data_8D17
#
_model_server_result.job_id            vvi8Rqx2cBb3WyftcLaFnQ 
_model_server_result.datetime_utc      '2024-12-19 07:13:51' 
_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          8d17 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":401}' 
#
_entry.id    8D17 
#
_exptl.entry_id    8D17 
_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    7 
_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            8D17 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8D17 
_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    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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 
_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 H N N 
? 2 J N N 
? 2 L N N 
? 2 N N N 
? 2 P N N 
? 2 R N N 
? 2 T 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 C GLU 74 A GLU 72 1_555 A N HIC 75 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C HIC 75 A HIC 73 1_555 A N GLY 76 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale3 B C GLU 74 B GLU 72 1_555 B N HIC 75 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B C HIC 75 B HIC 73 1_555 B N GLY 76 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale5 C C GLU 74 C GLU 72 1_555 C N HIC 75 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale6 C C HIC 75 C HIC 73 1_555 C N GLY 76 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale7 D C GLU 74 D GLU 72 1_555 D N HIC 75 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale8 D C HIC 75 D HIC 73 1_555 D N GLY 76 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale9 E C GLU 74 E GLU 72 1_555 E N HIC 75 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale10 E C HIC 75 E HIC 73 1_555 E N GLY 76 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale11 F C GLU 74 F GLU 72 1_555 F N HIC 75 F HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale12 F C HIC 75 F HIC 73 1_555 F N GLY 76 F GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale13 G C GLU 74 G GLU 72 1_555 G N HIC 75 G HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale14 G C HIC 75 G HIC 73 1_555 G N GLY 76 G GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
metalc ? metalc1 H O2B ADP . A ADP 401 1_555 I MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc2 J O3B ADP . B ADP 401 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? 
metalc ? metalc3 L O2B ADP . C ADP 401 1_555 M MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc4 N O2B ADP . D ADP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? 
metalc ? metalc5 N O3B ADP . D ADP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc6 E OE1 GLN 139 E GLN 137 1_555 Q MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? 
metalc ? metalc7 R O3B ADP . F ADP 401 1_555 S MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc8 G OE1 GLN 139 G GLN 137 1_555 U MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? 
metalc ? metalc9 T O2B ADP . G ADP 401 1_555 U MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? 
#
_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     ? 
#
_atom_sites.entry_id                     8D17 
_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
H 2 ADP A 1 401 376 ADP ADP . 
I 3 MG A 1 402 377 MG MG . 
J 2 ADP B 1 401 376 ADP ADP . 
K 3 MG B 1 402 377 MG MG . 
L 2 ADP C 1 401 376 ADP ADP . 
M 3 MG C 1 402 377 MG MG . 
N 2 ADP D 1 401 376 ADP ADP . 
O 3 MG D 1 402 377 MG MG . 
P 2 ADP E 1 401 376 ADP ADP . 
Q 3 MG E 1 402 377 MG MG . 
R 2 ADP F 1 401 376 ADP ADP . 
S 3 MG F 1 402 377 MG MG . 
T 2 ADP G 1 401 376 ADP ADP . 
U 3 MG G 1 402 377 MG MG . 
