data_3AKL
#
_model_server_result.job_id            Mu6ZebN9g6SMfTZaJs3-JQ 
_model_server_result.datetime_utc      '2025-08-31 09:18:34' 
_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":"K","auth_seq_id":500}' 
#
_entry.id    3AKL 
#
_exptl.entry_id    3AKL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             K 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 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 PB ADP . . . K 4 30.892 33.267 -1.774 1 71.64 ? PB ADP 500 C 1 
HETATM 2 O O1B ADP . . . K 4 31.447 32.568 -3.009 1 66.38 ? O1B ADP 500 C 1 
HETATM 3 O O2B ADP . . . K 4 31.277 32.69 -0.43 1 67.15 ? O2B ADP 500 C 1 
HETATM 4 O O3B ADP . . . K 4 29.421 33.602 -1.915 1 64.1 ? O3B ADP 500 C 1 
HETATM 5 P PA ADP . . . K 4 31.244 35.967 -2.454 1 75.52 ? PA ADP 500 C 1 
HETATM 6 O O1A ADP . . . K 4 32.237 36.411 -3.512 1 63.81 ? O1A ADP 500 C 1 
HETATM 7 O O2A ADP . . . K 4 29.786 35.806 -2.824 1 78.2 ? O2A ADP 500 C 1 
HETATM 8 O O3A ADP . . . K 4 31.687 34.658 -1.636 1 62.93 ? O3A ADP 500 C 1 
HETATM 9 O O5' ADP . . . K 4 31.229 37.071 -1.315 1 62.87 ? O5' ADP 500 C 1 
HETATM 10 C C5' ADP . . . K 4 30.321 38.053 -1.739 1 63.05 ? C5' ADP 500 C 1 
HETATM 11 C C4' ADP . . . K 4 29.762 38.799 -0.57 1 67.41 ? C4' ADP 500 C 1 
HETATM 12 O O4' ADP . . . K 4 30.788 39.677 -0.122 1 67.22 ? O4' ADP 500 C 1 
HETATM 13 C C3' ADP . . . K 4 28.633 39.621 -1.141 1 67.56 ? C3' ADP 500 C 1 
HETATM 14 O O3' ADP . . . K 4 27.502 39.577 -0.258 1 75.62 ? O3' ADP 500 C 1 
HETATM 15 C C2' ADP . . . K 4 29.189 41.02 -1.23 1 64.61 ? C2' ADP 500 C 1 
HETATM 16 O O2' ADP . . . K 4 28.354 41.834 -0.409 1 68.51 ? O2' ADP 500 C 1 
HETATM 17 C C1' ADP . . . K 4 30.606 40.979 -0.665 1 61.85 ? C1' ADP 500 C 1 
HETATM 18 N N9 ADP . . . K 4 31.627 41.161 -1.738 1 63.79 ? N9 ADP 500 C 1 
HETATM 19 C C8 ADP . . . K 4 31.956 40.218 -2.643 1 64.77 ? C8 ADP 500 C 1 
HETATM 20 N N7 ADP . . . K 4 32.903 40.647 -3.501 1 60.73 ? N7 ADP 500 C 1 
HETATM 21 C C5 ADP . . . K 4 33.204 41.909 -3.153 1 61.21 ? C5 ADP 500 C 1 
HETATM 22 C C6 ADP . . . K 4 34.143 42.94 -3.66 1 63.73 ? C6 ADP 500 C 1 
HETATM 23 N N6 ADP . . . K 4 34.954 42.692 -4.732 1 55.02 ? N6 ADP 500 C 1 
HETATM 24 N N1 ADP . . . K 4 34.151 44.128 -3 1 65.33 ? N1 ADP 500 C 1 
HETATM 25 C C2 ADP . . . K 4 33.349 44.377 -1.936 1 64.37 ? C2 ADP 500 C 1 
HETATM 26 N N3 ADP . . . K 4 32.477 43.486 -1.426 1 63.24 ? N3 ADP 500 C 1 
HETATM 27 C C4 ADP . . . K 4 32.363 42.252 -1.987 1 62.8 ? C4 ADP 500 C 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           356 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#