data_8F5S # _model_server_result.job_id yBQMCbLSh9ZeyAYTv6rPdg _model_server_result.datetime_utc '2025-01-10 14:10:29' _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 8f5s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8F5S # _exptl.entry_id 8F5S _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 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 90 _cell.entry_id 8F5S _cell.length_a 117.767 _cell.length_b 117.767 _cell.length_c 154.773 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8F5S _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,O 1 1 A,C,D,E,F,G,H,I,J,O 1 3 B,K,L,M,N,P 2 1 B,K,L,M,N,P 2 2 # 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' 5_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 117.767 0 0 3 'crystal symmetry operation' 6_545 x,-y-1,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 -117.767 77.3865 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 K 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 OD1 ASN 249 A ASN 249 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc2 A O VAL 298 A VAL 298 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc3 A O ASP 300 A ASP 300 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.196 ? metalc ? metalc4 A O PHE 303 A PHE 303 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.172 ? metalc ? metalc5 A O GLY 337 A GLY 337 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.422 ? metalc ? metalc6 C O3B ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc7 C O1A ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc8 C O2A ADP . A ADP 401 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc9 B OD1 ASN 249 B ASN 249 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc10 K O1B ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc11 K O1A ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? # _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 8F5S _atom_sites.fract_transf_matrix[1][1] 0.008491 _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] 0.008491 _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] 0.006461 _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 C 2 ADP A 1 401 401 ADP ADP . D 3 MG A 1 402 402 MG MG . E 4 K A 1 403 403 K K . F 5 XGT A 1 404 404 XGT PFE . G 6 SO4 A 1 405 1 SO4 SO4 . H 6 SO4 A 1 406 2 SO4 SO4 . I 6 SO4 A 1 407 4 SO4 SO4 . J 6 SO4 A 1 408 5 SO4 SO4 . K 2 ADP B 1 401 401 ADP ADP . L 3 MG B 1 402 402 MG MG . M 5 XGT B 1 403 404 XGT PFE . N 6 SO4 B 1 404 6 SO4 SO4 . O 7 HOH A 1 501 2 HOH HOH . O 7 HOH A 2 502 5 HOH HOH . O 7 HOH A 3 503 1 HOH HOH . O 7 HOH A 4 504 11 HOH HOH . O 7 HOH A 5 505 8 HOH HOH . O 7 HOH A 6 506 10 HOH HOH . O 7 HOH A 7 507 6 HOH HOH . O 7 HOH A 8 508 3 HOH HOH . O 7 HOH A 9 509 7 HOH HOH . O 7 HOH A 10 510 4 HOH HOH . O 7 HOH A 11 511 12 HOH HOH . P 7 HOH B 1 501 9 HOH HOH . # 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 . . . C 2 28.434 -39.815 31.176 1 79.32 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . C 2 28.013 -38.869 30.068 1 79.36 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . C 2 28.475 -39.163 32.542 1 78.7 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . C 2 29.705 -40.569 30.83 1 79.99 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . C 2 27.147 -42.5 31.434 1 77.3 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . C 2 28.292 -43.131 30.743 1 76.7 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . C 2 25.768 -42.915 31.083 1 77.4 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . C 2 27.267 -40.913 31.284 1 78.32 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . C 2 27.305 -42.682 33.011 1 77.2 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . C 2 26.399 -42.047 33.936 1 76.67 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . C 2 27.092 -41.965 35.272 1 76.12 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . C 2 27.426 -43.295 35.719 1 75.67 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . C 2 28.426 -41.239 35.243 1 76.29 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . C 2 28.275 -39.825 35.289 1 76.6 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . C 2 29.131 -41.808 36.473 1 76.4 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . C 2 28.831 -41.095 37.665 1 77.21 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . C 2 28.575 -43.24 36.543 1 75.7 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . C 2 29.52 -44.262 36.103 1 75 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . C 2 29.583 -44.882 34.883 1 74.54 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . C 2 30.588 -45.713 34.758 1 74.32 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . C 2 31.232 -45.637 35.984 1 74.21 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . C 2 32.371 -46.282 36.501 1 74.11 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . C 2 33.117 -47.136 35.805 1 74.35 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . C 2 32.739 -45.992 37.768 1 74.15 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . C 2 32.018 -45.108 38.461 1 74.43 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . C 2 30.929 -44.437 38.08 1 74.7 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . C 2 30.585 -44.748 36.822 1 74.68 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #