data_8XAY # _model_server_result.job_id AMYcr2Rywl5oLxI8jKlGZg _model_server_result.datetime_utc '2025-03-07 00:20:47' _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 8xay # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":601}' # _entry.id 8XAY # _exptl.entry_id 8XAY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 4 _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 8XAY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XAY _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 20-meric _pdbx_struct_assembly.oligomeric_count 20 _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 _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 ? 5 U N N ? 5 W N N ? 5 Y N N ? 5 AA 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 B NE2 GLN 466 B GLN 466 1_555 W O3G AGS . B AGS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.304 ? covale ? covale2 W S1G AGS . B AGS 601 1_555 C NH1 ARG 455 C ARG 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.629 ? covale ? covale3 E CA GLY 156 E GLY 156 1_555 CA O1A ADP . E ADP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? metalc ? metalc1 A OG SER 158 A SER 158 1_555 V MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc2 A OE2 GLU 192 A GLU 192 1_555 V MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc3 U O2G AGS . A AGS 601 1_555 V MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc4 U O2B AGS . A AGS 601 1_555 V MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc5 B OG SER 158 B SER 158 1_555 X MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc6 W O2G AGS . B AGS 601 1_555 X MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc7 W O2B AGS . B AGS 601 1_555 X MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc8 C OG SER 158 C SER 158 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc9 Y O2G AGS . C AGS 601 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc10 Y O2B AGS . C AGS 601 1_555 Z MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc11 D OG SER 158 D SER 158 1_555 BA MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc12 AA O2G AGS . D AGS 601 1_555 BA MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc13 AA O2B AGS . D AGS 601 1_555 BA MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc14 E OG SER 158 E SER 158 1_555 DA MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc15 E OE2 GLU 192 E GLU 192 1_555 DA MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc16 CA O2B ADP . E ADP 601 1_555 DA MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc17 F OG SER 158 F SER 158 1_555 FA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc18 EA O2B ADP . F ADP 601 1_555 FA MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? hydrog 'DG-DC PAIR' hydrog1 S N2 DG 1 S DG 1 1_555 T O2 DC 59 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 S N3 DC 2 S DC 2 1_555 T N1 DG 58 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 S N4 DC 2 S DC 2 1_555 T O6 DG 58 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 S O2 DC 2 S DC 2 1_555 T N2 DG 58 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 S N3 DT 3 S DT 3 1_555 T N1 DA 57 T DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 S O4 DT 3 S DT 3 1_555 T N6 DA 57 T DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 S N3 DT 4 S DT 4 1_555 T N1 DA 56 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 S O4 DT 4 S DT 4 1_555 T N6 DA 56 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 S N3 DT 5 S DT 5 1_555 T N1 DA 55 T DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 S O4 DT 5 S DT 5 1_555 T N6 DA 55 T DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 S N1 DA 6 S DA 6 1_555 T N3 DT 54 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 S N6 DA 6 S DA 6 1_555 T O4 DT 54 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 S N3 DT 7 S DT 7 1_555 T N1 DA 53 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 S O4 DT 7 S DT 7 1_555 T N6 DA 53 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog15 S N3 DC 8 S DC 8 1_555 T N2 DG 52 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog16 S O2 DC 8 S DC 8 1_555 T N1 DG 52 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DC MISPAIR' hydrog17 S N1 DA 9 S DA 9 1_555 T N4 DC 50 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog18 S N1 DG 10 S DG 10 1_555 T O2 DC 50 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog19 S N2 DG 10 S DG 10 1_555 T N3 DC 50 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 S N1 DA 11 S DA 11 1_555 T N3 DT 49 T DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 S N6 DA 11 S DA 11 1_555 T O4 DT 49 T DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 S N1 DA 12 S DA 12 1_555 T N3 DT 48 T DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 S N6 DA 12 S DA 12 1_555 T O4 DT 48 T DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog24 S N1 DG 13 S DG 13 1_555 T O2 DC 47 T DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog25 S N2 DG 13 S DG 13 1_555 T N3 DC 47 T DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 PG S1G AGS doub 45 n n PG O2G AGS sing 46 n n PG O3G AGS sing 47 n n PG O3B AGS sing 48 n n PB O1B AGS doub 49 n n PB O2B AGS sing 50 n n PB O3B AGS sing 51 n n PB O3A AGS sing 52 n n PA O1A AGS doub 53 n n PA O2A AGS sing 54 n n PA O3A AGS sing 55 n n PA O5' AGS sing 56 n n O5' C5' AGS sing 57 n n C5' C4' AGS sing 58 n n C4' O4' AGS sing 59 n n C4' C3' AGS sing 60 n n O4' C1' AGS sing 61 n n C3' O3' AGS sing 62 n n C3' C2' AGS sing 63 n n C2' O2' AGS sing 64 n n C2' C1' AGS sing 65 n n C1' N9 AGS sing 66 n n N9 C8 AGS sing 67 n y N9 C4 AGS sing 68 n y C8 N7 AGS doub 69 n y N7 C5 AGS sing 70 n y C5 C6 AGS sing 71 n y C5 C4 AGS doub 72 n y C6 N6 AGS sing 73 n n C6 N1 AGS doub 74 n y N1 C2 AGS sing 75 n y C2 N3 AGS doub 76 n y N3 C4 AGS sing 77 n y O2G HOG2 AGS sing 78 n n O3G H21 AGS sing 79 n n O2B HOB2 AGS sing 80 n n O2A HOA2 AGS sing 81 n n C5' "H5'1" AGS sing 82 n n C5' "H5'2" AGS sing 83 n n C4' H4' AGS sing 84 n n C3' H3' AGS sing 85 n n O3' HO3' AGS sing 86 n n C2' H2' AGS sing 87 n n O2' HO2' AGS sing 88 n n C1' H1' AGS sing 89 n n C8 H8 AGS sing 90 n n N6 HN61 AGS sing 91 n n N6 HN62 AGS sing 92 n n C2 H2 AGS sing 93 n n # _atom_sites.entry_id 8XAY _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 U 5 AGS A 1 601 601 AGS AGS . V 6 MG A 1 602 701 MG MG . W 5 AGS B 1 601 601 AGS AGS . X 6 MG B 1 602 701 MG MG . Y 5 AGS C 1 601 601 AGS AGS . Z 6 MG C 1 602 701 MG MG . AA 5 AGS D 1 601 601 AGS AGS . BA 6 MG D 1 602 701 MG MG . CA 7 ADP E 1 601 601 ADP ADP . DA 6 MG E 1 602 701 MG MG . EA 7 ADP F 1 601 601 ADP ADP . FA 6 MG F 1 602 701 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 PG AGS . . . W 5 171.623 175.414 177.226 1 5.85 ? PG AGS 601 B 1 HETATM 2 S S1G AGS . . . W 5 173.563 175.349 177.39 1 0 ? S1G AGS 601 B 1 HETATM 3 O O2G AGS . . . W 5 171.071 176.531 178.156 1 11.49 ? O2G AGS 601 B 1 HETATM 4 O O3G AGS . . . W 5 171.014 174.046 177.667 1 14.07 ? O3G AGS 601 B 1 HETATM 5 P PB AGS . . . W 5 170.934 177.217 175.247 1 5.53 ? PB AGS 601 B 1 HETATM 6 O O1B AGS . . . W 5 169.67 177.223 174.491 1 0.81 ? O1B AGS 601 B 1 HETATM 7 O O2B AGS . . . W 5 170.899 178.112 176.49 1 1.4 ? O2B AGS 601 B 1 HETATM 8 O O3B AGS . . . W 5 171.257 175.737 175.741 1 7.76 ? O3B AGS 601 B 1 HETATM 9 P PA AGS . . . W 5 172.233 179.338 174.141 1 0 ? PA AGS 601 B 1 HETATM 10 O O1A AGS . . . W 5 170.935 180.02 174.175 1 0 ? O1A AGS 601 B 1 HETATM 11 O O2A AGS . . . W 5 173.192 179.819 175.226 1 13.73 ? O2A AGS 601 B 1 HETATM 12 O O3A AGS . . . W 5 172.1 177.778 174.337 1 6.94 ? O3A AGS 601 B 1 HETATM 13 O O5' AGS . . . W 5 172.876 179.516 172.722 1 2.43 ? O5' AGS 601 B 1 HETATM 14 C C5' AGS . . . W 5 174.296 179.347 172.521 1 3.88 ? C5' AGS 601 B 1 HETATM 15 C C4' AGS . . . W 5 174.729 180.252 171.399 1 3.47 ? C4' AGS 601 B 1 HETATM 16 O O4' AGS . . . W 5 173.662 180.368 170.448 1 5.42 ? O4' AGS 601 B 1 HETATM 17 C C3' AGS . . . W 5 175.046 181.686 171.813 1 7.37 ? C3' AGS 601 B 1 HETATM 18 O O3' AGS . . . W 5 176.44 181.832 172.051 1 12.9 ? O3' AGS 601 B 1 HETATM 19 C C2' AGS . . . W 5 174.586 182.534 170.613 1 6.92 ? C2' AGS 601 B 1 HETATM 20 O O2' AGS . . . W 5 175.676 183.173 169.96 1 7.69 ? O2' AGS 601 B 1 HETATM 21 C C1' AGS . . . W 5 173.907 181.523 169.681 1 4.07 ? C1' AGS 601 B 1 HETATM 22 N N9 AGS . . . W 5 172.642 181.989 169.133 1 3.99 ? N9 AGS 601 B 1 HETATM 23 C C8 AGS . . . W 5 171.424 182.01 169.76 1 4.39 ? C8 AGS 601 B 1 HETATM 24 N N7 AGS . . . W 5 170.454 182.495 169.026 1 8.87 ? N7 AGS 601 B 1 HETATM 25 C C5 AGS . . . W 5 171.077 182.82 167.83 1 6 ? C5 AGS 601 B 1 HETATM 26 C C6 AGS . . . W 5 170.597 183.378 166.631 1 5.96 ? C6 AGS 601 B 1 HETATM 27 N N6 AGS . . . W 5 169.323 183.721 166.43 1 2.65 ? N6 AGS 601 B 1 HETATM 28 N N1 AGS . . . W 5 171.484 183.569 165.629 1 8.96 ? N1 AGS 601 B 1 HETATM 29 C C2 AGS . . . W 5 172.759 183.223 165.824 1 6.43 ? C2 AGS 601 B 1 HETATM 30 N N3 AGS . . . W 5 173.327 182.693 166.91 1 7.14 ? N3 AGS 601 B 1 HETATM 31 C C4 AGS . . . W 5 172.425 182.514 167.885 1 5.18 ? C4 AGS 601 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 365 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #