data_8DGT
#
_model_server_result.job_id            dakxmZYYm0_7PmsuwtCSTQ 
_model_server_result.datetime_utc      '2025-07-07 23:16:16' 
_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          8dgt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":801}' 
#
_entry.id    8DGT 
#
_exptl.entry_id    8DGT 
_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    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            8DGT 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DGT 
_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    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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 
_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
? 5 F N N 
? 5 J 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
disulf ? disulf1 A SG CYS 275 A CYS 248 1_555 A SG CYS 278 A CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? 
covale ? covale1 A C SER 391 A SER 364 1_555 A N SEP 392 A SEP 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 A C SEP 392 A SEP 365 1_555 A N ALA 393 A ALA 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale3 A C ALA 755 A ALA 728 1_555 A N SEP 756 A SEP 729 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale4 A C SEP 756 A SEP 729 1_555 A N GLU 757 A GLU 730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
metalc ? metalc1 A ND1 HIS 262 A HIS 235 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc2 A SG CYS 275 A CYS 248 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc3 A SG CYS 278 A CYS 251 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? 
metalc ? metalc4 A SG CYS 288 A CYS 261 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc5 A SG CYS 291 A CYS 264 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc6 A ND1 HIS 296 A HIS 269 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc7 A SG CYS 299 A CYS 272 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc8 A SG CYS 307 A CYS 280 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc9 B OD1 ASN 217 B ASN 195 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc10 B OD2 ASP 230 B ASP 208 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc11 I MG MG . B MG 401 1_555 J O3G AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? 
metalc ? metalc12 I MG MG . B MG 401 1_555 J O3A AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc13 I MG MG . B MG 401 1_555 J O1A AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? 
metalc ? metalc14 I MG MG . B MG 401 1_555 J O5' AGS . B AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? 
metalc ? metalc15 E OG SER 39 F SER 17 1_555 L MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc16 E OG1 THR 57 F THR 35 1_555 L MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc17 L MG MG . F MG 201 1_555 M O2B GNP . F GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc18 L MG MG . F MG 201 1_555 M O2G GNP . F GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
#
_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 1 n n 
PG O2G AGS sing 2 n n 
PG O3G AGS sing 3 n n 
PG O3B AGS sing 4 n n 
PB O1B AGS doub 5 n n 
PB O2B AGS sing 6 n n 
PB O3B AGS sing 7 n n 
PB O3A AGS sing 8 n n 
PA O1A AGS doub 9 n n 
PA O2A AGS sing 10 n n 
PA O3A AGS sing 11 n n 
PA O5' AGS sing 12 n n 
O5' C5' AGS sing 13 n n 
C5' C4' AGS sing 14 n n 
C4' O4' AGS sing 15 n n 
C4' C3' AGS sing 16 n n 
O4' C1' AGS sing 17 n n 
C3' O3' AGS sing 18 n n 
C3' C2' AGS sing 19 n n 
C2' O2' AGS sing 20 n n 
C2' C1' AGS sing 21 n n 
C1' N9 AGS sing 22 n n 
N9 C8 AGS sing 23 n y 
N9 C4 AGS sing 24 n y 
C8 N7 AGS doub 25 n y 
N7 C5 AGS sing 26 n y 
C5 C6 AGS sing 27 n y 
C5 C4 AGS doub 28 n y 
C6 N6 AGS sing 29 n n 
C6 N1 AGS doub 30 n y 
N1 C2 AGS sing 31 n y 
C2 N3 AGS doub 32 n y 
N3 C4 AGS sing 33 n y 
O2G HOG2 AGS sing 34 n n 
O3G H21 AGS sing 35 n n 
O2B HOB2 AGS sing 36 n n 
O2A HOA2 AGS sing 37 n n 
C5' "H5'1" AGS sing 38 n n 
C5' "H5'2" AGS sing 39 n n 
C4' H4' AGS sing 40 n n 
C3' H3' AGS sing 41 n n 
O3' HO3' AGS sing 42 n n 
C2' H2' AGS sing 43 n n 
O2' HO2' AGS sing 44 n n 
C1' H1' AGS sing 45 n n 
C8 H8 AGS sing 46 n n 
N6 HN61 AGS sing 47 n n 
N6 HN62 AGS sing 48 n n 
C2 H2 AGS sing 49 n n 
#
_atom_sites.entry_id                     8DGT 
_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
F 5 AGS A 1 801 801 AGS AGS . 
G 6 ZN A 1 802 901 ZN ZN . 
H 6 ZN A 1 803 902 ZN ZN . 
