data_8ARP # _model_server_result.job_id gwGjFYepCpIp8O-l5zyBlA _model_server_result.datetime_utc '2025-02-05 18:01:10' _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 8arp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":2001}' # _entry.id 8ARP # _exptl.entry_id 8ARP _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 6 _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 8ARP _cell.length_a 145.939 _cell.length_b 168.843 _cell.length_c 168.87 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ARP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 G N N ? 2 J N N ? 2 L N N ? 2 O N N ? 2 Q N N ? 2 V 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 N GLY 160 A GLY 160 1_555 G O1B ADP . A ADP 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? covale ? covale2 B N GLY 160 B GLY 160 1_555 J O3B ADP . B ADP 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.294 ? covale ? covale3 D CZ ARG 422 D ARG 422 1_555 O O2A ADP . D ADP 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale4 D NH1 ARG 422 D ARG 422 1_555 O O2A ADP . D ADP 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.259 ? covale ? covale5 E NZ LYS 163 E LYS 163 1_555 Q O2B ADP . E ADP 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? metalc ? metalc1 A OG1 THR 164 A THR 164 1_555 I MG MG . A MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc2 A OD2 ASP 267 A ASP 267 1_555 I MG MG . A MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc3 G O2B ADP . A ADP 2001 1_555 I MG MG . A MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc4 C OE2 GLU 268 C GLU 268 1_555 N MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc5 L O1B ADP . C ADP 2001 1_555 N MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc6 L O2B ADP . C ADP 2001 1_555 N MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc7 E OD2 ASP 267 E ASP 267 1_555 U MG MG . E MG 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? # _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 8ARP _atom_sites.fract_transf_matrix[1][1] 0.006852 _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] 0.005923 _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] 0.005922 _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 ADP A 1 2001 2001 ADP ADP . H 3 SO4 A 1 2002 1 SO4 SO4 . I 4 MG A 1 2003 1 MG MG . J 2 ADP B 1 2001 2001 ADP ADP . K 3 SO4 B 1 2002 2 SO4 SO4 . L 2 ADP C 1 2001 2001 ADP ADP . M 3 SO4 C 1 2002 5 SO4 SO4 . N 4 MG C 1 2003 2 MG MG . O 2 ADP D 1 2001 2001 ADP ADP . P 3 SO4 D 1 2002 4 SO4 SO4 . Q 2 ADP E 1 2001 2001 ADP ADP . R 3 SO4 E 1 2002 3 SO4 SO4 . S 3 SO4 E 1 2003 7 SO4 SO4 . T 3 SO4 E 1 2004 8 SO4 SO4 . U 4 MG E 1 2005 3 MG MG . V 2 ADP F 1 2001 2001 ADP ADP . W 3 SO4 F 1 2002 6 SO4 SO4 . # 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 . . . V 2 -11.708 -32.373 -16.878 1 71.13 ? PB ADP 2001 F 1 HETATM 2 O O1B ADP . . . V 2 -11.441 -32.958 -18.243 1 80.08 ? O1B ADP 2001 F 1 HETATM 3 O O2B ADP . . . V 2 -11.824 -30.868 -16.86 1 86.16 -1 O2B ADP 2001 F 1 HETATM 4 O O3B ADP . . . V 2 -10.885 -32.97 -15.763 1 70.05 ? O3B ADP 2001 F 1 HETATM 5 P PA ADP . . . V 2 -13.401 -34.097 -15.512 1 66.19 ? PA ADP 2001 F 1 HETATM 6 O O1A ADP . . . V 2 -12.456 -35.216 -15.871 1 67.55 -1 O1A ADP 2001 F 1 HETATM 7 O O2A ADP . . . V 2 -13.408 -33.518 -14.118 1 86.01 ? O2A ADP 2001 F 1 HETATM 8 O O3A ADP . . . V 2 -13.189 -32.899 -16.563 1 86.86 ? O3A ADP 2001 F 1 HETATM 9 O O5' ADP . . . V 2 -14.867 -34.623 -15.881 1 64.8 ? O5' ADP 2001 F 1 HETATM 10 C C5' ADP . . . V 2 -15.276 -35.869 -15.347 1 74.09 ? C5' ADP 2001 F 1 HETATM 11 C C4' ADP . . . V 2 -16.78 -36.023 -15.47 1 75.94 ? C4' ADP 2001 F 1 HETATM 12 O O4' ADP . . . V 2 -17.056 -36.797 -16.636 1 62.69 ? O4' ADP 2001 F 1 HETATM 13 C C3' ADP . . . V 2 -17.257 -36.824 -14.281 1 79.62 ? C3' ADP 2001 F 1 HETATM 14 O O3' ADP . . . V 2 -18.602 -36.452 -13.973 1 79.97 ? O3' ADP 2001 F 1 HETATM 15 C C2' ADP . . . V 2 -17.232 -38.246 -14.782 1 73.04 ? C2' ADP 2001 F 1 HETATM 16 O O2' ADP . . . V 2 -18.251 -38.999 -14.123 1 83.08 ? O2' ADP 2001 F 1 HETATM 17 C C1' ADP . . . V 2 -17.507 -38.099 -16.269 1 65.72 ? C1' ADP 2001 F 1 HETATM 18 N N9 ADP . . . V 2 -16.769 -39.11 -17.065 1 74.91 ? N9 ADP 2001 F 1 HETATM 19 C C8 ADP . . . V 2 -15.432 -39.216 -17.171 1 77.96 ? C8 ADP 2001 F 1 HETATM 20 N N7 ADP . . . V 2 -15.089 -40.247 -17.986 1 80.6 ? N7 ADP 2001 F 1 HETATM 21 C C5 ADP . . . V 2 -16.224 -40.824 -18.42 1 77.15 ? C5 ADP 2001 F 1 HETATM 22 C C6 ADP . . . V 2 -16.584 -41.96 -19.306 1 70.23 ? C6 ADP 2001 F 1 HETATM 23 N N6 ADP . . . V 2 -15.641 -42.717 -19.916 1 72.8 ? N6 ADP 2001 F 1 HETATM 24 N N1 ADP . . . V 2 -17.896 -42.217 -19.489 1 68.71 ? N1 ADP 2001 F 1 HETATM 25 C C2 ADP . . . V 2 -18.85 -41.479 -18.894 1 82.58 ? C2 ADP 2001 F 1 HETATM 26 N N3 ADP . . . V 2 -18.597 -40.439 -18.081 1 86.64 ? N3 ADP 2001 F 1 HETATM 27 C C4 ADP . . . V 2 -17.326 -40.068 -17.808 1 80.03 ? C4 ADP 2001 F 1 # _model_server_stats.io_time_ms 90 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 435 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #