data_9C57
#
_model_server_result.job_id            Ysa9GWWNuOKSD2cwehe9QA 
_model_server_result.datetime_utc      '2024-11-14 19:33:02' 
_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          9c57 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":3201}' 
#
_entry.id    9C57 
#
_exptl.entry_id    9C57 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    7 
_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            9C57 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9C57 
_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    tridecameric 
_pdbx_struct_assembly.oligomeric_count      13 
_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,R,S,T,U 
_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
? 9 N N N 
? 9 O N N 
? 9 P N N 
? 9 Q N N 
? 9 R N N 
? 9 S N N 
? 9 U N N 
#
_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                     9C57 
_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
N 9 AGS E 1 501 501 AGS AGS . 
O 9 AGS B 1 501 501 AGS AGS . 
P 9 AGS C 1 501 501 AGS AGS . 
Q 9 AGS D 1 501 501 AGS AGS . 
R 9 AGS F 1 501 501 AGS AGS . 
S 9 AGS G 1 3201 2301 AGS AGS . 
T 10 ATP L 1 501 501 ATP ATP . 
U 9 AGS A 1 501 501 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 . . . S 9 158.315 149.947 143.022 1 121.83 ? PG AGS 3201 G 1 
HETATM 2 S S1G AGS . . . S 9 158.589 148.041 143.317 1 106.69 ? S1G AGS 3201 G 1 
HETATM 3 O O2G AGS . . . S 9 158.617 150.3 141.537 1 124.06 ? O2G AGS 3201 G 1 
HETATM 4 O O3G AGS . . . S 9 156.832 150.3 143.338 1 119.88 ? O3G AGS 3201 G 1 
HETATM 5 P PB AGS . . . S 9 160.119 151.969 143.354 1 125.53 ? PB AGS 3201 G 1 
HETATM 6 O O1B AGS . . . S 9 161.117 151.46 142.388 1 117.23 ? O1B AGS 3201 G 1 
HETATM 7 O O2B AGS . . . S 9 159.101 152.923 142.727 1 123.4 ? O2B AGS 3201 G 1 
HETATM 8 O O3B AGS . . . S 9 159.265 150.77 143.946 1 122.87 ? O3B AGS 3201 G 1 
HETATM 9 P PA AGS . . . S 9 161.142 154.334 144.357 1 135.58 ? PA AGS 3201 G 1 
HETATM 10 O O1A AGS . . . S 9 160.533 154.849 143.112 1 127.17 ? O1A AGS 3201 G 1 
HETATM 11 O O2A AGS . . . S 9 160.647 155.018 145.634 1 125.7 ? O2A AGS 3201 G 1 
HETATM 12 O O3A AGS . . . S 9 160.831 152.78 144.524 1 128.08 ? O3A AGS 3201 G 1 
HETATM 13 O O5' AGS . . . S 9 162.717 154.458 144.22 1 120.01 ? O5' AGS 3201 G 1 
HETATM 14 C C5' AGS . . . S 9 163.359 155.526 143.499 1 115.58 ? C5' AGS 3201 G 1 
HETATM 15 C C4' AGS . . . S 9 163.277 155.28 142.015 1 116.72 ? C4' AGS 3201 G 1 
HETATM 16 O O4' AGS . . . S 9 164.565 155.563 141.421 1 117.06 ? O4' AGS 3201 G 1 
HETATM 17 C C3' AGS . . . S 9 162.893 153.864 141.575 1 119.02 ? C3' AGS 3201 G 1 
HETATM 18 O O3' AGS . . . S 9 161.896 153.93 140.56 1 124.89 ? O3' AGS 3201 G 1 
HETATM 19 C C2' AGS . . . S 9 164.22 153.277 141.089 1 118.84 ? C2' AGS 3201 G 1 
HETATM 20 O O2' AGS . . . S 9 164.064 152.256 140.108 1 123.6 ? O2' AGS 3201 G 1 
HETATM 21 C C1' AGS . . . S 9 164.909 154.521 140.536 1 116.44 ? C1' AGS 3201 G 1 
HETATM 22 N N9 AGS . . . S 9 166.366 154.448 140.428 1 115.51 ? N9 AGS 3201 G 1 
HETATM 23 C C8 AGS . . . S 9 167.203 155.45 140.01 1 116.41 ? C8 AGS 3201 G 1 
HETATM 24 N N7 AGS . . . S 9 168.471 155.114 139.992 1 121.1 ? N7 AGS 3201 G 1 
HETATM 25 C C5 AGS . . . S 9 168.469 153.798 140.424 1 123.16 ? C5 AGS 3201 G 1 
HETATM 26 C C6 AGS . . . S 9 169.51 152.864 140.613 1 124.15 ? C6 AGS 3201 G 1 
HETATM 27 N N6 AGS . . . S 9 170.8 153.138 140.394 1 123.58 ? N6 AGS 3201 G 1 
HETATM 28 N N1 AGS . . . S 9 169.174 151.628 141.044 1 123.02 ? N1 AGS 3201 G 1 
HETATM 29 C C2 AGS . . . S 9 167.884 151.357 141.266 1 121.11 ? C2 AGS 3201 G 1 
HETATM 30 N N3 AGS . . . S 9 166.82 152.155 141.119 1 119.72 ? N3 AGS 3201 G 1 
HETATM 31 C C4 AGS . . . S 9 167.18 153.369 140.688 1 119.3 ? C4 AGS 3201 G 1 
HETATM 32 H "H5'1" AGS . . . S 9 164.3 155.569 143.747 1 119.29 ? "H5'1" AGS 3201 G 1 
HETATM 33 H "H5'2" AGS . . . S 9 162.934 156.377 143.711 1 120.25 ? "H5'2" AGS 3201 G 1 
HETATM 34 H H4' AGS . . . S 9 162.62 155.89 141.643 1 120.72 ? H4' AGS 3201 G 1 
HETATM 35 H H3' AGS . . . S 9 162.571 153.334 142.321 1 120.03 ? H3' AGS 3201 G 1 
HETATM 36 H HO3' AGS . . . S 9 161.706 153.117 140.262 1 121.77 ? HO3' AGS 3201 G 1 
HETATM 37 H H2' AGS . . . S 9 164.687 152.929 141.863 1 119.33 ? H2' AGS 3201 G 1 
HETATM 38 H HO2' AGS . . . S 9 163.83 152.599 139.324 1 121.62 ? HO2' AGS 3201 G 1 
HETATM 39 H H1' AGS . . . S 9 164.548 154.74 139.659 1 120.4 ? H1' AGS 3201 G 1 
HETATM 40 H H8 AGS . . . S 9 166.881 156.332 139.76 1 119.52 ? H8 AGS 3201 G 1 
HETATM 41 H HN61 AGS . . . S 9 171.439 152.51 140.545 1 119.96 ? HN61 AGS 3201 G 1 
HETATM 42 H HN62 AGS . . . S 9 171.031 153.956 140.075 1 120.7 ? HN62 AGS 3201 G 1 
HETATM 43 H H2 AGS . . . S 9 167.688 150.454 141.568 1 119.36 ? H2 AGS 3201 G 1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    58 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           43 
#