data_8UZ1 # _model_server_result.job_id jzUcBF5GrZc_0-zIFUTagw _model_server_result.datetime_utc '2024-11-22 13:27:17' _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 8uz1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":401}' # _entry.id 8UZ1 # _exptl.entry_id 8UZ1 _exptl.method 'ELECTRON MICROSCOPY' # _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 9 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _pdbx_struct_assembly.details author_and_software_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,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 x,y,z _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 ? 2 J N N ? 2 M N N ? 2 P N N ? 2 S N N ? 2 V N N ? 2 Y N N ? 2 BA N N ? 2 EA N N ? 2 HA 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 A C GLU 69 J GLU 72 1_555 A N HIC 70 J HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C HIC 70 J HIC 73 1_555 A N GLY 71 J GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale3 B C GLU 69 K GLU 72 1_555 B N HIC 70 K HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 B C HIC 70 K HIC 73 1_555 B N GLY 71 K GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale5 C C GLU 69 L GLU 72 1_555 C N HIC 70 L HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 C C HIC 70 L HIC 73 1_555 C N GLY 71 L GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale7 D C GLU 69 M GLU 72 1_555 D N HIC 70 M HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 D C HIC 70 M HIC 73 1_555 D N GLY 71 M GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 E C GLU 69 N GLU 72 1_555 E N HIC 70 N HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 E C HIC 70 N HIC 73 1_555 E N GLY 71 N GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale11 F C GLU 69 O GLU 72 1_555 F N HIC 70 O HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 F C HIC 70 O HIC 73 1_555 F N GLY 71 O GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 G C GLU 69 P GLU 72 1_555 G N HIC 70 P HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale14 G C HIC 70 P HIC 73 1_555 G N GLY 71 P GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale15 H C GLU 69 Q GLU 72 1_555 H N HIC 70 Q HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 H C HIC 70 Q HIC 73 1_555 H N GLY 71 Q GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale17 I C GLU 69 R GLU 72 1_555 I N HIC 70 R HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 I C HIC 70 R HIC 73 1_555 I N GLY 71 R GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? metalc ? metalc1 A OE1 GLN 134 J GLN 137 1_555 K MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc2 J O2B ADP . J ADP 401 1_555 K MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.858 ? metalc ? metalc3 J O3B ADP . J ADP 401 1_555 K MG MG . J MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.924 ? metalc ? metalc4 B OE1 GLN 134 K GLN 137 1_555 N MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc5 M O2B ADP . K ADP 401 1_555 N MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc6 M O3B ADP . K ADP 401 1_555 N MG MG . K MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc7 C OE1 GLN 134 L GLN 137 1_555 Q MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc8 P O2B ADP . L ADP 401 1_555 Q MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? metalc ? metalc9 P O3B ADP . L ADP 401 1_555 Q MG MG . L MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? metalc ? metalc10 D OE1 GLN 134 M GLN 137 1_555 T MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc11 S O2B ADP . M ADP 401 1_555 T MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? metalc ? metalc12 S O3B ADP . M ADP 401 1_555 T MG MG . M MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc13 E OE1 GLN 134 N GLN 137 1_555 W MG MG . N MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc14 V O2B ADP . N ADP 401 1_555 W MG MG . N MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.853 ? metalc ? metalc15 V O3B ADP . N ADP 401 1_555 W MG MG . N MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc16 F OE1 GLN 134 O GLN 137 1_555 Z MG MG . O MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc17 Y O2B ADP . O ADP 401 1_555 Z MG MG . O MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? metalc ? metalc18 Y O3B ADP . O ADP 401 1_555 Z MG MG . O MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc19 G OE1 GLN 134 P GLN 137 1_555 CA MG MG . P MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc20 BA O2B ADP . P ADP 401 1_555 CA MG MG . P MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? metalc ? metalc21 BA O3B ADP . P ADP 401 1_555 CA MG MG . P MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc22 H OE1 GLN 134 Q GLN 137 1_555 FA MG MG . Q MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc23 EA O2B ADP . Q ADP 401 1_555 FA MG MG . Q MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc24 EA O3B ADP . Q ADP 401 1_555 FA MG MG . Q MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc25 I OE1 GLN 134 R GLN 137 1_555 IA MG MG . R MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc26 HA O2B ADP . R ADP 401 1_555 IA MG MG . R MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? metalc ? metalc27 HA O3B ADP . R ADP 401 1_555 IA MG MG . R MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? # _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 8UZ1 _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 J 2 ADP J 1 401 401 ADP ADP . K 3 MG J 1 402 402 MG MG . L 4 BEF J 1 403 403 BEF BEF . M 2 ADP K 1 401 401 ADP ADP . N 3 MG K 1 402 402 MG MG . O 4 BEF K 1 403 403 BEF BEF . P 2 ADP L 1 401 401 ADP ADP . Q 3 MG L 1 402 402 MG MG . R 4 BEF L 1 403 403 BEF BEF . S 2 ADP M 1 401 401 ADP ADP . T 3 MG M 1 402 402 MG MG . U 4 BEF M 1 403 403 BEF BEF . V 2 ADP N 1 401 401 ADP ADP . W 3 MG N 1 402 402 MG MG . X 4 BEF N 1 403 403 BEF BEF . Y 2 ADP O 1 401 401 ADP ADP . Z 3 MG O 1 402 402 MG MG . AA 4 BEF O 1 403 403 BEF BEF . BA 2 ADP P 1 401 401 ADP ADP . CA 3 MG P 1 402 402 MG MG . DA 4 BEF P 1 403 403 BEF BEF . EA 2 ADP Q 1 401 401 ADP ADP . FA 3 MG Q 1 402 402 MG MG . GA 4 BEF Q 1 403 403 BEF BEF . HA 2 ADP R 1 401 401 ADP ADP . IA 3 MG R 1 402 402 MG MG . JA 4 BEF R 1 403 403 BEF BEF . # 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 . . . Y 2 160.322 184.108 186.25 1 22.71 ? PB ADP 401 O 1 HETATM 2 O O1B ADP . . . Y 2 160.155 185.496 185.81 1 22.71 ? O1B ADP 401 O 1 HETATM 3 O O2B ADP . . . Y 2 159.816 184.062 187.64 1 22.71 ? O2B ADP 401 O 1 HETATM 4 O O3B ADP . . . Y 2 161.766 183.831 186.441 1 22.71 ? O3B ADP 401 O 1 HETATM 5 P PA ADP . . . Y 2 158.128 183.094 185.027 1 22.71 ? PA ADP 401 O 1 HETATM 6 O O1A ADP . . . Y 2 157.656 184.221 184.195 1 22.71 ? O1A ADP 401 O 1 HETATM 7 O O2A ADP . . . Y 2 157.281 182.998 186.234 1 22.71 ? O2A ADP 401 O 1 HETATM 8 O O3A ADP . . . Y 2 159.66 183.057 185.311 1 22.71 ? O3A ADP 401 O 1 HETATM 9 O O5' ADP . . . Y 2 157.998 181.718 184.232 1 22.71 ? O5' ADP 401 O 1 HETATM 10 C C5' ADP . . . Y 2 158.439 181.611 182.879 1 22.71 ? C5' ADP 401 O 1 HETATM 11 C C4' ADP . . . Y 2 158.762 180.121 182.631 1 22.71 ? C4' ADP 401 O 1 HETATM 12 O O4' ADP . . . Y 2 157.573 179.357 182.934 1 22.71 ? O4' ADP 401 O 1 HETATM 13 C C3' ADP . . . Y 2 159.112 179.785 181.171 1 22.71 ? C3' ADP 401 O 1 HETATM 14 O O3' ADP . . . Y 2 160.037 178.694 181.134 1 22.71 ? O3' ADP 401 O 1 HETATM 15 C C2' ADP . . . Y 2 157.763 179.354 180.612 1 22.71 ? C2' ADP 401 O 1 HETATM 16 O O2' ADP . . . Y 2 157.862 178.502 179.471 1 22.71 ? O2' ADP 401 O 1 HETATM 17 C C1' ADP . . . Y 2 157.09 178.659 181.787 1 22.71 ? C1' ADP 401 O 1 HETATM 18 N N9 ADP . . . Y 2 155.647 178.75 181.759 1 22.71 ? N9 ADP 401 O 1 HETATM 19 C C8 ADP . . . Y 2 154.87 179.901 181.699 1 22.71 ? C8 ADP 401 O 1 HETATM 20 N N7 ADP . . . Y 2 153.551 179.643 181.613 1 22.71 ? N7 ADP 401 O 1 HETATM 21 C C5 ADP . . . Y 2 153.549 178.279 181.646 1 22.71 ? C5 ADP 401 O 1 HETATM 22 C C6 ADP . . . Y 2 152.477 177.407 181.577 1 22.71 ? C6 ADP 401 O 1 HETATM 23 N N6 ADP . . . Y 2 151.204 177.81 181.456 1 22.71 ? N6 ADP 401 O 1 HETATM 24 N N1 ADP . . . Y 2 152.623 176.104 181.578 1 22.71 ? N1 ADP 401 O 1 HETATM 25 C C2 ADP . . . Y 2 153.88 175.668 181.67 1 22.71 ? C2 ADP 401 O 1 HETATM 26 N N3 ADP . . . Y 2 154.986 176.416 181.735 1 22.71 ? N3 ADP 401 O 1 HETATM 27 C C4 ADP . . . Y 2 154.775 177.727 181.736 1 22.71 ? C4 ADP 401 O 1 HETATM 28 H "H5'1" ADP . . . Y 2 157.652 181.952 182.195 1 22.71 ? "H5'1" ADP 401 O 1 HETATM 29 H "H5'2" ADP . . . Y 2 159.335 182.221 182.709 1 22.71 ? "H5'2" ADP 401 O 1 HETATM 30 H H4' ADP . . . Y 2 159.582 179.819 183.295 1 22.71 ? H4' ADP 401 O 1 HETATM 31 H H3' ADP . . . Y 2 159.504 180.658 180.635 1 22.71 ? H3' ADP 401 O 1 HETATM 32 H HO3' ADP . . . Y 2 160.913 179.109 181.047 1 22.71 ? HO3' ADP 401 O 1 HETATM 33 H H2' ADP . . . Y 2 157.202 180.259 180.351 1 22.71 ? H2' ADP 401 O 1 HETATM 34 H HO2' ADP . . . Y 2 157.226 178.855 178.825 1 22.71 ? HO2' ADP 401 O 1 HETATM 35 H H1' ADP . . . Y 2 157.383 177.604 181.839 1 22.71 ? H1' ADP 401 O 1 HETATM 36 H H8 ADP . . . Y 2 155.322 180.883 181.71 1 22.71 ? H8 ADP 401 O 1 HETATM 37 H HN61 ADP . . . Y 2 151.111 178.743 181.076 1 22.71 ? HN61 ADP 401 O 1 HETATM 38 H HN62 ADP . . . Y 2 150.593 177.092 181.087 1 22.71 ? HN62 ADP 401 O 1 HETATM 39 H H2 ADP . . . Y 2 154.017 174.589 181.656 1 22.71 ? H2 ADP 401 O 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 329 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #