data_5XG3
#
_model_server_result.job_id            8pltoupm6XvFJgwCKEHQ7Q 
_model_server_result.datetime_utc      '2025-08-05 11:28:13' 
_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          5xg3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":1201}' 
#
_entry.id    5XG3 
#
_exptl.entry_id    5XG3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          3 
_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            5XG3 
_cell.length_a            88.103 
_cell.length_b            104.783 
_cell.length_c            185.22 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XG3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J 
_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    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
? 3 E N N 
? 3 H 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 OE1 GLN 143 A GLN 143 1_555 F MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? 
metalc ? metalc2 E O3G AGS . A AGS 1201 1_555 F MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? 
metalc ? metalc3 E O1B AGS . A AGS 1201 1_555 F MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? 
metalc ? metalc4 B OE1 GLN 143 B GLN 143 1_555 I MG MG . B MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc5 H O1B AGS . B AGS 1201 1_555 I MG MG . B MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? 
#
_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                     5XG3 
_atom_sites.fract_transf_matrix[1][1]    0.01135 
_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]    0.009544 
_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]    0.005399 
_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
E 3 AGS A 1 1201 3 AGS AGS . 
F 4 MG A 1 1202 4 MG MG . 
G 5 CO A 1 1203 1 CO CO . 
H 3 AGS B 1 1201 1 AGS AGS . 
I 4 MG B 1 1202 2 MG MG . 
J 6 HOH B 1 1301 4 HOH HOH . 
J 6 HOH B 2 1302 2 HOH HOH . 
J 6 HOH B 3 1303 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 . . . H 3 28.676 1.075 -24.881 1 73.28 ? PG AGS 1201 B 1 
HETATM 2 S S1G AGS . . . H 3 27.41 -0.223 -25.494 1 41.64 ? S1G AGS 1201 B 1 
HETATM 3 O O2G AGS . . . H 3 28.094 1.507 -23.548 1 58.25 ? O2G AGS 1201 B 1 
HETATM 4 O O3G AGS . . . H 3 30.08 0.553 -24.58 1 67.3 ? O3G AGS 1201 B 1 
HETATM 5 P PB AGS . . . H 3 29.231 1.956 -27.384 1 28.82 ? PB AGS 1201 B 1 
HETATM 6 O O1B AGS . . . H 3 28.605 0.79 -28.099 1 28.42 ? O1B AGS 1201 B 1 
HETATM 7 O O2B AGS . . . H 3 30.738 1.775 -27.297 1 51.99 ? O2B AGS 1201 B 1 
HETATM 8 O O3B AGS . . . H 3 28.798 2.2 -25.906 1 36.91 ? O3B AGS 1201 B 1 
HETATM 9 P PA AGS . . . H 3 29.568 3.59 -29.601 1 39.98 ? PA AGS 1201 B 1 
HETATM 10 O O1A AGS . . . H 3 28.812 2.574 -30.482 1 23.4 ? O1A AGS 1201 B 1 
HETATM 11 O O2A AGS . . . H 3 31.019 3.382 -29.734 1 54.82 ? O2A AGS 1201 B 1 
HETATM 12 O O3A AGS . . . H 3 28.972 3.342 -28.153 1 29.18 ? O3A AGS 1201 B 1 
HETATM 13 O O5' AGS . . . H 3 29.38 5.167 -29.741 1 39.24 ? O5' AGS 1201 B 1 
HETATM 14 C C5' AGS . . . H 3 28.01 5.629 -29.738 1 58.7 ? C5' AGS 1201 B 1 
HETATM 15 C C4' AGS . . . H 3 27.987 7.091 -29.418 1 44.97 ? C4' AGS 1201 B 1 
HETATM 16 O O4' AGS . . . H 3 29.34 7.558 -29.476 1 34.64 ? O4' AGS 1201 B 1 
HETATM 17 C C3' AGS . . . H 3 27.148 7.944 -30.365 1 44.73 ? C3' AGS 1201 B 1 
HETATM 18 O O3' AGS . . . H 3 26.03 8.475 -29.649 1 59.74 ? O3' AGS 1201 B 1 
HETATM 19 C C2' AGS . . . H 3 28.014 9.133 -30.701 1 48.72 ? C2' AGS 1201 B 1 
HETATM 20 O O2' AGS . . . H 3 27.568 10.307 -30.038 1 80.01 ? O2' AGS 1201 B 1 
HETATM 21 C C1' AGS . . . H 3 29.425 8.718 -30.29 1 44.65 ? C1' AGS 1201 B 1 
HETATM 22 N N9 AGS . . . H 3 30.207 8.385 -31.412 1 48.66 ? N9 AGS 1201 B 1 
HETATM 23 C C8 AGS . . . H 3 30.522 7.17 -31.931 1 41.25 ? C8 AGS 1201 B 1 
HETATM 24 N N7 AGS . . . H 3 31.303 7.223 -33.024 1 46.02 ? N7 AGS 1201 B 1 
HETATM 25 C C5 AGS . . . H 3 31.485 8.573 -33.21 1 46.68 ? C5 AGS 1201 B 1 
HETATM 26 C C6 AGS . . . H 3 32.201 9.318 -34.179 1 38.71 ? C6 AGS 1201 B 1 
HETATM 27 N N6 AGS . . . H 3 32.882 8.781 -35.167 1 37.55 ? N6 AGS 1201 B 1 
HETATM 28 N N1 AGS . . . H 3 32.179 10.651 -34.076 1 34.27 ? N1 AGS 1201 B 1 
HETATM 29 C C2 AGS . . . H 3 31.496 11.215 -33.076 1 42.09 ? C2 AGS 1201 B 1 
HETATM 30 N N3 AGS . . . H 3 30.788 10.627 -32.11 1 57.73 ? N3 AGS 1201 B 1 
HETATM 31 C C4 AGS . . . H 3 30.819 9.309 -32.228 1 55.25 ? C4 AGS 1201 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#