data_8ARP # _model_server_result.job_id KjohxM2KhCZh5dQKm7TySw _model_server_result.datetime_utc '2025-02-05 17:50:51' _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":"J","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 . . . J 2 -14.773 -21.548 63.86 1 133.35 ? PB ADP 2001 B 1 HETATM 2 O O1B ADP . . . J 2 -15.863 -22.205 63.021 1 122.58 ? O1B ADP 2001 B 1 HETATM 3 O O2B ADP . . . J 2 -13.896 -22.476 64.709 1 125.87 -1 O2B ADP 2001 B 1 HETATM 4 O O3B ADP . . . J 2 -15.3 -20.408 64.657 1 146.37 ? O3B ADP 2001 B 1 HETATM 5 P PA ADP . . . J 2 -12.286 -20.502 63.242 1 112.54 ? PA ADP 2001 B 1 HETATM 6 O O1A ADP . . . J 2 -12.47 -19.131 63.834 1 117.07 -1 O1A ADP 2001 B 1 HETATM 7 O O2A ADP . . . J 2 -11.619 -21.657 63.956 1 118.91 ? O2A ADP 2001 B 1 HETATM 8 O O3A ADP . . . J 2 -13.779 -20.864 62.776 1 126.82 ? O3A ADP 2001 B 1 HETATM 9 O O5' ADP . . . J 2 -11.394 -20.342 61.926 1 103.53 ? O5' ADP 2001 B 1 HETATM 10 C C5' ADP . . . J 2 -9.987 -20.351 62.162 1 101.42 ? C5' ADP 2001 B 1 HETATM 11 C C4' ADP . . . J 2 -9.518 -18.956 62.54 1 100.35 ? C4' ADP 2001 B 1 HETATM 12 O O4' ADP . . . J 2 -9.094 -18.925 63.904 1 95.76 ? O4' ADP 2001 B 1 HETATM 13 C C3' ADP . . . J 2 -8.329 -18.603 61.675 1 90.95 ? C3' ADP 2001 B 1 HETATM 14 O O3' ADP . . . J 2 -8.579 -17.34 61.055 1 76.97 ? O3' ADP 2001 B 1 HETATM 15 C C2' ADP . . . J 2 -7.146 -18.502 62.613 1 105.04 ? C2' ADP 2001 B 1 HETATM 16 O O2' ADP . . . J 2 -6.453 -17.276 62.366 1 108.16 ? O2' ADP 2001 B 1 HETATM 17 C C1' ADP . . . J 2 -7.733 -18.506 64.015 1 101.69 ? C1' ADP 2001 B 1 HETATM 18 N N9 ADP . . . J 2 -7.023 -19.471 64.892 1 111.68 ? N9 ADP 2001 B 1 HETATM 19 C C8 ADP . . . J 2 -7.273 -20.792 64.962 1 102.24 ? C8 ADP 2001 B 1 HETATM 20 N N7 ADP . . . J 2 -6.464 -21.399 65.867 1 98.22 ? N7 ADP 2001 B 1 HETATM 21 C C5 ADP . . . J 2 -5.672 -20.452 66.399 1 101.41 ? C5 ADP 2001 B 1 HETATM 22 C C6 ADP . . . J 2 -4.591 -20.411 67.412 1 117.24 ? C6 ADP 2001 B 1 HETATM 23 N N6 ADP . . . J 2 -4.179 -21.53 68.058 1 123.61 ? N6 ADP 2001 B 1 HETATM 24 N N1 ADP . . . J 2 -4.031 -19.209 67.669 1 130.2 ? N1 ADP 2001 B 1 HETATM 25 C C2 ADP . . . J 2 -4.428 -18.087 67.038 1 111.17 ? C2 ADP 2001 B 1 HETATM 26 N N3 ADP . . . J 2 -5.397 -18.051 66.11 1 98.04 ? N3 ADP 2001 B 1 HETATM 27 C C4 ADP . . . J 2 -6.046 -19.182 65.754 1 104.23 ? C4 ADP 2001 B 1 # _model_server_stats.io_time_ms 283 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 63 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #