data_3AKL
#
_model_server_result.job_id            2Vg-_jfeSYf3NpcQJrmuVg 
_model_server_result.datetime_utc      '2025-08-31 12:22:06' 
_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          3akl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":602}' 
#
_entry.id    3AKL 
#
_exptl.entry_id    3AKL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              506.196 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         78.84 
_cell.angle_beta          71.36 
_cell.angle_gamma         85.44 
_cell.entry_id            3AKL 
_cell.length_a            60.133 
_cell.length_b            74.835 
_cell.length_c            75.815 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3AKL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,I,J,P,Q 1 1 
C,D,K,L,M,N,O,R,S 2 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 E N N 
? 2 H N N 
? 2 M 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
disulf ? disulf1 A SG CYS 61 A CYS 61 1_555 A SG CYS 180 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc1 A OD1 ASN 160 A ASN 160 1_555 G MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? 
metalc ? metalc2 A OD2 ASP 179 A ASP 179 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? 
metalc ? metalc3 A OD1 ASP 179 A ASP 179 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
metalc ? metalc4 G MG MG . A MG 405 1_555 E O1G ANP . A ANP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc5 G MG MG . A MG 405 1_555 E O3A ANP . A ANP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc6 G MG MG . A MG 405 1_555 E O2A ANP . A ANP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? 
metalc ? metalc7 B OD1 ASN 160 B ASN 160 1_555 J MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? 
metalc ? metalc8 B OD1 ASP 179 B ASP 179 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? 
metalc ? metalc9 B OD2 ASP 179 B ASP 179 1_555 J MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? 
metalc ? metalc10 B OG SER 182 B SER 182 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? 
metalc ? metalc11 I MG MG . B MG 401 1_555 H O1G ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? 
metalc ? metalc12 I MG MG . B MG 401 1_555 H O2B ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.912 ? 
metalc ? metalc13 J MG MG . B MG 404 1_555 H O2A ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc14 J MG MG . B MG 404 1_555 H O3G ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? 
metalc ? metalc15 J MG MG . B MG 404 1_555 H O3' ANP . B ANP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? 
metalc ? metalc16 C OD1 ASN 160 C ASN 160 1_555 L MG MG . C MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? 
metalc ? metalc17 C OD2 ASP 179 C ASP 179 1_555 L MG MG . C MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc18 L MG MG . C MG 400 1_555 K O3B ADP . C ADP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? 
metalc ? metalc19 L MG MG . C MG 400 1_555 K O2A ADP . C ADP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? 
metalc ? metalc20 D OD2 ASP 179 D ASP 179 1_555 O MG MG . D MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? 
metalc ? metalc21 O MG MG . D MG 406 1_555 M O2G ANP . D ANP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
#
_chem_comp.formula           'C10 H17 N6 O12 P3' 
_chem_comp.formula_weight    506.196 
_chem_comp.id                ANP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 O1G ANP doub 57 n n 
PG O2G ANP sing 58 n n 
PG O3G ANP sing 59 n n 
PG N3B ANP sing 60 n n 
O2G HOG2 ANP sing 61 n n 
O3G HOG3 ANP sing 62 n n 
PB O1B ANP doub 63 n n 
PB O2B ANP sing 64 n n 
PB N3B ANP sing 65 n n 
PB O3A ANP sing 66 n n 
O2B HOB2 ANP sing 67 n n 
N3B HNB1 ANP sing 68 n n 
PA O1A ANP doub 69 n n 
PA O2A ANP sing 70 n n 
PA O3A ANP sing 71 n n 
PA O5' ANP sing 72 n n 
O2A HOA2 ANP sing 73 n n 
O5' C5' ANP sing 74 n n 
C5' C4' ANP sing 75 n n 
C5' "H5'1" ANP sing 76 n n 
C5' "H5'2" ANP sing 77 n n 
C4' O4' ANP sing 78 n n 
C4' C3' ANP sing 79 n n 
C4' H4' ANP sing 80 n n 
O4' C1' ANP sing 81 n n 
C3' O3' ANP sing 82 n n 
C3' C2' ANP sing 83 n n 
C3' H3' ANP sing 84 n n 
O3' HO3' ANP sing 85 n n 
C2' O2' ANP sing 86 n n 
C2' C1' ANP sing 87 n n 
C2' H2' ANP sing 88 n n 
O2' HO2' ANP sing 89 n n 
C1' N9 ANP sing 90 n n 
C1' H1' ANP sing 91 n n 
N9 C8 ANP sing 92 n y 
N9 C4 ANP sing 93 n y 
C8 N7 ANP doub 94 n y 
C8 H8 ANP sing 95 n n 
N7 C5 ANP sing 96 n y 
C5 C6 ANP sing 97 n y 
C5 C4 ANP doub 98 n y 
C6 N6 ANP sing 99 n n 
C6 N1 ANP doub 100 n y 
N6 HN61 ANP sing 101 n n 
N6 HN62 ANP sing 102 n n 
N1 C2 ANP sing 103 n y 
C2 N3 ANP doub 104 n y 
C2 H2 ANP sing 105 n n 
N3 C4 ANP sing 106 n y 
#
_atom_sites.entry_id                     3AKL 
_atom_sites.fract_transf_matrix[1][1]    0.01663 
_atom_sites.fract_transf_matrix[1][2]    -0.001327 
_atom_sites.fract_transf_matrix[1][3]    -0.005462 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013405 
_atom_sites.fract_transf_matrix[2][3]    -0.002425 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.014147 
_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
E 2 ANP A 1 601 601 ANP ANP . 
F 3 MG A 1 402 402 MG MG . 
G 3 MG A 1 405 405 MG MG . 
H 2 ANP B 1 600 600 ANP ANP . 
I 3 MG B 1 401 401 MG MG . 
J 3 MG B 1 404 404 MG MG . 
K 4 ADP C 1 500 500 ADP ADP . 
L 3 MG C 1 400 400 MG MG . 
M 2 ANP D 1 602 602 ANP ANP . 
N 3 MG D 1 403 403 MG MG . 
O 3 MG D 1 406 406 MG MG . 
P 5 HOH A 1 326 6 HOH HOH . 
P 5 HOH A 2 327 9 HOH HOH . 
P 5 HOH A 3 328 13 HOH HOH . 
P 5 HOH A 4 329 15 HOH HOH . 
P 5 HOH A 5 330 16 HOH HOH . 
P 5 HOH A 6 331 20 HOH HOH . 
P 5 HOH A 7 332 21 HOH HOH . 
P 5 HOH A 8 333 29 HOH HOH . 
P 5 HOH A 9 334 31 HOH HOH . 
P 5 HOH A 10 335 36 HOH HOH . 
P 5 HOH A 11 336 37 HOH HOH . 
P 5 HOH A 12 337 41 HOH HOH . 
P 5 HOH A 13 338 56 HOH HOH . 
Q 5 HOH B 1 326 2 HOH HOH . 
Q 5 HOH B 2 327 7 HOH HOH . 
Q 5 HOH B 3 328 11 HOH HOH . 
Q 5 HOH B 4 329 14 HOH HOH . 
Q 5 HOH B 5 330 17 HOH HOH . 
Q 5 HOH B 6 331 27 HOH HOH . 
Q 5 HOH B 7 332 30 HOH HOH . 
Q 5 HOH B 8 333 39 HOH HOH . 
Q 5 HOH B 9 334 42 HOH HOH . 
Q 5 HOH B 10 335 43 HOH HOH . 
Q 5 HOH B 11 336 46 HOH HOH . 
Q 5 HOH B 12 337 49 HOH HOH . 
Q 5 HOH B 13 338 51 HOH HOH . 
Q 5 HOH B 14 339 54 HOH HOH . 
Q 5 HOH B 15 340 58 HOH HOH . 
Q 5 HOH B 16 341 59 HOH HOH . 
R 5 HOH C 1 326 19 HOH HOH . 
R 5 HOH C 2 327 22 HOH HOH . 
R 5 HOH C 3 328 25 HOH HOH . 
R 5 HOH C 4 329 32 HOH HOH . 
R 5 HOH C 5 330 33 HOH HOH . 
R 5 HOH C 6 331 40 HOH HOH . 
R 5 HOH C 7 332 44 HOH HOH . 
R 5 HOH C 8 333 50 HOH HOH . 
R 5 HOH C 9 334 55 HOH HOH . 
R 5 HOH C 10 335 57 HOH HOH . 
S 5 HOH D 1 326 1 HOH HOH . 
S 5 HOH D 2 327 3 HOH HOH . 
S 5 HOH D 3 328 4 HOH HOH . 
S 5 HOH D 4 329 5 HOH HOH . 
S 5 HOH D 5 330 8 HOH HOH . 
S 5 HOH D 6 331 10 HOH HOH . 
S 5 HOH D 7 332 12 HOH HOH . 
S 5 HOH D 8 333 18 HOH HOH . 
S 5 HOH D 9 334 23 HOH HOH . 
S 5 HOH D 10 335 24 HOH HOH . 
S 5 HOH D 11 336 26 HOH HOH . 
S 5 HOH D 12 337 28 HOH HOH . 
S 5 HOH D 13 338 34 HOH HOH . 
