data_8GIY
#
_model_server_result.job_id            uWt9nxs-S8MHjaq1bvPI-A 
_model_server_result.datetime_utc      '2024-11-05 12:41:30' 
_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          8giy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":501}' 
#
_entry.id    8GIY 
#
_exptl.entry_id    8GIY 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    3 
_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            8GIY 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8GIY 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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
? 6 I N N 
? 6 L N N 
? 6 O 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
metalc ? metalc1 B OG1 THR 52 B THR 52 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc2 B SG CYS 64 B CYS 64 1_555 K ZN ZN . B ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc3 B SG CYS 73 B CYS 73 1_555 K ZN ZN . B ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc4 B SG CYS 76 B CYS 76 1_555 K ZN ZN . B ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc5 B SG CYS 79 B CYS 79 1_555 K ZN ZN . B ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc6 I O2G AGS . B AGS 501 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc7 I O3G AGS . B AGS 501 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? 
metalc ? metalc8 I O2B AGS . B AGS 501 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc9 C OG1 THR 52 C THR 52 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc10 C SG CYS 64 C CYS 64 1_555 N ZN ZN . C ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc11 C SG CYS 73 C CYS 73 1_555 N ZN ZN . C ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc12 C SG CYS 76 C CYS 76 1_555 N ZN ZN . C ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc13 C SG CYS 79 C CYS 79 1_555 N ZN ZN . C ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc14 L O2G AGS . C AGS 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc15 L O2B AGS . C AGS 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc16 D OG1 THR 52 D THR 52 1_555 P MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc17 D SG CYS 64 D CYS 64 1_555 Q ZN ZN . D ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc18 D SG CYS 73 D CYS 73 1_555 Q ZN ZN . D ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc19 D SG CYS 76 D CYS 76 1_555 Q ZN ZN . D ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc20 D SG CYS 79 D CYS 79 1_555 Q ZN ZN . D ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc21 O O2G AGS . D AGS 501 1_555 P MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc22 O O2B AGS . D AGS 501 1_555 P MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc23 E SG CYS 50 E CYS 50 1_555 R ZN ZN . E ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc24 E SG CYS 59 E CYS 59 1_555 R ZN ZN . E ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc25 E SG CYS 62 E CYS 62 1_555 R ZN ZN . E ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc26 E SG CYS 65 E CYS 65 1_555 R ZN ZN . E ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
#
_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                     8GIY 
_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
I 6 AGS B 1 501 1000 AGS AGS . 
J 7 MG B 1 502 1001 MG MG . 
K 8 ZN B 1 503 2001 ZN ZN . 
L 6 AGS C 1 501 1000 AGS AGS . 
M 7 MG C 1 502 1001 MG MG . 
N 8 ZN C 1 503 2001 ZN ZN . 
O 6 AGS D 1 501 1000 AGS AGS . 
P 7 MG D 1 502 1001 MG MG . 
Q 8 ZN D 1 503 2001 ZN ZN . 
R 8 ZN E 1 2001 2001 ZN ZN . 
#
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 . . . O 6 155.203 162.532 168.492 1 273.36 ? PG AGS 501 D 1 