#
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 . . . J 2 259.283 280.556 214.153 1 33.98 ? PB ADP 401 B 1 
HETATM 2 O O1B ADP . . . J 2 259.592 281.617 213.212 1 33.98 ? O1B ADP 401 B 1 
HETATM 3 O O2B ADP . . . J 2 260.485 279.74 214.214 1 33.98 ? O2B ADP 401 B 1 
HETATM 4 O O3B ADP . . . J 2 259.238 281.208 215.453 1 33.98 ? O3B ADP 401 B 1 
HETATM 5 P PA ADP . . . J 2 256.565 280.595 213.348 1 33.98 ? PA ADP 401 B 1 
HETATM 6 O O1A ADP . . . J 2 256.938 281.783 212.602 1 33.98 ? O1A ADP 401 B 1 
HETATM 7 O O2A ADP . . . J 2 255.927 281.173 214.521 1 33.98 ? O2A ADP 401 B 1 
HETATM 8 O O3A ADP . . . J 2 257.913 279.756 213.745 1 33.98 ? O3A ADP 401 B 1 
HETATM 9 O O5' ADP . . . J 2 255.507 279.673 212.502 1 33.98 ? O5' ADP 401 B 1 
HETATM 10 C C5' ADP . . . J 2 255.894 279.21 211.247 1 33.98 ? C5' ADP 401 B 1 
HETATM 11 C C4' ADP . . . J 2 255.127 277.962 210.969 1 33.98 ? C4' ADP 401 B 1 
HETATM 12 O O4' ADP . . . J 2 253.742 278.149 211.377 1 33.98 ? O4' ADP 401 B 1 
HETATM 13 C C3' ADP . . . J 2 255.112 277.692 209.507 1 33.98 ? C3' ADP 401 B 1 
HETATM 14 O O3' ADP . . . J 2 255.205 276.285 209.281 1 33.98 ? O3' ADP 401 B 1 
HETATM 15 C C2' ADP . . . J 2 253.809 278.169 209.038 1 33.98 ? C2' ADP 401 B 1 
HETATM 16 O O2' ADP . . . J 2 253.38 277.408 207.908 1 33.98 ? O2' ADP 401 B 1 
HETATM 17 C C1' ADP . . . J 2 252.908 277.933 210.201 1 33.98 ? C1' ADP 401 B 1 
HETATM 18 N N9 ADP . . . J 2 251.801 278.822 210.168 1 33.98 ? N9 ADP 401 B 1 
HETATM 19 C C8 ADP . . . J 2 251.979 280.104 210.12 1 33.98 ? C8 ADP 401 B 1 
HETATM 20 N N7 ADP . . . J 2 250.732 280.743 210.089 1 33.98 ? N7 ADP 401 B 1 
HETATM 21 C C5 ADP . . . J 2 249.871 279.5 210.131 1 33.98 ? C5 ADP 401 B 1 
HETATM 22 C C6 ADP . . . J 2 248.504 279.336 210.128 1 33.98 ? C6 ADP 401 B 1 
HETATM 23 N N6 ADP . . . J 2 247.634 280.491 210.078 1 33.98 ? N6 ADP 401 B 1 
HETATM 24 N N1 ADP . . . J 2 247.989 278.112 210.171 1 33.98 ? N1 ADP 401 B 1 
HETATM 25 C C2 ADP . . . J 2 248.847 277.104 210.217 1 33.98 ? C2 ADP 401 B 1 
HETATM 26 N N3 ADP . . . J 2 250.156 277.161 210.223 1 33.98 ? N3 ADP 401 B 1 
HETATM 27 C C4 ADP . . . J 2 250.645 278.359 210.18 1 33.98 ? C4 ADP 401 B 1 
HETATM 28 H "H5'1" ADP . . . J 2 256.845 279.02 211.246 1 33.98 ? "H5'1" ADP 401 B 1 
HETATM 29 H "H5'2" ADP . . . J 2 255.692 279.877 210.573 1 33.98 ? "H5'2" ADP 401 B 1 
HETATM 30 H H4' ADP . . . J 2 255.517 277.211 211.443 1 33.98 ? H4' ADP 401 B 1 
HETATM 31 H H3' ADP . . . J 2 255.832 278.167 209.062 1 33.98 ? H3' ADP 401 B 1 
HETATM 32 H HO3' ADP . . . J 2 255.77 275.949 209.82 1 33.98 ? HO3' ADP 401 B 1 
HETATM 33 H H2' ADP . . . J 2 253.857 279.112 208.819 1 33.98 ? H2' ADP 401 B 1 
HETATM 34 H HO2' ADP . . . J 2 253.633 277.793 207.193 1 33.98 ? HO2' ADP 401 B 1 
HETATM 35 H H1' ADP . . . J 2 252.597 277.015 210.189 1 33.98 ? H1' ADP 401 B 1 
HETATM 36 H H8 ADP . . . J 2 252.804 280.533 210.107 1 33.98 ? H8 ADP 401 B 1 
HETATM 37 H HN61 ADP . . . J 2 247.971 281.283 210.083 1 33.98 ? HN61 ADP 401 B 1 
HETATM 38 H HN62 ADP . . . J 2 246.782 280.386 210.044 1 33.98 ? HN62 ADP 401 B 1 
HETATM 39 H H2 ADP . . . J 2 248.473 276.256 210.245 1 33.98 ? H2 ADP 401 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    61 
_model_server_stats.query_time_ms           215 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#