S 5 HOH D 14 339 35 HOH HOH . 
S 5 HOH D 15 340 38 HOH HOH . 
S 5 HOH D 16 341 45 HOH HOH . 
S 5 HOH D 17 342 47 HOH HOH . 
S 5 HOH D 18 343 48 HOH HOH . 
S 5 HOH D 19 344 52 HOH HOH . 
S 5 HOH D 20 345 53 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 ANP . . . M 2 15.181 36.125 8.038 1 65.73 ? PG ANP 602 D 1 
HETATM 2 O O1G ANP . . . M 2 15.593 36.119 6.616 1 68.35 ? O1G ANP 602 D 1 
HETATM 3 O O2G ANP . . . M 2 16.287 36.829 9.001 1 53.37 ? O2G ANP 602 D 1 
HETATM 4 O O3G ANP . . . M 2 14.985 34.595 8.555 1 64.84 ? O3G ANP 602 D 1 
HETATM 5 P PB ANP . . . M 2 13.556 38.203 7.466 1 54.25 ? PB ANP 602 D 1 
HETATM 6 O O1B ANP . . . M 2 13.938 38.046 6.058 1 52.06 ? O1B ANP 602 D 1 
HETATM 7 O O2B ANP . . . M 2 12.171 38.609 7.765 1 59.74 ? O2B ANP 602 D 1 
HETATM 8 N N3B ANP . . . M 2 13.753 36.85 8.329 1 59.99 ? N3B ANP 602 D 1 
HETATM 9 P PA ANP . . . M 2 14.071 40.744 8.445 1 45.44 ? PA ANP 602 D 1 
HETATM 10 O O1A ANP . . . M 2 12.947 40.877 7.52 1 57.11 ? O1A ANP 602 D 1 
HETATM 11 O O2A ANP . . . M 2 13.867 41.138 9.858 1 42.26 ? O2A ANP 602 D 1 
HETATM 12 O O3A ANP . . . M 2 14.592 39.233 8.226 1 49.47 ? O3A ANP 602 D 1 
HETATM 13 O O5' ANP . . . M 2 15.191 41.623 7.774 1 48.19 ? O5' ANP 602 D 1 
HETATM 14 C C5' ANP . . . M 2 15.343 41.701 6.367 1 42.1 ? C5' ANP 602 D 1 
HETATM 15 C C4' ANP . . . M 2 16.673 42.41 6.129 1 51.99 ? C4' ANP 602 D 1 
HETATM 16 O O4' ANP . . . M 2 16.481 43.874 6.237 1 47.26 ? O4' ANP 602 D 1 
HETATM 17 C C3' ANP . . . M 2 17.725 41.982 7.188 1 49.88 ? C3' ANP 602 D 1 
HETATM 18 O O3' ANP . . . M 2 18.736 41.14 6.586 1 44.96 ? O3' ANP 602 D 1 
HETATM 19 C C2' ANP . . . M 2 18.364 43.301 7.661 1 51.34 ? C2' ANP 602 D 1 
HETATM 20 O O2' ANP . . . M 2 19.669 43.526 7.055 1 44.44 ? O2' ANP 602 D 1 
HETATM 21 C C1' ANP . . . M 2 17.408 44.424 7.217 1 46.58 ? C1' ANP 602 D 1 
HETATM 22 N N9 ANP . . . M 2 16.552 44.942 8.289 1 42.48 ? N9 ANP 602 D 1 
HETATM 23 C C8 ANP . . . M 2 15.865 44.252 9.184 1 42.15 ? C8 ANP 602 D 1 
HETATM 24 N N7 ANP . . . M 2 15.198 45.091 9.971 1 41.02 ? N7 ANP 602 D 1 
HETATM 25 C C5 ANP . . . M 2 15.463 46.327 9.569 1 40.78 ? C5 ANP 602 D 1 
HETATM 26 C C6 ANP . . . M 2 15.074 47.592 9.989 1 41.01 ? C6 ANP 602 D 1 
HETATM 27 N N6 ANP . . . M 2 14.25 47.762 11.003 1 41.67 ? N6 ANP 602 D 1 
HETATM 28 N N1 ANP . . . M 2 15.542 48.658 9.335 1 44.11 ? N1 ANP 602 D 1 
HETATM 29 C C2 ANP . . . M 2 16.369 48.52 8.308 1 46.05 ? C2 ANP 602 D 1 
HETATM 30 N N3 ANP . . . M 2 16.77 47.336 7.883 1 44.4 ? N3 ANP 602 D 1 
HETATM 31 C C4 ANP . . . M 2 16.319 46.226 8.49 1 44.45 ? C4 ANP 602 D 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           390 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#