data_4NAH
#
_model_server_result.job_id            ovg7JHSovhyNzUWY116_MQ 
_model_server_result.datetime_utc      '2025-07-03 08:43:07' 
_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          4nah 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":201}' 
#
_entry.id    4NAH 
#
_exptl.entry_id    4NAH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.247 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.69 
_cell.angle_gamma         90 
_cell.entry_id            4NAH 
_cell.length_a            68.476 
_cell.length_b            105.36 
_cell.length_c            79.98 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NAH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_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,V,W,X 
_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    x,y,z 
_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
? 2 G N N 
? 2 J N N 
? 2 L N N 
? 2 M N N 
? 2 O N N 
? 2 P 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 64 n n 
PG O2G AGS sing 65 n n 
PG O3G AGS sing 66 n n 
PG O3B AGS sing 67 n n 
PB O1B AGS doub 68 n n 
PB O2B AGS sing 69 n n 
PB O3B AGS sing 70 n n 
PB O3A AGS sing 71 n n 
PA O1A AGS doub 72 n n 
PA O2A AGS sing 73 n n 
PA O3A AGS sing 74 n n 
PA O5' AGS sing 75 n n 
O5' C5' AGS sing 76 n n 
C5' C4' AGS sing 77 n n 
C4' O4' AGS sing 78 n n 
C4' C3' AGS sing 79 n n 
O4' C1' AGS sing 80 n n 
C3' O3' AGS sing 81 n n 
C3' C2' AGS sing 82 n n 
C2' O2' AGS sing 83 n n 
C2' C1' AGS sing 84 n n 
C1' N9 AGS sing 85 n n 
N9 C8 AGS sing 86 n y 
N9 C4 AGS sing 87 n y 
C8 N7 AGS doub 88 n y 
N7 C5 AGS sing 89 n y 
C5 C6 AGS sing 90 n y 
C5 C4 AGS doub 91 n y 
C6 N6 AGS sing 92 n n 
C6 N1 AGS doub 93 n y 
N1 C2 AGS sing 94 n y 
C2 N3 AGS doub 95 n y 
N3 C4 AGS sing 96 n y 
O2G HOG2 AGS sing 97 n n 
O3G H21 AGS sing 98 n n 
O2B HOB2 AGS sing 99 n n 
O2A HOA2 AGS sing 100 n n 
C5' "H5'1" AGS sing 101 n n 
C5' "H5'2" AGS sing 102 n n 
C4' H4' AGS sing 103 n n 
C3' H3' AGS sing 104 n n 
O3' HO3' AGS sing 105 n n 
C2' H2' AGS sing 106 n n 
O2' HO2' AGS sing 107 n n 
C1' H1' AGS sing 108 n n 
C8 H8 AGS sing 109 n n 
N6 HN61 AGS sing 110 n n 
N6 HN62 AGS sing 111 n n 
C2 H2 AGS sing 112 n n 
#
_atom_sites.entry_id                     4NAH 
_atom_sites.fract_transf_matrix[1][1]    0.014604 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001198 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009491 
_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]    0.012545 
_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
G 2 AGS A 1 201 1 AGS AGS . 
H 3 2VJ A 1 202 1 2VJ INH . 
I 3 2VJ A 1 203 1 2VJ INH . 
J 2 AGS B 1 201 1 AGS AGS . 
K 3 2VJ B 1 202 1 2VJ INH . 
L 2 AGS C 1 201 1 AGS AGS . 
M 2 AGS D 1 201 1 AGS AGS . 
N 3 2VJ D 1 202 1 2VJ INH . 
O 2 AGS E 1 201 1 AGS AGS . 
P 2 AGS F 1 201 1 AGS AGS . 
Q 3 2VJ F 1 202 1 2VJ INH . 
R 3 2VJ F 1 203 1 2VJ INH . 
S 4 HOH A 1 301 2 HOH HOH . 
S 4 HOH A 2 302 11 HOH HOH . 
S 4 HOH A 3 303 14 HOH HOH . 
S 4 HOH A 4 304 17 HOH HOH . 
S 4 HOH A 5 305 20 HOH HOH . 
S 4 HOH A 6 306 22 HOH HOH . 
S 4 HOH A 7 307 26 HOH HOH . 
S 4 HOH A 8 308 27 HOH HOH . 
S 4 HOH A 9 309 37 HOH HOH . 
