data_9C57
#
_model_server_result.job_id            VDAkpas6_UUwgRw_tXCWTA 
_model_server_result.datetime_utc      '2024-11-14 19:46:16' 
_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":"N","auth_seq_id":501}' 
#
_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 . . . N 9 235.365 182.478 215.341 1 95.23 ? PG AGS 501 E 1 
HETATM 2 S S1G AGS . . . N 9 233.488 182.125 214.953 1 86.79 ? S1G AGS 501 E 1 
HETATM 3 O O2G AGS . . . N 9 235.793 181.707 216.624 1 68.04 ? O2G AGS 501 E 1 
HETATM 4 O O3G AGS . . . N 9 236.236 182.017 214.139 1 66.03 ? O3G AGS 501 E 1 
HETATM 5 P PB AGS . . . N 9 236.757 184.683 214.699 1 66.69 ? PB AGS 501 E 1 
HETATM 6 O O1B AGS . . . N 9 237.9 183.76 214.532 1 50.78 ? O1B AGS 501 E 1 
HETATM 7 O O2B AGS . . . N 9 236.117 185.128 213.383 1 57.69 ? O2B AGS 501 E 1 
HETATM 8 O O3B AGS . . . N 9 235.611 183.998 215.54 1 68.24 ? O3B AGS 501 E 1 
HETATM 9 P PA AGS . . . N 9 237.011 187.377 214.675 1 70.58 ? PA AGS 501 E 1 
HETATM 10 O O1A AGS . . . N 9 236.897 187.15 213.218 1 49.61 ? O1A AGS 501 E 1 
HETATM 11 O O2A AGS . . . N 9 235.793 188.045 215.316 1 61.24 ? O2A AGS 501 E 1 
HETATM 12 O O3A AGS . . . N 9 237.204 186.005 215.427 1 66.22 ? O3A AGS 501 E 1 
HETATM 13 O O5' AGS . . . N 9 238.338 188.179 214.963 1 56.31 ? O5' AGS 501 E 1 
HETATM 14 C C5' AGS . . . N 9 238.498 188.963 216.156 1 50.13 ? C5' AGS 501 E 1 
HETATM 15 C C4' AGS . . . N 9 238.466 190.424 215.79 1 54.92 ? C4' AGS 501 E 1 
HETATM 16 O O4' AGS . . . N 9 239.7 190.777 215.131 1 60.12 ? O4' AGS 501 E 1 
HETATM 17 C C3' AGS . . . N 9 237.362 190.832 214.821 1 54.61 ? C3' AGS 501 E 1 
HETATM 18 O O3' AGS . . . N 9 236.985 192.189 215.018 1 56.66 ? O3' AGS 501 E 1 
HETATM 19 C C2' AGS . . . N 9 238.023 190.625 213.46 1 54.82 ? C2' AGS 501 E 1 
HETATM 20 O O2' AGS . . . N 9 237.456 191.472 212.469 1 56.5 ? O2' AGS 501 E 1 
HETATM 21 C C1' AGS . . . N 9 239.477 191.008 213.752 1 56.94 ? C1' AGS 501 E 1 
HETATM 22 N N9 AGS . . . N 9 240.456 190.234 213.001 1 53.74 ? N9 AGS 501 E 1 
HETATM 23 C C8 AGS . . . N 9 240.641 188.878 213.037 1 53.24 ? C8 AGS 501 E 1 
HETATM 24 N N7 AGS . . . N 9 241.603 188.449 212.257 1 53.71 ? N7 AGS 501 E 1 
HETATM 25 C C5 AGS . . . N 9 242.09 189.606 211.671 1 52.17 ? C5 AGS 501 E 1 
HETATM 26 C C6 AGS . . . N 9 243.122 189.836 210.742 1 49.01 ? C6 AGS 501 E 1 
HETATM 27 N N6 AGS . . . N 9 243.878 188.869 210.218 1 55.95 ? N6 AGS 501 E 1 
HETATM 28 N N1 AGS . . . N 9 243.351 191.112 210.363 1 51.81 ? N1 AGS 501 E 1 
HETATM 29 C C2 AGS . . . N 9 242.596 192.083 210.882 1 51.97 ? C2 AGS 501 E 1 
HETATM 30 N N3 AGS . . . N 9 241.601 191.987 211.766 1 52.5 ? N3 AGS 501 E 1 
HETATM 31 C C4 AGS . . . N 9 241.394 190.714 212.12 1 53.3 ? C4 AGS 501 E 1 
HETATM 32 H "H5'1" AGS . . . N 9 239.351 188.753 216.574 1 54.97 ? "H5'1" AGS 501 E 1 
HETATM 33 H "H5'2" AGS . . . N 9 237.774 188.767 216.776 1 55.49 ? "H5'2" AGS 501 E 1 
HETATM 34 H H4' AGS . . . N 9 238.382 190.95 216.602 1 55.99 ? H4' AGS 501 E 1 
HETATM 35 H H3' AGS . . . N 9 236.595 190.246 214.918 1 55.65 ? H3' AGS 501 E 1 
HETATM 36 H HO3' AGS . . . N 9 236.187 192.329 214.655 1 54.76 ? HO3' AGS 501 E 1 
HETATM 37 H H2' AGS . . . N 9 237.962 189.695 213.188 1 55.78 ? H2' AGS 501 E 1 
HETATM 38 H HO2' AGS . . . N 9 236.674 191.78 212.753 1 54.6 ? HO2' AGS 501 E 1 
HETATM 39 H H1' AGS . . . N 9 239.6 191.954 213.561 1 55.79 ? H1' AGS 501 E 1 
HETATM 40 H H8 AGS . . . N 9 240.105 188.286 213.585 1 55.55 ? H8 AGS 501 E 1 
HETATM 41 H HN61 AGS . . . N 9 244.572 189.083 209.671 1 54.54 ? HN61 AGS 501 E 1 
HETATM 42 H HN62 AGS . . . N 9 243.7 187.998 210.406 1 55.49 ? HN62 AGS 501 E 1 
HETATM 43 H H2 AGS . . . N 9 242.803 192.983 210.577 1 54.24 ? H2 AGS 501 E 1 
#
_model_server_stats.io_time_ms              115 
_model_server_stats.parse_time_ms           32 
_model_server_stats.create_model_time_ms    122 
_model_server_stats.query_time_ms           665 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#