data_8AMD
#
_model_server_result.job_id            O8BUP_JsGDXevndA0Gkb4Q 
_model_server_result.datetime_utc      '2024-12-27 01:58:13' 
_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          8amd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":500}' 
#
_entry.id    8AMD 
#
_exptl.entry_id    8AMD 
_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    4 
_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            8AMD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8AMD 
_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    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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 
_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 F N N 
? 3 G N N 
? 3 H N N 
? 3 I 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
covale ? covale1 A CA SER 82 A SER 82 1_555 F O1B AGS . A AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? 
covale ? covale2 A N GLY 84 A GLY 84 1_555 F O2A AGS . A AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale3 A CD1 TYR 116 A TYR 116 1_555 F N6 AGS . A AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale4 A NZ LYS 257 A LYS 257 1_555 F O3' AGS . A AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale5 C CA SER 82 B SER 82 1_555 G O1B AGS . B AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? 
covale ? covale6 C N GLY 84 B GLY 84 1_555 G O2A AGS . B AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale7 C CD1 TYR 116 B TYR 116 1_555 G N6 AGS . B AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale8 C NZ LYS 257 B LYS 257 1_555 G O3' AGS . B AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? 
covale ? covale9 D CA SER 82 F SER 82 1_555 H O1B AGS . F AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? 
covale ? covale10 D N GLY 84 F GLY 84 1_555 H O2A AGS . F AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale11 D CD1 TYR 116 F TYR 116 1_555 H N6 AGS . F AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale12 D NZ LYS 257 F LYS 257 1_555 H O3' AGS . F AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? 
covale ? covale13 E CA SER 82 G SER 82 1_555 I O1B AGS . G AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? 
covale ? covale14 E CA GLY 84 G GLY 84 1_555 I O2A AGS . G AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? 
covale ? covale15 E CD1 TYR 116 G TYR 116 1_555 I N6 AGS . G AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale16 E NZ LYS 257 G LYS 257 1_555 I O3' AGS . G AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
#
_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                     8AMD 
_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
F 3 AGS A 1 500 500 AGS AGS . 
G 3 AGS B 1 500 500 AGS AGS . 
H 3 AGS F 1 500 500 AGS AGS . 
I 3 AGS G 1 500 500 AGS AGS . 
#
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 3 118.722 132.948 110.308 1 103.75 ? PG AGS 500 B 1 
HETATM 2 S S1G AGS . . . G 3 116.868 133.187 109.776 1 103.75 ? S1G AGS 500 B 1 
HETATM 3 O O2G AGS . . . G 3 119.489 134.296 110.383 1 103.75 ? O2G AGS 500 B 1 
HETATM 4 O O3G AGS . . . G 3 119.428 132.025 109.283 1 103.75 ? O3G AGS 500 B 1 
HETATM 5 P PB AGS . . . G 3 120.158 132.02 112.349 1 103.75 ? PB AGS 500 B 1 
HETATM 6 O O1B AGS . . . G 3 120.065 130.915 113.338 1 103.75 ? O1B AGS 500 B 1 
HETATM 7 O O2B AGS . . . G 3 121.069 131.777 111.146 1 103.75 ? O2B AGS 500 B 1 
HETATM 8 O O3B AGS . . . G 3 118.755 132.311 111.716 1 103.75 ? O3B AGS 500 B 1 
HETATM 9 P PA AGS . . . G 3 122.185 133.753 112.565 1 103.75 ? PA AGS 500 B 1 
HETATM 10 O O1A AGS . . . G 3 122.126 134.203 111.168 1 103.75 ? O1A AGS 500 B 1 
HETATM 11 O O2A AGS . . . G 3 123.121 132.564 112.83 1 103.75 ? O2A AGS 500 B 1 
HETATM 12 O O3A AGS . . . G 3 120.746 133.314 113.009 1 103.75 ? O3A AGS 500 B 1 
HETATM 13 O O5' AGS . . . G 3 122.484 135.012 113.481 1 103.75 ? O5' AGS 500 B 1 
HETATM 14 C C5' AGS . . . G 3 123.442 135.03 114.579 1 103.75 ? C5' AGS 500 B 1 
HETATM 15 C C4' AGS . . . G 3 122.781 135.164 115.936 1 103.75 ? C4' AGS 500 B 1 
HETATM 16 O O4' AGS . . . G 3 122.825 136.525 116.398 1 103.75 ? O4' AGS 500 B 1 
HETATM 17 C C3' AGS . . . G 3 121.324 134.741 116.059 1 103.75 ? C3' AGS 500 B 1 
HETATM 18 O O3' AGS . . . G 3 121.117 134.162 117.343 1 103.75 ? O3' AGS 500 B 1 
HETATM 19 C C2' AGS . . . G 3 120.551 136.053 115.854 1 103.75 ? C2' AGS 500 B 1 
HETATM 20 O O2' AGS . . . G 3 119.394 136.099 116.678 1 103.75 ? O2' AGS 500 B 1 
HETATM 21 C C1' AGS . . . G 3 121.555 137.137 116.27 1 103.75 ? C1' AGS 500 B 1 
HETATM 22 N N9 AGS . . . G 3 121.705 138.215 115.305 1 103.75 ? N9 AGS 500 B 1 
HETATM 23 C C8 AGS . . . G 3 121.961 138.063 113.97 1 103.75 ? C8 AGS 500 B 1 
HETATM 24 N N7 AGS . . . G 3 122.1 139.191 113.322 1 103.75 ? N7 AGS 500 B 1 
HETATM 25 C C5 AGS . . . G 3 121.917 140.154 114.299 1 103.75 ? C5 AGS 500 B 1 
HETATM 26 C C6 AGS . . . G 3 121.961 141.561 114.257 1 103.75 ? C6 AGS 500 B 1 
HETATM 27 N N6 AGS . . . G 3 122.202 142.262 113.142 1 103.75 ? N6 AGS 500 B 1 
HETATM 28 N N1 AGS . . . G 3 121.756 142.228 115.416 1 103.75 ? N1 AGS 500 B 1 
HETATM 29 C C2 AGS . . . G 3 121.542 141.527 116.532 1 103.75 ? C2 AGS 500 B 1 
HETATM 30 N N3 AGS . . . G 3 121.495 140.202 116.692 1 103.75 ? N3 AGS 500 B 1 
HETATM 31 C C4 AGS . . . G 3 121.699 139.569 115.531 1 103.75 ? C4 AGS 500 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#