S 4 HOH A 10 310 40 HOH HOH . 
S 4 HOH A 11 311 41 HOH HOH . 
S 4 HOH A 12 312 48 HOH HOH . 
S 4 HOH A 13 313 51 HOH HOH . 
S 4 HOH A 14 314 57 HOH HOH . 
S 4 HOH A 15 315 61 HOH HOH . 
S 4 HOH A 16 316 71 HOH HOH . 
S 4 HOH A 17 317 75 HOH HOH . 
T 4 HOH B 1 301 4 HOH HOH . 
T 4 HOH B 2 302 5 HOH HOH . 
T 4 HOH B 3 303 10 HOH HOH . 
T 4 HOH B 4 304 12 HOH HOH . 
T 4 HOH B 5 305 16 HOH HOH . 
T 4 HOH B 6 306 24 HOH HOH . 
T 4 HOH B 7 307 36 HOH HOH . 
T 4 HOH B 8 308 39 HOH HOH . 
T 4 HOH B 9 309 44 HOH HOH . 
T 4 HOH B 10 310 45 HOH HOH . 
T 4 HOH B 11 311 46 HOH HOH . 
T 4 HOH B 12 312 50 HOH HOH . 
T 4 HOH B 13 313 55 HOH HOH . 
T 4 HOH B 14 314 56 HOH HOH . 
T 4 HOH B 15 315 58 HOH HOH . 
T 4 HOH B 16 316 62 HOH HOH . 
T 4 HOH B 17 317 65 HOH HOH . 
T 4 HOH B 18 318 67 HOH HOH . 
T 4 HOH B 19 319 68 HOH HOH . 
T 4 HOH B 20 320 69 HOH HOH . 
T 4 HOH B 21 321 74 HOH HOH . 
T 4 HOH B 22 322 76 HOH HOH . 
U 4 HOH C 1 301 1 HOH HOH . 
U 4 HOH C 2 302 3 HOH HOH . 
U 4 HOH C 3 303 13 HOH HOH . 
U 4 HOH C 4 304 19 HOH HOH . 
U 4 HOH C 5 305 25 HOH HOH . 
U 4 HOH C 6 306 34 HOH HOH . 
U 4 HOH C 7 307 38 HOH HOH . 
U 4 HOH C 8 308 49 HOH HOH . 
U 4 HOH C 9 309 53 HOH HOH . 
U 4 HOH C 10 310 54 HOH HOH . 
U 4 HOH C 11 311 63 HOH HOH . 
U 4 HOH C 12 312 64 HOH HOH . 
U 4 HOH C 13 313 70 HOH HOH . 
V 4 HOH D 1 301 6 HOH HOH . 
V 4 HOH D 2 302 9 HOH HOH . 
V 4 HOH D 3 303 21 HOH HOH . 
V 4 HOH D 4 304 29 HOH HOH . 
V 4 HOH D 5 305 30 HOH HOH . 
V 4 HOH D 6 306 31 HOH HOH . 
V 4 HOH D 7 307 32 HOH HOH . 
V 4 HOH D 8 308 60 HOH HOH . 
V 4 HOH D 9 309 72 HOH HOH . 
V 4 HOH D 10 310 78 HOH HOH . 
W 4 HOH E 1 301 33 HOH HOH . 
W 4 HOH E 2 302 43 HOH HOH . 
W 4 HOH E 3 303 77 HOH HOH . 
X 4 HOH F 1 301 7 HOH HOH . 
X 4 HOH F 2 302 8 HOH HOH . 
X 4 HOH F 3 303 15 HOH HOH . 
X 4 HOH F 4 304 18 HOH HOH . 
X 4 HOH F 5 305 23 HOH HOH . 
X 4 HOH F 6 306 28 HOH HOH . 
X 4 HOH F 7 307 35 HOH HOH . 
X 4 HOH F 8 308 42 HOH HOH . 
X 4 HOH F 9 309 47 HOH HOH . 
X 4 HOH F 10 310 52 HOH HOH . 
X 4 HOH F 11 311 59 HOH HOH . 
X 4 HOH F 12 312 66 HOH HOH . 
X 4 HOH F 13 313 73 HOH HOH . 