HETATM 2 S S1G AGS . . . O 6 153.398 161.851 168.767 1 273.36 ? S1G AGS 501 D 1 
HETATM 3 O O2G AGS . . . O 6 155.276 163.288 167.132 1 273.36 ? O2G AGS 501 D 1 
HETATM 4 O O3G AGS . . . O 6 156.201 161.338 168.455 1 273.36 ? O3G AGS 501 D 1 
HETATM 5 P PB AGS . . . O 6 157.103 163.775 169.992 1 273.36 ? PB AGS 501 D 1 
HETATM 6 O O1B AGS . . . O 6 157.749 162.646 170.703 1 273.36 ? O1B AGS 501 D 1 
HETATM 7 O O2B AGS . . . O 6 157.739 164.074 168.634 1 273.36 ? O2B AGS 501 D 1 
HETATM 8 O O3B AGS . . . O 6 155.581 163.472 169.678 1 273.36 ? O3B AGS 501 D 1 
HETATM 9 P PA AGS . . . O 6 156.836 166.493 170.115 1 273.36 ? PA AGS 501 D 1 
HETATM 10 O O1A AGS . . . O 6 158.034 167.202 169.608 1 273.36 ? O1A AGS 501 D 1 
HETATM 11 O O2A AGS . . . O 6 155.796 166.183 169.033 1 273.36 ? O2A AGS 501 D 1 
HETATM 12 O O3A AGS . . . O 6 157.225 165.118 170.815 1 273.36 ? O3A AGS 501 D 1 
HETATM 13 O O5' AGS . . . O 6 156.214 167.37 171.275 1 273.36 ? O5' AGS 501 D 1 
HETATM 14 C C5' AGS . . . O 6 154.897 167.953 171.155 1 273.36 ? C5' AGS 501 D 1 
HETATM 15 C C4' AGS . . . O 6 154.802 169.151 172.064 1 273.36 ? C4' AGS 501 D 1 
HETATM 16 O O4' AGS . . . O 6 154.858 168.712 173.439 1 273.36 ? O4' AGS 501 D 1 
HETATM 17 C C3' AGS . . . O 6 155.93 170.167 171.905 1 273.36 ? C3' AGS 501 D 1 
HETATM 18 O O3' AGS . . . O 6 155.599 171.162 170.942 1 273.36 ? O3' AGS 501 D 1 
HETATM 19 C C2' AGS . . . O 6 156.057 170.747 173.313 1 273.36 ? C2' AGS 501 D 1 
HETATM 20 O O2' AGS . . . O 6 155.107 171.779 173.556 1 273.36 ? O2' AGS 501 D 1 
HETATM 21 C C1' AGS . . . O 6 155.757 169.52 174.177 1 273.36 ? C1' AGS 501 D 1 
HETATM 22 N N9 AGS . . . O 6 156.927 168.714 174.507 1 273.36 ? N9 AGS 501 D 1 
HETATM 23 C C8 AGS . . . O 6 157.102 167.376 174.269 1 273.36 ? C8 AGS 501 D 1 
HETATM 24 N N7 AGS . . . O 6 158.257 166.907 174.674 1 273.36 ? N7 AGS 501 D 1 
HETATM 25 C C5 AGS . . . O 6 158.889 168.016 175.216 1 273.36 ? C5 AGS 501 D 1 
HETATM 26 C C6 AGS . . . O 6 160.151 168.19 175.818 1 273.36 ? C6 AGS 501 D 1 
HETATM 27 N N6 AGS . . . O 6 161.037 167.205 175.981 1 273.36 ? N6 AGS 501 D 1 
HETATM 28 N N1 AGS . . . O 6 160.473 169.429 176.253 1 273.36 ? N1 AGS 501 D 1 
HETATM 29 C C2 AGS . . . O 6 159.588 170.418 176.093 1 273.36 ? C2 AGS 501 D 1 
HETATM 30 N N3 AGS . . . O 6 158.373 170.373 175.542 1 273.36 ? N3 AGS 501 D 1 
HETATM 31 C C4 AGS . . . O 6 158.081 169.137 175.12 1 273.36 ? C4 AGS 501 D 1 
HETATM 32 H "H5'1" AGS . . . O 6 154.222 167.302 171.414 1 273.36 ? "H5'1" AGS 501 D 1 
HETATM 33 H "H5'2" AGS . . . O 6 154.746 168.24 170.238 1 273.36 ? "H5'2" AGS 501 D 1 
HETATM 34 H H4' AGS . . . O 6 153.952 169.593 171.909 1 273.36 ? H4' AGS 501 D 1 
HETATM 35 H H3' AGS . . . O 6 156.752 169.714 171.655 1 273.36 ? H3' AGS 501 D 1 
HETATM 36 H HO3' AGS . . . O 6 155.375 170.772 170.177 1 273.36 ? HO3' AGS 501 D 1 
HETATM 37 H H2' AGS . . . O 6 156.959 171.071 173.469 1 273.36 ? H2' AGS 501 D 1 
HETATM 38 H HO2' AGS . . . O 6 154.409 171.68 173.017 1 273.36 ? HO2' AGS 501 D 1 
HETATM 39 H H1' AGS . . . O 6 155.328 169.811 175 1 273.36 ? H1' AGS 501 D 1 
HETATM 40 H H8 AGS . . . O 6 156.431 166.823 173.841 1 273.36 ? H8 AGS 501 D 1 
HETATM 41 H HN61 AGS . . . O 6 160.853 166.371 175.671 1 273.36 ? HN61 AGS 501 D 1 
HETATM 42 H HN62 AGS . . . O 6 161.825 167.367 176.405 1 273.36 ? HN62 AGS 501 D 1 
HETATM 43 H H2 AGS . . . O 6 159.868 171.289 176.423 1 273.36 ? H2 AGS 501 D 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    133 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#