I 7 MG B 1 401 503 MG MG . 
J 5 AGS B 1 402 607 AGS AGS . 
K 8 LCJ B 1 403 803 LCJ LCJ . 
L 7 MG F 1 201 201 MG MG . 
M 9 GNP F 1 202 202 GNP GNP . 
#
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 . . . F 5 138.535 117.372 147.008 1 92.79 ? PG AGS 801 A 1 
HETATM 2 S S1G AGS . . . F 5 137.931 119.22 147.14 1 92.79 ? S1G AGS 801 A 1 
HETATM 3 O O2G AGS . . . F 5 138.723 116.993 145.512 1 92.79 ? O2G AGS 801 A 1 
HETATM 4 O O3G AGS . . . F 5 137.468 116.447 147.653 1 92.79 ? O3G AGS 801 A 1 
HETATM 5 P PB AGS . . . F 5 141.195 117.735 147.009 1 92.79 ? PB AGS 801 A 1 
HETATM 6 O O1B AGS . . . F 5 141.066 117.496 145.556 1 92.79 ? O1B AGS 801 A 1 
HETATM 7 O O2B AGS . . . F 5 141.337 119.211 147.388 1 92.79 ? O2B AGS 801 A 1 
HETATM 8 O O3B AGS . . . F 5 139.897 117.214 147.739 1 92.79 ? O3B AGS 801 A 1 
HETATM 9 P PA AGS . . . F 5 142.456 115.432 147.679 1 92.79 ? PA AGS 801 A 1 
HETATM 10 O O1A AGS . . . F 5 142.291 114.826 146.35 1 92.79 ? O1A AGS 801 A 1 
HETATM 11 O O2A AGS . . . F 5 141.335 115.081 148.66 1 92.79 ? O2A AGS 801 A 1 
HETATM 12 O O3A AGS . . . F 5 142.478 117.007 147.569 1 92.79 ? O3A AGS 801 A 1 
HETATM 13 O O5' AGS . . . F 5 143.879 115.03 148.24 1 92.79 ? O5' AGS 801 A 1 
HETATM 14 C C5' AGS . . . F 5 144.993 115.943 148.169 1 92.79 ? C5' AGS 801 A 1 
HETATM 15 C C4' AGS . . . F 5 145.983 115.435 147.149 1 92.79 ? C4' AGS 801 A 1 
HETATM 16 O O4' AGS . . . F 5 145.545 114.165 146.64 1 92.79 ? O4' AGS 801 A 1 
HETATM 17 C C3' AGS . . . F 5 146.145 116.295 145.901 1 92.79 ? C3' AGS 801 A 1 
HETATM 18 O O3' AGS . . . F 5 147.093 117.335 146.12 1 92.79 ? O3' AGS 801 A 1 
HETATM 19 C C2' AGS . . . F 5 146.645 115.287 144.852 1 92.79 ? C2' AGS 801 A 1 
HETATM 20 O O2' AGS . . . F 5 148.061 115.317 144.723 1 92.79 ? O2' AGS 801 A 1 
HETATM 21 C C1' AGS . . . F 5 146.197 113.928 145.41 1 92.79 ? C1' AGS 801 A 1 
HETATM 22 N N9 AGS . . . F 5 145.293 113.188 144.541 1 92.79 ? N9 AGS 801 A 1 
HETATM 23 C C8 AGS . . . F 5 143.925 113.23 144.547 1 92.79 ? C8 AGS 801 A 1 
HETATM 24 N N7 AGS . . . F 5 143.36 112.451 143.654 1 92.79 ? N7 AGS 801 A 1 
HETATM 25 C C5 AGS . . . F 5 144.435 111.854 143.015 1 92.79 ? C5 AGS 801 A 1 
HETATM 26 C C6 AGS . . . F 5 144.511 110.921 141.967 1 92.79 ? C6 AGS 801 A 1 
HETATM 27 N N6 AGS . . . F 5 143.445 110.404 141.352 1 92.79 ? N6 AGS 801 A 1 
HETATM 28 N N1 AGS . . . F 5 145.742 110.531 141.566 1 92.79 ? N1 AGS 801 A 1 
HETATM 29 C C2 AGS . . . F 5 146.814 111.043 142.176 1 92.79 ? C2 AGS 801 A 1 
HETATM 30 N N3 AGS . . . F 5 146.864 111.928 143.173 1 92.79 ? N3 AGS 801 A 1 
HETATM 31 C C4 AGS . . . F 5 145.631 112.297 143.55 1 92.79 ? C4 AGS 801 A 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#