#
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 . . . M 2 -32.248 -12.292 -17.527 1 50 ? PG AGS 201 D 1 
HETATM 2 S S1G AGS . . . M 2 -31.671 -10.984 -16.334 1 50 ? S1G AGS 201 D 1 
HETATM 3 O O2G AGS . . . M 2 -33.582 -12.988 -16.957 1 45.02 ? O2G AGS 201 D 1 
HETATM 4 O O3G AGS . . . M 2 -31.097 -13.403 -17.702 1 50 ? O3G AGS 201 D 1 
HETATM 5 P PB AGS . . . M 2 -31.156 -11.477 -19.725 1 50 ? PB AGS 201 D 1 
HETATM 6 O O1B AGS . . . M 2 -31.398 -11.396 -21.183 1 48.65 ? O1B AGS 201 D 1 
HETATM 7 O O2B AGS . . . M 2 -30.24 -12.762 -19.405 1 50 ? O2B AGS 201 D 1 
HETATM 8 O O3B AGS . . . M 2 -32.563 -11.616 -18.955 1 50 ? O3B AGS 201 D 1 
HETATM 9 P PA AGS . . . M 2 -31.174 -8.898 -19.892 1 36.81 ? PA AGS 201 D 1 
HETATM 10 O O1A AGS . . . M 2 -31.108 -9.016 -21.497 1 43.8 ? O1A AGS 201 D 1 
HETATM 11 O O2A AGS . . . M 2 -32.588 -8.907 -19.454 1 40.86 ? O2A AGS 201 D 1 
HETATM 12 O O3A AGS . . . M 2 -30.401 -10.144 -19.231 1 46.4 ? O3A AGS 201 D 1 
HETATM 13 O O5' AGS . . . M 2 -30.478 -7.524 -19.426 1 38.68 ? O5' AGS 201 D 1 
HETATM 14 C C5' AGS . . . M 2 -29.392 -7.285 -20.323 1 36.65 ? C5' AGS 201 D 1 
HETATM 15 C C4' AGS . . . M 2 -28.067 -7.425 -19.574 1 35.92 ? C4' AGS 201 D 1 
HETATM 16 O O4' AGS . . . M 2 -28.277 -7.299 -18.15 1 32.89 ? O4' AGS 201 D 1 
HETATM 17 C C3' AGS . . . M 2 -27.483 -8.842 -19.763 1 33.15 ? C3' AGS 201 D 1 
HETATM 18 O O3' AGS . . . M 2 -26.493 -8.843 -20.793 1 35.72 ? O3' AGS 201 D 1 
HETATM 19 C C2' AGS . . . M 2 -26.844 -9.171 -18.394 1 30.84 ? C2' AGS 201 D 1 
HETATM 20 O O2' AGS . . . M 2 -25.438 -9.385 -18.537 1 28.9 ? O2' AGS 201 D 1 
HETATM 21 C C1' AGS . . . M 2 -27.124 -7.916 -17.539 1 30.63 ? C1' AGS 201 D 1 
HETATM 22 N N9 AGS . . . M 2 -27.422 -8.297 -16.156 1 30.51 ? N9 AGS 201 D 1 
HETATM 23 C C8 AGS . . . M 2 -28.491 -9.029 -15.735 1 31.43 ? C8 AGS 201 D 1 
HETATM 24 N N7 AGS . . . M 2 -28.445 -9.181 -14.444 1 27.72 ? N7 AGS 201 D 1 
HETATM 25 C C5 AGS . . . M 2 -27.346 -8.558 -13.955 1 26.66 ? C5 AGS 201 D 1 
HETATM 26 C C6 AGS . . . M 2 -26.792 -8.389 -12.675 1 24.82 ? C6 AGS 201 D 1 
HETATM 27 N N6 AGS . . . M 2 -27.408 -8.933 -11.561 1 25.26 ? N6 AGS 201 D 1 
HETATM 28 N N1 AGS . . . M 2 -25.665 -7.697 -12.558 1 24.58 ? N1 AGS 201 D 1 
HETATM 29 C C2 AGS . . . M 2 -25.071 -7.174 -13.616 1 26.73 ? C2 AGS 201 D 1 
HETATM 30 N N3 AGS . . . M 2 -25.552 -7.306 -14.834 1 26.32 ? N3 AGS 201 D 1 
HETATM 31 C C4 AGS . . . M 2 -26.676 -7.983 -15.048 1 28.73 ? C4 AGS 201 D 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#