data_9B16
#
_model_server_result.job_id            i87Dz5TJOF3fgmbEcel9yQ 
_model_server_result.datetime_utc      '2025-03-02 23:51:56' 
_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          9b16 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":401}' 
#
_entry.id    9B16 
#
_exptl.entry_id    9B16 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_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            9B16 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9B16 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,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    ? 
_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 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q N N 
? 2 S N N 
? 2 U N N 
? 2 W 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
covale ? covale1 A SG CYS 306 A CYS 278 1_555 J C5 KLU . A KLU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.73 ? 
covale ? covale2 B SG CYS 306 B CYS 278 1_555 L C5 KLU . B KLU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.711 ? 
covale ? covale3 C SG CYS 306 C CYS 278 1_555 N C5 KLU . C KLU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? 
covale ? covale4 D SG CYS 306 D CYS 278 1_555 P C5 KLU . D KLU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.713 ? 
covale ? covale5 E SG CYS 306 E CYS 278 1_555 R C5 KLU . E KLU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.708 ? 
covale ? covale6 F SG CYS 306 F CYS 278 1_555 T C5 KLU . F KLU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.754 ? 
covale ? covale7 G SG CYS 306 G CYS 278 1_555 V C5 KLU . G KLU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? 
covale ? covale8 H SG CYS 306 H CYS 278 1_555 X C5 KLU . H KLU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.732 ? 
#
_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                     9B16 
_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
I 2 ADP A 1 401 402 ADP ADP . 
J 3 KLU A 1 402 403 KLU KLU . 
K 2 ADP B 1 401 402 ADP ADP . 
L 3 KLU B 1 402 403 KLU KLU . 
M 2 ADP C 1 401 402 ADP ADP . 
N 3 KLU C 1 402 403 KLU KLU . 
O 2 ADP D 1 401 402 ADP ADP . 
P 3 KLU D 1 402 403 KLU KLU . 
Q 2 ADP E 1 401 402 ADP ADP . 
R 3 KLU E 1 402 403 KLU KLU . 
S 2 ADP F 1 401 402 ADP ADP . 
T 3 KLU F 1 402 403 KLU KLU . 
U 2 ADP G 1 401 402 ADP ADP . 
V 3 KLU G 1 402 403 KLU KLU . 
W 2 ADP H 1 401 402 ADP ADP . 
X 3 KLU H 1 402 403 KLU KLU . 
#
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 . . . U 2 175.422 113.414 152.397 1 160.21 ? PB ADP 401 G 1 
HETATM 2 O O1B ADP . . . U 2 174.263 112.589 151.895 1 157.65 ? O1B ADP 401 G 1 
HETATM 3 O O2B ADP . . . U 2 175.301 113.851 153.836 1 155.66 ? O2B ADP 401 G 1 
HETATM 4 O O3B ADP . . . U 2 175.872 114.5 151.452 1 143.84 ? O3B ADP 401 G 1 
HETATM 5 P PA ADP . . . U 2 176.897 111.429 151.13 1 162.91 ? PA ADP 401 G 1 
HETATM 6 O O1A ADP . . . U 2 176.607 110.003 151.526 1 162.97 ? O1A ADP 401 G 1 
HETATM 7 O O2A ADP . . . U 2 176.197 112.061 149.952 1 154.67 ? O2A ADP 401 G 1 
HETATM 8 O O3A ADP . . . U 2 176.653 112.38 152.403 1 161.46 ? O3A ADP 401 G 1 
HETATM 9 O O5' ADP . . . U 2 178.481 111.586 150.899 1 154.78 ? O5' ADP 401 G 1 
HETATM 10 C C5' ADP . . . U 2 178.992 111.724 149.577 1 154.47 ? C5' ADP 401 G 1 
HETATM 11 C C4' ADP . . . U 2 180.514 111.768 149.606 1 152.05 ? C4' ADP 401 G 1 
HETATM 12 O O4' ADP . . . U 2 180.983 112.455 150.769 1 148.04 ? O4' ADP 401 G 1 
HETATM 13 C C3' ADP . . . U 2 181.121 110.374 149.639 1 159.52 ? C3' ADP 401 G 1 
HETATM 14 O O3' ADP . . . U 2 181.76 110.084 148.392 1 161.31 ? O3' ADP 401 G 1 
HETATM 15 C C2' ADP . . . U 2 182.126 110.392 150.773 1 156.72 ? C2' ADP 401 G 1 
HETATM 16 O O2' ADP . . . U 2 183.411 109.932 150.346 1 157.93 ? O2' ADP 401 G 1 
HETATM 17 C C1' ADP . . . U 2 182.189 111.839 151.225 1 150.45 ? C1' ADP 401 G 1 
HETATM 18 N N9 ADP . . . U 2 182.321 111.913 152.7 1 152.65 ? N9 ADP 401 G 1 
HETATM 19 C C8 ADP . . . U 2 181.315 112.006 153.588 1 152.69 ? C8 ADP 401 G 1 
HETATM 20 N N7 ADP . . . U 2 181.8 112.055 154.856 1 148.8 ? N7 ADP 401 G 1 
HETATM 21 C C5 ADP . . . U 2 183.141 111.989 154.784 1 150.62 ? C5 ADP 401 G 1 
HETATM 22 C C6 ADP . . . U 2 184.268 111.993 155.743 1 155.62 ? C6 ADP 401 G 1 
HETATM 23 N N6 ADP . . . U 2 184.055 112.074 157.077 1 159.83 ? N6 ADP 401 G 1 
HETATM 24 N N1 ADP . . . U 2 185.52 111.908 155.243 1 158.6 ? N1 ADP 401 G 1 
HETATM 25 C C2 ADP . . . U 2 185.76 111.825 153.921 1 158.19 ? C2 ADP 401 G 1 
HETATM 26 N N3 ADP . . . U 2 184.78 111.819 153 1 155.61 ? N3 ADP 401 G 1 
HETATM 27 C C4 ADP . . . U 2 183.478 111.897 153.36 1 152.12 ? C4 ADP 401 G 1 
HETATM 28 H "H5'1" ADP . . . U 2 178.607 112.643 149.13 1 150.53 ? "H5'1" ADP 401 G 1 
HETATM 29 H "H5'2" ADP . . . U 2 178.659 110.884 148.963 1 157.53 ? "H5'2" ADP 401 G 1 
HETATM 30 H H4' ADP . . . U 2 180.868 112.285 148.703 1 151.77 ? H4' ADP 401 G 1 
HETATM 31 H H3' ADP . . . U 2 180.338 109.635 149.855 1 160.49 ? H3' ADP 401 G 1 
HETATM 32 H HO3' ADP . . . U 2 182.064 109.167 148.386 1 162.28 ? HO3' ADP 401 G 1 
HETATM 33 H H2' ADP . . . U 2 181.751 109.771 151.599 1 158.55 ? H2' ADP 401 G 1 
HETATM 34 H HO2' ADP . . . U 2 183.375 108.979 150.186 1 160.8 ? HO2' ADP 401 G 1 
HETATM 35 H H1' ADP . . . U 2 183.054 112.32 150.75 1 152.05 ? H1' ADP 401 G 1 
HETATM 36 H H8 ADP . . . U 2 180.264 112.04 153.328 1 151.24 ? H8 ADP 401 G 1 
HETATM 37 H HN61 ADP . . . U 2 183.113 112.136 157.436 1 153.75 ? HN61 ADP 401 G 1 
HETATM 38 H HN62 ADP . . . U 2 184.839 112.074 157.713 1 157.08 ? HN62 ADP 401 G 1 
HETATM 39 H H2 ADP . . . U 2 186.787 111.761 153.584 1 157.94 ? H2 ADP 401 G 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    595 
_model_server_stats.query_time_ms           717 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           39 
#