data_9C57
#
_model_server_result.job_id            dHCDuDxYp_7LtkECKXJBMQ 
_model_server_result.datetime_utc      '2024-11-14 19:33:01' 
_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":"O","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 . . . O 9 208.717 145.993 238.247 1 80.31 ? PG AGS 501 B 1 
HETATM 2 S S1G AGS . . . O 9 208.195 147.102 236.732 1 62.64 ? S1G AGS 501 B 1 
HETATM 3 O O2G AGS . . . O 9 209.522 146.839 239.272 1 59.45 ? O2G AGS 501 B 1 
HETATM 4 O O3G AGS . . . O 9 209.626 144.837 237.736 1 71.19 ? O3G AGS 501 B 1 
HETATM 5 P PB AGS . . . O 9 206.011 145.957 238.759 1 76.13 ? PB AGS 501 B 1 
HETATM 6 O O1B AGS . . . O 9 206.032 147.408 238.49 1 69.24 ? O1B AGS 501 B 1 
HETATM 7 O O2B AGS . . . O 9 205.259 145.622 240.048 1 58.7 ? O2B AGS 501 B 1 
HETATM 8 O O3B AGS . . . O 9 207.473 145.383 238.961 1 69.85 ? O3B AGS 501 B 1 
HETATM 9 P PA AGS . . . O 9 203.824 144.572 237.895 1 76.38 ? PA AGS 501 B 1 
HETATM 10 O O1A AGS . . . O 9 202.807 145.634 237.995 1 67.97 ? O1A AGS 501 B 1 
HETATM 11 O O2A AGS . . . O 9 203.539 143.546 236.794 1 49.45 ? O2A AGS 501 B 1 
HETATM 12 O O3A AGS . . . O 9 205.258 145.18 237.605 1 68.78 ? O3A AGS 501 B 1 
HETATM 13 O O5' AGS . . . O 9 203.973 143.895 239.318 1 63.01 ? O5' AGS 501 B 1 
HETATM 14 C C5' AGS . . . O 9 204.952 142.859 239.511 1 63.87 ? C5' AGS 501 B 1 
HETATM 15 C C4' AGS . . . O 9 204.7 142.156 240.819 1 64.81 ? C4' AGS 501 B 1 
HETATM 16 O O4' AGS . . . O 9 204.494 143.12 241.867 1 60.4 ? O4' AGS 501 B 1 
HETATM 17 C C3' AGS . . . O 9 203.455 141.284 240.879 1 60.81 ? C3' AGS 501 B 1 
HETATM 18 O O3' AGS . . . O 9 203.674 140.012 240.281 1 70.52 ? O3' AGS 501 B 1 
HETATM 19 C C2' AGS . . . O 9 203.228 141.166 242.385 1 59.89 ? C2' AGS 501 B 1 
HETATM 20 O O2' AGS . . . O 9 203.963 140.077 242.933 1 58.98 ? O2' AGS 501 B 1 
HETATM 21 C C1' AGS . . . O 9 203.745 142.517 242.907 1 64.02 ? C1' AGS 501 B 1 
HETATM 22 N N9 AGS . . . O 9 202.685 143.437 243.303 1 56.1 ? N9 AGS 501 B 1 
HETATM 23 C C8 AGS . . . O 9 202.264 144.549 242.625 1 59.27 ? C8 AGS 501 B 1 
HETATM 24 N N7 AGS . . . O 9 201.281 145.19 243.208 1 63.14 ? N7 AGS 501 B 1 
HETATM 25 C C5 AGS . . . O 9 201.031 144.442 244.347 1 58.56 ? C5 AGS 501 B 1 
HETATM 26 C C6 AGS . . . O 9 200.101 144.59 245.394 1 61.41 ? C6 AGS 501 B 1 
HETATM 27 N N6 AGS . . . O 9 199.216 145.586 245.465 1 69.44 ? N6 AGS 501 B 1 
HETATM 28 N N1 AGS . . . O 9 200.116 143.668 246.381 1 51.86 ? N1 AGS 501 B 1 
HETATM 29 C C2 AGS . . . O 9 201.003 142.672 246.316 1 58.87 ? C2 AGS 501 B 1 
HETATM 30 N N3 AGS . . . O 9 201.926 142.43 245.382 1 62.07 ? N3 AGS 501 B 1 
HETATM 31 C C4 AGS . . . O 9 201.888 143.358 244.419 1 58.34 ? C4 AGS 501 B 1 
HETATM 32 H "H5'1" AGS . . . O 9 205.845 143.246 239.52 1 61.55 ? "H5'1" AGS 501 B 1 
HETATM 33 H "H5'2" AGS . . . O 9 204.887 142.215 238.784 1 62.79 ? "H5'2" AGS 501 B 1 
HETATM 34 H H4' AGS . . . O 9 205.475 141.612 241.038 1 62.53 ? H4' AGS 501 B 1 
HETATM 35 H H3' AGS . . . O 9 202.706 141.738 240.459 1 60.73 ? H3' AGS 501 B 1 
HETATM 36 H HO3' AGS . . . O 9 204.12 139.494 240.847 1 62.13 ? HO3' AGS 501 B 1 
HETATM 37 H H2' AGS . . . O 9 202.281 141.075 242.577 1 60.65 ? H2' AGS 501 B 1 
HETATM 38 H HO2' AGS . . . O 9 204.804 140.322 243.069 1 61.93 ? HO2' AGS 501 B 1 
HETATM 39 H H1' AGS . . . O 9 204.329 142.358 243.669 1 62.09 ? H1' AGS 501 B 1 
HETATM 40 H H8 AGS . . . O 9 202.663 144.837 241.791 1 60.43 ? H8 AGS 501 B 1 
HETATM 41 H HN61 AGS . . . O 9 199.183 146.211 244.805 1 60.97 ? HN61 AGS 501 B 1 
HETATM 42 H HN62 AGS . . . O 9 198.648 145.642 246.172 1 60.93 ? HN62 AGS 501 B 1 
HETATM 43 H H2 AGS . . . O 9 200.972 142.035 247.051 1 61.83 ? H2 AGS 501 B 1 
#
_model_server_stats.io_time_ms              366 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    76 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#