data_6Z4X
#
_model_server_result.job_id            eCi5SE-Xee0b3RZrTzX3lg 
_model_server_result.datetime_utc      '2025-09-01 07:30:13' 
_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          6z4x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":501}' 
#
_entry.id    6Z4X 
#
_exptl.entry_id    6Z4X 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          4 
_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          96.197 
_cell.angle_gamma         90 
_cell.entry_id            6Z4X 
_cell.length_a            89.97 
_cell.length_b            84.903 
_cell.length_c            154.477 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6Z4X 
_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
? trimeric 3 author_defined_assembly 1 
? trimeric 3 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,B,C,G,H,I,L 1 1 
D,E,F,J,K 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
? 4 G N N 
? 4 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
metalc ? metalc1 G O1B AGS . B AGS 501 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc2 E OD1 ASN 225 E ASN 225 1_555 K MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? 
#
_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                     6Z4X 
_atom_sites.fract_transf_matrix[1][1]    0.011115 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001207 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011778 
_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]    0.006512 
_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
G 4 AGS B 1 501 401 AGS ATG . 
H 5 MG B 1 502 1 MG MG . 
I 6 CL B 1 503 1 CL CL . 
J 4 AGS E 1 501 401 AGS ATG . 
K 5 MG E 1 502 2 MG MG . 
L 7 HOH B 1 601 1 HOH HOH . 
#
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 . . . G 4 -35.95 -27.872 -21.367 1 144.42 ? PG AGS 501 B 1 
HETATM 2 S S1G AGS . . . G 4 -33.929 -27.737 -20.9 1 84.49 ? S1G AGS 501 B 1 
HETATM 3 O O2G AGS . . . G 4 -36.38 -26.644 -22.073 1 105.98 ? O2G AGS 501 B 1 
HETATM 4 O O3G AGS . . . G 4 -36.824 -28.059 -20.029 1 116.79 ? O3G AGS 501 B 1 
HETATM 5 P PB AGS . . . G 4 -37.179 -29.167 -23.57 1 112.77 ? PB AGS 501 B 1 
HETATM 6 O O1B AGS . . . G 4 -37.98 -27.885 -23.556 1 105.86 ? O1B AGS 501 B 1 
HETATM 7 O O2B AGS . . . G 4 -36.348 -29.53 -24.775 1 74.52 ? O2B AGS 501 B 1 
HETATM 8 O O3B AGS . . . G 4 -36.253 -29.179 -22.253 1 123.9 ? O3B AGS 501 B 1 
HETATM 9 P PA AGS . . . G 4 -39.566 -30.629 -24.006 1 118.25 ? PA AGS 501 B 1 
HETATM 10 O O1A AGS . . . G 4 -40.558 -31.175 -23.008 1 79.88 ? O1A AGS 501 B 1 
HETATM 11 O O2A AGS . . . G 4 -39.952 -29.397 -24.787 1 108.92 ? O2A AGS 501 B 1 
HETATM 12 O O3A AGS . . . G 4 -38.176 -30.383 -23.22 1 109.72 ? O3A AGS 501 B 1 
HETATM 13 O O5' AGS . . . G 4 -39.131 -31.839 -24.986 1 90.13 ? O5' AGS 501 B 1 
HETATM 14 C C5' AGS . . . G 4 -38.225 -31.653 -26.086 1 72.42 ? C5' AGS 501 B 1 
HETATM 15 C C4' AGS . . . G 4 -38.086 -32.972 -26.851 1 45.33 ? C4' AGS 501 B 1 
HETATM 16 O O4' AGS . . . G 4 -39.381 -33.513 -27.172 1 44.73 ? O4' AGS 501 B 1 
HETATM 17 C C3' AGS . . . G 4 -37.322 -32.951 -28.184 1 75.82 ? C3' AGS 501 B 1 
HETATM 18 O O3' AGS . . . G 4 -36.248 -33.884 -28.086 1 83.18 ? O3' AGS 501 B 1 
HETATM 19 C C2' AGS . . . G 4 -38.291 -33.405 -29.279 1 76.03 ? C2' AGS 501 B 1 
HETATM 20 O O2' AGS . . . G 4 -37.683 -34.368 -30.133 1 79.5 ? O2' AGS 501 B 1 
HETATM 21 C C1' AGS . . . G 4 -39.434 -34.056 -28.505 1 68.46 ? C1' AGS 501 B 1 
HETATM 22 N N9 AGS . . . G 4 -40.775 -33.824 -29.107 1 70.2 ? N9 AGS 501 B 1 
HETATM 23 C C8 AGS . . . G 4 -41.271 -34.494 -30.168 1 60.84 ? C8 AGS 501 B 1 
HETATM 24 N N7 AGS . . . G 4 -42.523 -34.065 -30.474 1 37.41 ? N7 AGS 501 B 1 
HETATM 25 C C5 AGS . . . G 4 -42.848 -33.107 -29.59 1 29.64 ? C5 AGS 501 B 1 
HETATM 26 C C6 AGS . . . G 4 -44.021 -32.242 -29.348 1 38.52 ? C6 AGS 501 B 1 
HETATM 27 N N6 AGS . . . G 4 -45.111 -32.326 -30.137 1 38.69 ? N6 AGS 501 B 1 
HETATM 28 N N1 AGS . . . G 4 -43.966 -31.368 -28.32 1 55.89 ? N1 AGS 501 B 1 
HETATM 29 C C2 AGS . . . G 4 -42.884 -31.268 -27.523 1 62.78 ? C2 AGS 501 B 1 
HETATM 30 N N3 AGS . . . G 4 -41.783 -32.028 -27.69 1 73.08 ? N3 AGS 501 B 1 
HETATM 31 C C4 AGS . . . G 4 -41.699 -32.95 -28.685 1 55.12 ? C4 AGS 501 B 1 
HETATM 32 H H21 AGS . . . G 4 -37.606 -27.509 -19.882 1 140.7 ? H21 AGS 501 B 1 
HETATM 33 H "H5'1" AGS . . . G 4 -37.249 -31.334 -25.715 1 87.45 ? "H5'1" AGS 501 B 1 
HETATM 34 H "H5'2" AGS . . . G 4 -38.603 -30.875 -26.752 1 87.45 ? "H5'2" AGS 501 B 1 
HETATM 35 H H4' AGS . . . G 4 -37.498 -33.573 -26.143 1 54.94 ? H4' AGS 501 B 1 
HETATM 36 H H3' AGS . . . G 4 -36.927 -31.952 -28.414 1 91.53 ? H3' AGS 501 B 1 
HETATM 37 H HO3' AGS . . . G 4 -35.741 -33.88 -28.909 1 100.36 ? HO3' AGS 501 B 1 
HETATM 38 H H2' AGS . . . G 4 -38.609 -32.576 -29.926 1 91.79 ? H2' AGS 501 B 1 
HETATM 39 H HO2' AGS . . . G 4 -37.148 -33.916 -30.8 1 95.94 ? HO2' AGS 501 B 1 
HETATM 40 H H1' AGS . . . G 4 -39.291 -35.145 -28.529 1 82.7 ? H1' AGS 501 B 1 
HETATM 41 H H8 AGS . . . G 4 -40.741 -35.271 -30.705 1 73.55 ? H8 AGS 501 B 1 
HETATM 42 H HN61 AGS . . . G 4 -45.902 -31.725 -29.961 1 46.97 ? HN61 AGS 501 B 1 
HETATM 43 H HN62 AGS . . . G 4 -45.128 -32.988 -30.897 1 46.97 ? HN62 AGS 501 B 1 
HETATM 44 H H2 AGS . . . G 4 -42.9 -30.548 -26.714 1 75.88 ? H2 AGS 501 B 1 
HETATM 45 H HSG3 AGS . . . G 4 -33.206 -28.192 -21.92 1 101.93 ? HSG3 AGS 501 B 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           338 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           45 
#