data_9UBG
#
_model_server_result.job_id            LHmMHugfLrI08j0MoXKIyg 
_model_server_result.datetime_utc      '2025-06-16 09:08:59' 
_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          9ubg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":1102}' 
#
_entry.id    9UBG 
#
_exptl.entry_id    9UBG 
_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    4 
_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            9UBG 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9UBG 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 E N N 
? 2 H N N 
? 2 L N N 
? 2 O 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
metalc ? metalc1 A OD2 ASP 533 A ASP 533 1_555 F ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? 
metalc ? metalc2 A NE2 HIS 732 A HIS 732 1_555 F ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc3 A NE2 HIS 734 A HIS 734 1_555 F ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc4 B OD2 ASP 533 B ASP 533 1_555 I ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? 
metalc ? metalc5 B NE2 HIS 732 B HIS 732 1_555 I ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc6 B NE2 HIS 734 B HIS 734 1_555 I ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc7 C OD2 ASP 533 C ASP 533 1_555 M ZN ZN . C ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? 
metalc ? metalc8 C NE2 HIS 732 C HIS 732 1_555 M ZN ZN . C ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc9 C NE2 HIS 734 C HIS 734 1_555 M ZN ZN . C ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc10 D OD2 ASP 533 D ASP 533 1_555 P ZN ZN . D ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? 
metalc ? metalc11 D NE2 HIS 732 D HIS 732 1_555 P ZN ZN . D ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc12 D NE2 HIS 734 D HIS 734 1_555 P ZN ZN . D ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
#
_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 92 n n 
PB O2B ADP sing 93 n n 
PB O3B ADP sing 94 n n 
PB O3A ADP sing 95 n n 
O2B HOB2 ADP sing 96 n n 
O3B HOB3 ADP sing 97 n n 
PA O1A ADP doub 98 n n 
PA O2A ADP sing 99 n n 
PA O3A ADP sing 100 n n 
PA O5' ADP sing 101 n n 
O2A HOA2 ADP sing 102 n n 
O5' C5' ADP sing 103 n n 
C5' C4' ADP sing 104 n n 
C5' "H5'1" ADP sing 105 n n 
C5' "H5'2" ADP sing 106 n n 
C4' O4' ADP sing 107 n n 
C4' C3' ADP sing 108 n n 
C4' H4' ADP sing 109 n n 
O4' C1' ADP sing 110 n n 
C3' O3' ADP sing 111 n n 
C3' C2' ADP sing 112 n n 
C3' H3' ADP sing 113 n n 
O3' HO3' ADP sing 114 n n 
C2' O2' ADP sing 115 n n 
C2' C1' ADP sing 116 n n 
C2' H2' ADP sing 117 n n 
O2' HO2' ADP sing 118 n n 
C1' N9 ADP sing 119 n n 
C1' H1' ADP sing 120 n n 
N9 C8 ADP sing 121 n y 
N9 C4 ADP sing 122 n y 
C8 N7 ADP doub 123 n y 
C8 H8 ADP sing 124 n n 
N7 C5 ADP sing 125 n y 
C5 C6 ADP sing 126 n y 
C5 C4 ADP doub 127 n y 
C6 N6 ADP sing 128 n n 
C6 N1 ADP doub 129 n y 
N6 HN61 ADP sing 130 n n 
N6 HN62 ADP sing 131 n n 
N1 C2 ADP sing 132 n y 
C2 N3 ADP doub 133 n y 
C2 H2 ADP sing 134 n n 
N3 C4 ADP sing 135 n y 
#
_atom_sites.entry_id                     9UBG 
_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
E 2 ADP A 1 1101 1101 ADP ADP . 
F 3 ZN A 1 1102 1103 ZN ZN . 
G 4 ACO A 1 1103 1102 ACO ACO . 
H 2 ADP B 1 1101 1101 ADP ADP . 
I 3 ZN B 1 1102 1103 ZN ZN . 
J 4 ACO B 1 1103 1102 ACO ACO . 
K 4 ACO C 1 1101 1102 ACO ACO . 
L 2 ADP C 1 1102 1101 ADP ADP . 
M 3 ZN C 1 1103 1103 ZN ZN . 
N 4 ACO D 1 1101 1102 ACO ACO . 
O 2 ADP D 1 1102 1101 ADP ADP . 
P 3 ZN D 1 1103 1103 ZN ZN . 
Q 5 HOH A 1 1201 1107 HOH HOH . 
Q 5 HOH A 2 1202 1105 HOH HOH . 
Q 5 HOH A 3 1203 1106 HOH HOH . 
Q 5 HOH A 4 1204 1104 HOH HOH . 
R 5 HOH B 1 1201 1106 HOH HOH . 
R 5 HOH B 2 1202 1104 HOH HOH . 
R 5 HOH B 3 1203 1105 HOH HOH . 
S 5 HOH C 1 1201 1104 HOH HOH . 
S 5 HOH C 2 1202 1107 HOH HOH . 
S 5 HOH C 3 1203 1106 HOH HOH . 
S 5 HOH C 4 1204 1105 HOH HOH . 
T 5 HOH D 1 1201 1105 HOH HOH . 
T 5 HOH D 2 1202 1104 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 . . . O 2 166.324 218.436 180.358 1 151.69 ? PB ADP 1102 D 1 
HETATM 2 O O1B ADP . . . O 2 165.378 217.265 180.469 1 151.56 ? O1B ADP 1102 D 1 
HETATM 3 O O2B ADP . . . O 2 166.218 219.198 179.059 1 135.94 ? O2B ADP 1102 D 1 
HETATM 4 O O3B ADP . . . O 2 167.737 218.144 180.802 1 143.93 ? O3B ADP 1102 D 1 
HETATM 5 P PA ADP . . . O 2 165.883 219.161 183.03 1 153.49 ? PA ADP 1102 D 1 
HETATM 6 O O1A ADP . . . O 2 165.685 217.678 183.232 1 147.8 ? O1A ADP 1102 D 1 
HETATM 7 O O2A ADP . . . O 2 167.115 219.826 183.595 1 145.09 ? O2A ADP 1102 D 1 
HETATM 8 O O3A ADP . . . O 2 165.782 219.479 181.455 1 148.19 ? O3A ADP 1102 D 1 
HETATM 9 O O5' ADP . . . O 2 164.573 219.909 183.583 1 144.73 ? O5' ADP 1102 D 1 
HETATM 10 C C5' ADP . . . O 2 163.872 219.428 184.725 1 144.09 ? C5' ADP 1102 D 1 
HETATM 11 C C4' ADP . . . O 2 162.397 219.398 184.349 1 143.02 ? C4' ADP 1102 D 1 
HETATM 12 O O4' ADP . . . O 2 161.561 219.344 185.505 1 143.22 ? O4' ADP 1102 D 1 
HETATM 13 C C3' ADP . . . O 2 162.007 220.645 183.575 1 140.22 ? C3' ADP 1102 D 1 
HETATM 14 O O3' ADP . . . O 2 161.786 220.306 182.205 1 132.43 ? O3' ADP 1102 D 1 
HETATM 15 C C2' ADP . . . O 2 160.721 221.134 184.205 1 136.39 ? C2' ADP 1102 D 1 
HETATM 16 O O2' ADP . . . O 2 159.686 221.195 183.221 1 125.45 ? O2' ADP 1102 D 1 
HETATM 17 C C1' ADP . . . O 2 160.376 220.107 185.271 1 140.81 ? C1' ADP 1102 D 1 
HETATM 18 N N9 ADP . . . O 2 159.949 220.772 186.525 1 149.66 ? N9 ADP 1102 D 1 
HETATM 19 C C8 ADP . . . O 2 158.796 220.528 187.174 1 149.85 ? C8 ADP 1102 D 1 
HETATM 20 N N7 ADP . . . O 2 158.687 221.296 188.287 1 158.55 ? N7 ADP 1102 D 1 
HETATM 21 C C5 ADP . . . O 2 159.795 222.055 188.36 1 161.93 ? C5 ADP 1102 D 1 
HETATM 22 C C6 ADP . . . O 2 160.315 223.084 189.287 1 168.23 ? C6 ADP 1102 D 1 
HETATM 23 N N6 ADP . . . O 2 159.604 223.451 190.378 1 170.65 ? N6 ADP 1102 D 1 
HETATM 24 N N1 ADP . . . O 2 161.515 223.637 189.006 1 167.99 ? N1 ADP 1102 D 1 
HETATM 25 C C2 ADP . . . O 2 162.222 223.273 187.921 1 157.22 ? C2 ADP 1102 D 1 
HETATM 26 N N3 ADP . . . O 2 161.811 222.346 187.038 1 153.44 ? N3 ADP 1102 D 1 
HETATM 27 C C4 ADP . . . O 2 160.624 221.712 187.195 1 155.17 ? C4 ADP 1102 D 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    50 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#