data_8H5Z
#
_model_server_result.job_id            sLg6IDO0IQA3d6A6LlT9_Q 
_model_server_result.datetime_utc      '2025-09-08 12:50:38' 
_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          8h5z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":601}' 
#
_entry.id    8H5Z 
#
_exptl.entry_id    8H5Z 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          2 
_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          99.841 
_cell.angle_gamma         90 
_cell.entry_id            8H5Z 
_cell.length_a            82.589 
_cell.length_b            79.168 
_cell.length_c            109.824 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8H5Z 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D 1 1 
B,E,F 2 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 C N N 
? 2 E 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 A SG CYS 384 B CYS 384 1_555 D ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc2 A SG CYS 387 B CYS 387 1_555 D ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc3 A SG CYS 411 B CYS 411 1_555 D ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc4 A SG CYS 425 B CYS 425 1_555 D ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc5 B SG CYS 384 A CYS 384 1_555 F ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc6 B SG CYS 387 A CYS 387 1_555 F ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc7 B SG CYS 411 A CYS 411 1_555 F ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc8 B SG CYS 425 A CYS 425 1_555 F ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
#
_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                     8H5Z 
_atom_sites.fract_transf_matrix[1][1]    0.012108 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.0021 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012631 
_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]    0.009241 
_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
C 2 AGS B 1 601 2 AGS AGS . 
D 3 ZN B 1 602 2 ZN ZN . 
E 2 AGS A 1 601 1 AGS AGS . 
F 3 ZN A 1 602 1 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 . . . C 2 75.712 -6.21 121.433 1 146.65 ? PG AGS 601 B 1 
HETATM 2 S S1G AGS . . . C 2 73.812 -5.668 120.798 1 133.22 ? S1G AGS 601 B 1 
HETATM 3 O O2G AGS . . . C 2 75.682 -7.722 121.984 1 120.13 ? O2G AGS 601 B 1 
HETATM 4 O O3G AGS . . . C 2 76.149 -5.299 122.514 1 115 ? O3G AGS 601 B 1 
HETATM 5 P PB AGS . . . C 2 76.273 -6.516 118.711 1 112.19 ? PB AGS 601 B 1 
HETATM 6 O O1B AGS . . . C 2 77.447 -6.332 117.78 1 113.75 ? O1B AGS 601 B 1 
HETATM 7 O O2B AGS . . . C 2 74.964 -5.821 118.42 1 103.94 ? O2B AGS 601 B 1 
HETATM 8 O O3B AGS . . . C 2 76.739 -6.11 120.197 1 107.43 ? O3B AGS 601 B 1 
HETATM 9 P PA AGS . . . C 2 77.061 -9.171 118.328 1 102.45 ? PA AGS 601 B 1 
HETATM 10 O O1A AGS . . . C 2 77.08 -9.124 116.819 1 103.56 ? O1A AGS 601 B 1 
HETATM 11 O O2A AGS . . . C 2 78.341 -8.975 119.105 1 100.02 ? O2A AGS 601 B 1 
HETATM 12 O O3A AGS . . . C 2 75.984 -8.094 118.852 1 90.6 ? O3A AGS 601 B 1 
HETATM 13 O O5' AGS . . . C 2 76.407 -10.571 118.78 1 90.83 ? O5' AGS 601 B 1 
HETATM 14 C C5' AGS . . . C 2 77.203 -11.571 119.411 1 89.64 ? C5' AGS 601 B 1 
HETATM 15 C C4' AGS . . . C 2 77.587 -12.635 118.389 1 89.17 ? C4' AGS 601 B 1 
HETATM 16 O O4' AGS . . . C 2 76.508 -13.56 118.227 1 89.55 ? O4' AGS 601 B 1 
HETATM 17 C C3' AGS . . . C 2 77.879 -12.017 117.031 1 89.01 ? C3' AGS 601 B 1 
HETATM 18 O O3' AGS . . . C 2 79.219 -12.317 116.634 1 109.52 ? O3' AGS 601 B 1 
HETATM 19 C C2' AGS . . . C 2 76.897 -12.641 116.061 1 86.31 ? C2' AGS 601 B 1 
HETATM 20 O O2' AGS . . . C 2 77.602 -13.341 115.032 1 101.1 ? O2' AGS 601 B 1 
HETATM 21 C C1' AGS . . . C 2 76.055 -13.613 116.871 1 81.18 ? C1' AGS 601 B 1 
HETATM 22 N N9 AGS . . . C 2 74.627 -13.216 116.804 1 75.99 ? N9 AGS 601 B 1 
HETATM 23 C C8 AGS . . . C 2 74.066 -12.183 117.459 1 78.24 ? C8 AGS 601 B 1 
HETATM 24 N N7 AGS . . . C 2 72.74 -12.089 117.183 1 75.68 ? N7 AGS 601 B 1 
HETATM 25 C C5 AGS . . . C 2 72.434 -13.084 116.33 1 72.17 ? C5 AGS 601 B 1 
HETATM 26 C C6 AGS . . . C 2 71.212 -13.56 115.639 1 66.97 ? C6 AGS 601 B 1 
HETATM 27 N N6 AGS . . . C 2 70.021 -12.936 115.811 1 67.33 ? N6 AGS 601 B 1 
HETATM 28 N N1 AGS . . . C 2 71.326 -14.638 114.832 1 62.33 ? N1 AGS 601 B 1 
HETATM 29 C C2 AGS . . . C 2 72.503 -15.267 114.653 1 65.41 ? C2 AGS 601 B 1 
HETATM 30 N N3 AGS . . . C 2 73.649 -14.889 115.248 1 75.75 ? N3 AGS 601 B 1 
HETATM 31 C C4 AGS . . . C 2 73.681 -13.824 116.083 1 75.46 ? C4 AGS 601 B 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#