data_8DGS
#
_model_server_result.job_id            juEHthYpLYubOkDs1GhMSA 
_model_server_result.datetime_utc      '2025-02-05 04:41:46' 
_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          8dgs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":801}' 
#
_entry.id    8DGS 
#
_exptl.entry_id    8DGS 
_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            8DGS 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DGS 
_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 I 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 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale3 A C ALA 755 A ALA 728 1_555 A N SEP 756 A SEP 729 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale4 A C SEP 756 A SEP 729 1_555 A N GLU 757 A GLU 730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? 
metalc ? metalc1 A ND1 HIS 262 A HIS 235 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? 
metalc ? metalc2 A SG CYS 275 A CYS 248 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc3 A SG CYS 278 A CYS 251 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc4 A SG CYS 288 A CYS 261 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc5 A SG CYS 291 A CYS 264 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc6 A ND1 HIS 296 A HIS 269 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
metalc ? metalc7 A SG CYS 299 A CYS 272 1_555 G ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc8 A SG CYS 307 A CYS 280 1_555 H ZN ZN . A ZN 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc9 I O2G AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc10 I O3B AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? 
metalc ? metalc11 I O1A AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc12 I O2A AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc13 I O3A AGS . B AGS 801 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? 
metalc ? metalc14 J MG MG . B MG 802 1_555 K O05 LCJ . B LCJ 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc15 E OG SER 39 E SER 17 1_555 L MG MG . E MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc16 E OG1 THR 57 E THR 35 1_555 L MG MG . E MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc17 L MG MG . E MG 201 1_555 M O2G GNP . E GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc18 L MG MG . E MG 201 1_555 M O2B GNP . E GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_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                     8DGS 
_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 5 AGS B 1 801 801 AGS AGS . 
J 7 MG B 1 802 802 MG MG . 
K 8 LCJ B 1 803 803 LCJ LCJ . 
L 7 MG E 1 201 201 MG MG . 
M 9 GNP E 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 . . . I 5 122.781 138.475 158.747 1 245.32 ? PG AGS 801 B 1 
HETATM 2 S S1G AGS . . . I 5 124.699 138.541 158.415 1 245.32 ? S1G AGS 801 B 1 
HETATM 3 O O2G AGS . . . I 5 122.505 138.017 160.208 1 245.32 ? O2G AGS 801 B 1 
HETATM 4 O O3G AGS . . . I 5 122.117 137.473 157.758 1 245.32 ? O3G AGS 801 B 1 
HETATM 5 P PB AGS . . . I 5 122.807 141.119 159.275 1 245.32 ? PB AGS 801 B 1 
HETATM 6 O O1B AGS . . . I 5 123.536 140.675 160.482 1 245.32 ? O1B AGS 801 B 1 
HETATM 7 O O2B AGS . . . I 5 123.678 141.843 158.245 1 245.32 ? O2B AGS 801 B 1 
HETATM 8 O O3B AGS . . . I 5 122.17 139.885 158.533 1 245.32 ? O3B AGS 801 B 1 
HETATM 9 P PA AGS . . . I 5 120.492 141.591 160.617 1 245.32 ? PA AGS 801 B 1 
HETATM 10 O O1A AGS . . . I 5 121.03 140.817 161.756 1 245.32 ? O1A AGS 801 B 1 
HETATM 11 O O2A AGS . . . I 5 119.504 140.825 159.734 1 245.32 ? O2A AGS 801 B 1 
HETATM 12 O O3A AGS . . . I 5 121.652 142.111 159.678 1 245.32 ? O3A AGS 801 B 1 
HETATM 13 O O5' AGS . . . I 5 119.869 142.923 161.185 1 245.32 ? O5' AGS 801 B 1 
HETATM 14 C C5' AGS . . . I 5 120.539 144.177 160.955 1 245.32 ? C5' AGS 801 B 1 
HETATM 15 C C4' AGS . . . I 5 121.024 144.714 162.277 1 245.32 ? C4' AGS 801 B 1 
HETATM 16 O O4' AGS . . . I 5 119.89 145.019 163.114 1 245.32 ? O4' AGS 801 B 1 
HETATM 17 C C3' AGS . . . I 5 121.876 143.753 163.097 1 245.32 ? C3' AGS 801 B 1 
HETATM 18 O O3' AGS . . . I 5 123.245 143.841 162.724 1 245.32 ? O3' AGS 801 B 1 
HETATM 19 C C2' AGS . . . I 5 121.64 144.248 164.524 1 245.32 ? C2' AGS 801 B 1 
HETATM 20 O O2' AGS . . . I 5 122.486 145.344 164.851 1 245.32 ? O2' AGS 801 B 1 
HETATM 21 C C1' AGS . . . I 5 120.177 144.699 164.464 1 245.32 ? C1' AGS 801 B 1 
HETATM 22 N N9 AGS . . . I 5 119.23 143.683 164.905 1 245.32 ? N9 AGS 801 B 1 
HETATM 23 C C8 AGS . . . I 5 118.826 142.571 164.216 1 245.32 ? C8 AGS 801 B 1 
HETATM 24 N N7 AGS . . . I 5 117.961 141.826 164.862 1 245.32 ? N7 AGS 801 B 1 
HETATM 25 C C5 AGS . . . I 5 117.782 142.499 166.06 1 245.32 ? C5 AGS 801 B 1 
HETATM 26 C C6 AGS . . . I 5 116.985 142.227 167.19 1 245.32 ? C6 AGS 801 B 1 
HETATM 27 N N6 AGS . . . I 5 116.19 141.161 167.299 1 245.32 ? N6 AGS 801 B 1 
HETATM 28 N N1 AGS . . . I 5 117.04 143.101 168.221 1 245.32 ? N1 AGS 801 B 1 
HETATM 29 C C2 AGS . . . I 5 117.837 144.168 168.119 1 245.32 ? C2 AGS 801 B 1 
HETATM 30 N N3 AGS . . . I 5 118.632 144.526 167.107 1 245.32 ? N3 AGS 801 B 1 
HETATM 31 C C4 AGS . . . I 5 118.558 143.644 166.103 1 245.32 ? C4 AGS 801 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           705 
_model_server_stats.encode_time_ms          28 
_model_server_stats.element_count           31 
#