 K GLY 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? metalc ? metalc1 G SG CYS 140 G CYS 137 1_555 X ZN ZN . G ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc2 G NE2 HIS 142 G HIS 139 1_555 X ZN ZN . G ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc3 G SG CYS 148 G CYS 145 1_555 X ZN ZN . G ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc4 G SG CYS 151 G CYS 148 1_555 X ZN ZN . G ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc5 G SG CYS 207 G CYS 204 1_555 Y ZN ZN . G ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc6 G NE2 HIS 211 G HIS 208 1_555 Y ZN ZN . G ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc7 G SG CYS 219 G CYS 216 1_555 Y ZN ZN . G ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc8 G SG CYS 222 G CYS 219 1_555 Y ZN ZN . G ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? # _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 8DAV _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 L 5 ATP A 1 901 901 ATP ATP . M 6 ADP A 1 902 902 ADP ADP . N 5 ATP B 1 901 901 ATP ATP . O 6 ADP B 1 902 902 ADP ADP . P 5 ATP C 1 901 901 ATP ATP . Q 6 ADP C 1 902 902 ADP ADP . R 5 ATP D 1 901 901 ATP ATP . S 6 ADP D 1 902 902 ADP ADP . T 6 ADP E 1 901 901 ADP ADP . U 6 ADP E 1 902 902 ADP ADP . V 5 ATP F 1 901 901 ATP ATP . W 6 ADP F 1 902 902 ADP ADP . X 7 ZN G 1 601 601 ZN ZN . Y 7 ZN G 1 602 602 ZN ZN . # 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 . . . O 6 254.826 212.705 199.307 1 147.86 ? PB ADP 902 B 1 HETATM 2 O O1B ADP . . . O 6 255.721 212.807 198.108 1 147.86 ? O1B ADP 902 B 1 HETATM 3 O O2B ADP . . . O 6 254.308 214.037 199.737 1 147.86 ? O2B ADP 902 B 1 HETATM 4 O O3B ADP . . . O 6 253.735 211.679 199.142 1 147.86 ? O3B ADP 902 B 1 HETATM 5 P PA ADP . . . O 6 255.423 212.162 202.093 1 147.86 ? PA ADP 902 B 1 HETATM 6 O O1A ADP . . . O 6 254.288 211.224 202.334 1 147.86 ? O1A ADP 902 B 1 HETATM 7 O O2A ADP . . . O 6 255.296 213.568 202.575 1 147.86 ? O2A ADP 902 B 1 HETATM 8 O O3A ADP . . . O 6 255.743 212.201 200.525 1 147.86 ? O3A ADP 902 B 1 HETATM 9 O O5' ADP . . . O 6 256.775 211.529 202.668 1 147.86 ? O5' ADP 902 B 1 HETATM 10 C C5' ADP . . . O 6 258.01 212.204 202.338 1 147.86 ? C5' ADP 902 B 1 HETATM 11 C C4' ADP . . . O 6 259.086 211.779 203.304 1 147.86 ? C4' ADP 902 B 1 HETATM 12 O O4' ADP . . . O 6 260.325 212.441 202.944 1 147.86 ? O4' ADP 902 B 1 HETATM 13 C C3' ADP . . . O 6 258.852 212.167 204.767 1 147.86 ? C3' ADP 902 B 1 HETATM 14 O O3' ADP . . . O 6 259.573 211.31 205.641 1 147.86 ? O3' ADP 902 B 1 HETATM 15 C C2' ADP . . . O 6 259.429 213.582 204.787 1 147.86 ? C2' ADP 902 B 1 HETATM 16 O O2' ADP . . . O 6 259.745 214.033 206.085 1 147.86 ? O2' ADP 902 B 1 HETATM 17 C C1' ADP . . . O 6 260.679 213.375 203.94 1 147.86 ? C1' ADP 902 B 1 HETATM 18 N N9 ADP . . . O 6 261.149 214.59 203.288 1 147.86 ? N9 ADP 902 B 1 HETATM 19 C C8 ADP . . . O 6 261.11 215.863 203.796 1 147.86 ? C8 ADP 902 B 1 HETATM 20 N N7 ADP . . . O 6 261.605 216.76 202.982 1 147.86 ? N7 ADP 902 B 1 HETATM 21 C C5 ADP . . . O 6 261.99 216.037 201.863 1 147.86 ? C5 ADP 902 B 1 HETATM 22 C C6 ADP . . . O 6 262.585 216.418 200.644 1 147.86 ? C6 ADP 902 B 1 HETATM 23 N N6 ADP . . . O 6 262.907 217.67 200.333 1 147.86 ? N6 ADP 902 B 1 HETATM 24 N N1 ADP . . . O 6 262.838 215.442 199.74 1 147.86 ? N1 ADP 902 B 1 HETATM 25 C C2 ADP . . . O 6 262.514 214.182 200.053 1 147.86 ? C2 ADP 902 B 1 HETATM 26 N N3 ADP . . . O 6 261.955 213.708 201.163 1 147.86 ? N3 ADP 902 B 1 HETATM 27 C C4 ADP . . . O 6 261.713 214.696 202.04 1 147.86 ? C4 ADP 902 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #