data_8DUE
#
_model_server_result.job_id            bC01sN6QakxESr34X3yazg 
_model_server_result.datetime_utc      '2024-11-09 23:22:48' 
_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          8due 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":501}' 
#
_entry.id    8DUE 
#
_exptl.entry_id    8DUE 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    5 
_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            8DUE 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DUE 
_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    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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 
_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
? 3 H N N 
? 3 J N N 
? 3 L N N 
? 3 N N N 
? 3 P 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 OG SER 204 B SER 204 1_555 I MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc2 B OE1 GLU 227 B GLU 227 1_555 I MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? 
metalc ? metalc3 B OE2 GLU 227 B GLU 227 1_555 I MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc4 H O3B AGS . B AGS 501 1_555 I MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? 
metalc ? metalc5 H O3A AGS . B AGS 501 1_555 I MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? 
metalc ? metalc6 J O2G AGS . C AGS 501 1_555 K MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? 
metalc ? metalc7 J O1B AGS . C AGS 501 1_555 K MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc8 J O1A AGS . C AGS 501 1_555 K MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc9 J O3A AGS . C AGS 501 1_555 K MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc10 L O3G AGS . D AGS 501 1_555 M MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? 
metalc ? metalc11 L O2B AGS . D AGS 501 1_555 M MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? 
metalc ? metalc12 L O3B AGS . D AGS 501 1_555 M MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc13 L O2A AGS . D AGS 501 1_555 M MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc14 E OE1 GLU 227 E GLU 227 1_555 O MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? 
metalc ? metalc15 N O3G AGS . E AGS 501 1_555 O MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc16 N O2B AGS . E AGS 501 1_555 O MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? 
metalc ? metalc17 F OG SER 204 F SER 204 1_555 Q MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc18 P O2G AGS . F AGS 501 1_555 Q MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc19 P O2B AGS . F AGS 501 1_555 Q MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc20 P O3B AGS . F AGS 501 1_555 Q MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? 
metalc ? metalc21 P O3A AGS . F AGS 501 1_555 Q MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
#
_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                     8DUE 
_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
H 3 AGS B 1 501 501 AGS AGS . 
I 4 MG B 1 502 502 MG MG . 
J 3 AGS C 1 501 501 AGS AGS . 
K 4 MG C 1 502 502 MG MG . 
L 3 AGS D 1 501 501 AGS AGS . 
M 4 MG D 1 502 502 MG MG . 
N 3 AGS E 1 501 501 AGS AGS . 
O 4 MG E 1 502 502 MG MG . 
P 3 AGS F 1 501 501 AGS AGS . 
Q 4 MG F 1 502 502 MG MG . 
#
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 . . . L 3 112.293 147.122 108.208 1 77.25 ? PG AGS 501 D 1 
HETATM 2 S S1G AGS . . . L 3 113.079 147.525 109.943 1 93.65 ? S1G AGS 501 D 1 
HETATM 3 O O2G AGS . . . L 3 111.449 145.817 108.286 1 69.38 ? O2G AGS 501 D 1 
HETATM 4 O O3G AGS . . . L 3 113.436 146.925 107.17 1 83.69 ? O3G AGS 501 D 1 
HETATM 5 P PB AGS . . . L 3 110.62 149.135 108.874 1 73.92 ? PB AGS 501 D 1 
HETATM 6 O O1B AGS . . . L 3 109.635 148.272 109.559 1 71.24 ? O1B AGS 501 D 1 
HETATM 7 O O2B AGS . . . L 3 111.709 149.674 109.804 1 77.08 ? O2B AGS 501 D 1 
HETATM 8 O O3B AGS . . . L 3 111.381 148.304 107.767 1 76.72 ? O3B AGS 501 D 1 
HETATM 9 P PA AGS . . . L 3 110.64 151.223 107.109 1 61.69 ? PA AGS 501 D 1 
HETATM 10 O O1A AGS . . . L 3 111.016 152.57 107.575 1 81.28 ? O1A AGS 501 D 1 
HETATM 11 O O2A AGS . . . L 3 111.822 150.36 106.668 1 62.26 ? O2A AGS 501 D 1 
HETATM 12 O O3A AGS . . . L 3 109.91 150.4 108.238 1 77.51 ? O3A AGS 501 D 1 
HETATM 13 O O5' AGS . . . L 3 109.557 151.385 105.97 1 67.99 ? O5' AGS 501 D 1 
HETATM 14 C C5' AGS . . . L 3 108.164 151.13 106.237 1 70.17 ? C5' AGS 501 D 1 
HETATM 15 C C4' AGS . . . L 3 107.344 151.554 105.044 1 78.12 ? C4' AGS 501 D 1 
HETATM 16 O O4' AGS . . . L 3 107.768 152.861 104.603 1 86.75 ? O4' AGS 501 D 1 
HETATM 17 C C3' AGS . . . L 3 107.471 150.661 103.817 1 79.53 ? C3' AGS 501 D 1 
HETATM 18 O O3' AGS . . . L 3 106.55 149.578 103.883 1 82.59 ? O3' AGS 501 D 1 
HETATM 19 C C2' AGS . . . L 3 107.134 151.622 102.677 1 77.35 ? C2' AGS 501 D 1 
HETATM 20 O O2' AGS . . . L 3 105.728 151.746 102.498 1 80.88 ? O2' AGS 501 D 1 
HETATM 21 C C1' AGS . . . L 3 107.717 152.943 103.19 1 75.77 ? C1' AGS 501 D 1 
HETATM 22 N N9 AGS . . . L 3 109.059 153.234 102.7 1 65.37 ? N9 AGS 501 D 1 
HETATM 23 C C8 AGS . . . L 3 110.239 152.741 103.19 1 64.27 ? C8 AGS 501 D 1 
HETATM 24 N N7 AGS . . . L 3 111.303 153.174 102.559 1 64.62 ? N7 AGS 501 D 1 
HETATM 25 C C5 AGS . . . L 3 110.787 154.011 101.582 1 74.81 ? C5 AGS 501 D 1 
HETATM 26 C C6 AGS . . . L 3 111.398 154.783 100.575 1 78.47 ? C6 AGS 501 D 1 
HETATM 27 N N6 AGS . . . L 3 112.718 154.84 100.381 1 77.33 ? N6 AGS 501 D 1 
HETATM 28 N N1 AGS . . . L 3 110.594 155.508 99.766 1 77.53 ? N1 AGS 501 D 1 
HETATM 29 C C2 AGS . . . L 3 109.272 155.456 99.958 1 77.28 ? C2 AGS 501 D 1 
HETATM 30 N N3 AGS . . . L 3 108.584 154.766 100.871 1 72.88 ? N3 AGS 501 D 1 
HETATM 31 C C4 AGS . . . L 3 109.405 154.059 101.657 1 71.94 ? C4 AGS 501 D 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           245 
_model_server_stats.encode_time_ms          22 
_model_server_stats.element_count           31 
#