data_7YK1 # _model_server_result.job_id Xwd5dDGH6a2Nsm4iM3t08Q _model_server_result.datetime_utc '2024-11-24 22:02:55' _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 7yk1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":401}' # _entry.id 7YK1 # _exptl.entry_id 7YK1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 12 _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 7YK1 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YK1 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,Z,AA,BA,CA,DA _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 ? 4 I N N ? 4 J N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 S N N ? 4 V N N ? 4 W N N ? 4 X N N ? 4 AA N N ? 4 BA 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 NH2 ARG 49 A ARG 49 1_555 J O1A ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? covale ? covale2 B NH2 ARG 49 B ARG 49 1_555 M O2A ADP . B ADP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? covale ? covale3 C NH2 ARG 49 C ARG 49 1_555 P O2A ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? covale ? covale4 D NH2 ARG 49 D ARG 49 1_555 S O2A ADP . D ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? covale ? covale5 E NH2 ARG 49 E ARG 49 1_555 W O1A ADP . E ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? covale ? covale6 F NH2 ARG 49 F ARG 49 1_555 BA O1A ADP . F ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? metalc ? metalc1 H MG MG . A MG 402 1_555 O O1A ADP . C ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc2 H MG MG . A MG 402 1_555 O O1B ADP . C ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc3 I O3B ADP . A ADP 403 1_555 R MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc4 I O2A ADP . A ADP 403 1_555 R MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc5 L MG MG . B MG 402 1_555 X O3B ADP . E ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc6 L MG MG . B MG 402 1_555 X O2A ADP . E ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc7 N O1B ADP . B ADP 404 1_555 Z MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc8 N O1A ADP . B ADP 404 1_555 Z MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc9 U MG MG . D MG 403 1_555 AA O2A ADP . F ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc10 U MG MG . D MG 403 1_555 AA O3B ADP . F ADP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc11 V O1B ADP . D ADP 404 1_555 DA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc12 V O1A ADP . D ADP 404 1_555 DA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? # _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 7YK1 _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 G 2 PO4 A 1 401 401 PO4 PO4 . H 3 MG A 1 402 404 MG MG . I 4 ADP A 1 403 403 ADP ADP . J 4 ADP A 1 404 402 ADP ADP . K 2 PO4 B 1 401 401 PO4 PO4 . L 3 MG B 1 402 404 MG MG . M 4 ADP B 1 403 402 ADP ADP . N 4 ADP B 1 404 403 ADP ADP . O 4 ADP C 1 401 403 ADP ADP . P 4 ADP C 1 402 402 ADP ADP . Q 2 PO4 C 1 403 401 PO4 PO4 . R 3 MG C 1 404 404 MG MG . S 4 ADP D 1 401 402 ADP ADP . T 2 PO4 D 1 402 401 PO4 PO4 . U 3 MG D 1 403 404 MG MG . V 4 ADP D 1 404 403 ADP ADP . W 4 ADP E 1 401 402 ADP ADP . X 4 ADP E 1 402 403 ADP ADP . Y 2 PO4 E 1 403 401 PO4 PO4 . Z 3 MG E 1 404 404 MG MG . AA 4 ADP F 1 401 403 ADP ADP . BA 4 ADP F 1 402 402 ADP ADP . CA 2 PO4 F 1 403 401 PO4 PO4 . DA 3 MG F 1 404 404 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 . . . W 4 117.58 140.434 113.704 1 38.23 ? PB ADP 401 E 1 HETATM 2 O O1B ADP . . . W 4 118.065 139.283 112.868 1 15.38 ? O1B ADP 401 E 1 HETATM 3 O O2B ADP . . . W 4 116.6 141.343 113.01 1 22.17 ? O2B ADP 401 E 1 HETATM 4 O O3B ADP . . . W 4 118.663 141.139 114.48 1 14.47 ? O3B ADP 401 E 1 HETATM 5 P PA ADP . . . W 4 117.413 139.055 116.108 1 35.74 ? PA ADP 401 E 1 HETATM 6 O O1A ADP . . . W 4 118.56 138.199 115.618 1 29.22 ? O1A ADP 401 E 1 HETATM 7 O O2A ADP . . . W 4 117.66 140.145 117.112 1 0 ? O2A ADP 401 E 1 HETATM 8 O O3A ADP . . . W 4 116.699 139.729 114.841 1 12.65 ? O3A ADP 401 E 1 HETATM 9 O O5' ADP . . . W 4 116.242 138.099 116.655 1 15.93 ? O5' ADP 401 E 1 HETATM 10 C C5' ADP . . . W 4 115.037 138.663 117.149 1 10.71 ? C5' ADP 401 E 1 HETATM 11 C C4' ADP . . . W 4 114.704 138.06 118.505 1 13.16 ? C4' ADP 401 E 1 HETATM 12 O O4' ADP . . . W 4 113.541 138.677 119.052 1 12.4 ? O4' ADP 401 E 1 HETATM 13 C C3' ADP . . . W 4 114.417 136.577 118.443 1 14.17 ? C3' ADP 401 E 1 HETATM 14 O O3' ADP . . . W 4 115.577 135.855 118.848 1 20.85 ? O3' ADP 401 E 1 HETATM 15 C C2' ADP . . . W 4 113.287 136.362 119.425 1 9.4 ? C2' ADP 401 E 1 HETATM 16 O O2' ADP . . . W 4 113.768 135.644 120.556 1 5.63 ? O2' ADP 401 E 1 HETATM 17 C C1' ADP . . . W 4 112.842 137.744 119.865 1 2.64 ? C1' ADP 401 E 1 HETATM 18 N N9 ADP . . . W 4 111.379 137.9 119.686 1 6.12 ? N9 ADP 401 E 1 HETATM 19 C C8 ADP . . . W 4 110.427 137.404 120.496 1 15.9 ? C8 ADP 401 E 1 HETATM 20 N N7 ADP . . . W 4 109.183 137.726 120.062 1 8.8 ? N7 ADP 401 E 1 HETATM 21 C C5 ADP . . . W 4 109.335 138.448 118.944 1 7.73 ? C5 ADP 401 E 1 HETATM 22 C C6 ADP . . . W 4 108.425 139.096 117.979 1 9.15 ? C6 ADP 401 E 1 HETATM 23 N N6 ADP . . . W 4 107.083 139.035 118.132 1 11.97 ? N6 ADP 401 E 1 HETATM 24 N N1 ADP . . . W 4 108.986 139.753 116.943 1 18.52 ? N1 ADP 401 E 1 HETATM 25 C C2 ADP . . . W 4 110.322 139.815 116.786 1 20.06 ? C2 ADP 401 E 1 HETATM 26 N N3 ADP . . . W 4 111.205 139.247 117.621 1 0.31 ? N3 ADP 401 E 1 HETATM 27 C C4 ADP . . . W 4 110.78 138.564 118.703 1 0 ? C4 ADP 401 E 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #