data_8G5D
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_model_server_result.job_id            pZ-VvCOMqwJuFsymIXSfbA 
_model_server_result.datetime_utc      '2025-07-31 02:24:06' 
_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          8g5d 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":3304}' 
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_entry.id    8G5D 
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_exptl.entry_id    8G5D 
_exptl.method      'ELECTRON MICROSCOPY' 
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_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          5 
_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                     ? 
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_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            8G5D 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 8G5D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
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_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 
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_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
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_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             N 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     8G5D 
_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 ACO A 1 3301 3301 ACO ACO . 
F 3 OAA A 1 3302 3302 OAA OAA . 
G 2 ACO B 1 3301 3301 ACO ACO . 
H 3 OAA B 1 3302 3302 OAA OAA . 
I 2 ACO C 1 3301 3301 ACO ACO . 
J 3 OAA C 1 3302 3302 OAA OAA . 
K 2 ACO D 1 3301 3301 ACO ACO . 
L 3 OAA D 1 3302 3302 OAA OAA . 
M 4 Q5B D 1 3303 3303 Q5B Q5B . 
N 5 ADP D 1 3304 3304 ADP ADP . 
O 6 PO4 D 1 3305 3305 PO4 PO4 . 
P 7 HOH A 1 3401 3402 HOH HOH . 
P 7 HOH A 2 3402 3408 HOH HOH . 
P 7 HOH A 3 3403 3401 HOH HOH . 
P 7 HOH A 4 3404 3403 HOH HOH . 
P 7 HOH A 5 3405 3404 HOH HOH . 
P 7 HOH A 6 3406 3405 HOH HOH . 
P 7 HOH A 7 3407 3409 HOH HOH . 
P 7 HOH A 8 3408 3406 HOH HOH . 
P 7 HOH A 9 3409 3407 HOH HOH . 
Q 7 HOH B 1 3401 3401 HOH HOH . 
Q 7 HOH B 2 3402 3403 HOH HOH . 
Q 7 HOH B 3 3403 3407 HOH HOH . 
Q 7 HOH B 4 3404 3402 HOH HOH . 
Q 7 HOH B 5 3405 3406 HOH HOH . 
Q 7 HOH B 6 3406 3408 HOH HOH . 
Q 7 HOH B 7 3407 3405 HOH HOH . 
Q 7 HOH B 8 3408 3410 HOH HOH . 
Q 7 HOH B 9 3409 3409 HOH HOH . 
Q 7 HOH B 10 3410 3411 HOH HOH . 
Q 7 HOH B 11 3411 3404 HOH HOH . 
R 7 HOH C 1 3401 3401 HOH HOH . 
R 7 HOH C 2 3402 3404 HOH HOH . 
R 7 HOH C 3 3403 3403 HOH HOH . 
R 7 HOH C 4 3404 3406 HOH HOH . 
R 7 HOH C 5 3405 3402 HOH HOH . 
R 7 HOH C 6 3406 3405 HOH HOH . 
R 7 HOH C 7 3407 3407 HOH HOH . 
R 7 HOH C 8 3408 3408 HOH HOH . 
S 7 HOH D 1 3401 3402 HOH HOH . 
S 7 HOH D 2 3402 3401 HOH HOH . 
S 7 HOH D 3 3403 3404 HOH HOH . 
S 7 HOH D 4 3404 3403 HOH HOH . 
S 7 HOH D 5 3405 3405 HOH HOH . 
S 7 HOH D 6 3406 3407 HOH HOH . 
S 7 HOH D 7 3407 3409 HOH HOH . 
S 7 HOH D 8 3408 3406 HOH HOH . 
S 7 HOH D 9 3409 3408 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 . . . N 5 49.043 129.721 33.763 1 121.75 ? PB ADP 3304 D 1 
HETATM 2 O O1B ADP . . . N 5 49.926 128.552 33.403 1 121.75 ? O1B ADP 3304 D 1 
HETATM 3 O O2B ADP . . . N 5 47.572 129.422 33.681 1 121.75 ? O2B ADP 3304 D 1 
HETATM 4 O O3B ADP . . . N 5 49.464 130.426 35.021 1 121.75 ? O3B ADP 3304 D 1 
HETATM 5 P PA ADP . . . N 5 50.69 131.224 32.026 1 121.75 ? PA ADP 3304 D 1 
HETATM 6 O O1A ADP . . . N 5 51.398 130.034 31.429 1 121.75 ? O1A ADP 3304 D 1 
HETATM 7 O O2A ADP . . . N 5 51.381 132.045 33.082 1 121.75 ? O2A ADP 3304 D 1 
HETATM 8 O O3A ADP . . . N 5 49.244 130.798 32.582 1 121.75 ? O3A ADP 3304 D 1 
HETATM 9 O O5' ADP . . . N 5 50.31 132.176 30.79 1 121.75 ? O5' ADP 3304 D 1 
HETATM 10 C C5' ADP . . . N 5 50.515 131.677 29.474 1 121.75 ? C5' ADP 3304 D 1 
HETATM 11 C C4' ADP . . . N 5 50.621 132.82 28.479 1 121.75 ? C4' ADP 3304 D 1 
HETATM 12 O O4' ADP . . . N 5 51.563 133.784 28.951 1 121.75 ? O4' ADP 3304 D 1 
HETATM 13 C C3' ADP . . . N 5 51.114 132.311 27.134 1 121.75 ? C3' ADP 3304 D 1 
HETATM 14 O O3' ADP . . . N 5 50.181 132.639 26.103 1 121.75 ? O3' ADP 3304 D 1 
HETATM 15 C C2' ADP . . . N 5 52.431 133.012 26.88 1 121.75 ? C2' ADP 3304 D 1 
HETATM 16 O O2' ADP . . . N 5 52.43 133.655 25.605 1 121.75 ? O2' ADP 3304 D 1 
HETATM 17 C C1' ADP . . . N 5 52.564 134.055 27.97 1 121.75 ? C1' ADP 3304 D 1 
HETATM 18 N N9 ADP . . . N 5 53.912 133.956 28.569 1 121.75 ? N9 ADP 3304 D 1 
HETATM 19 C C8 ADP . . . N 5 54.198 133.494 29.796 1 121.75 ? C8 ADP 3304 D 1 
HETATM 20 N N7 ADP . . . N 5 55.534 133.544 30.026 1 121.75 ? N7 ADP 3304 D 1 
HETATM 21 C C5 ADP . . . N 5 56.119 134.047 28.925 1 121.75 ? C5 ADP 3304 D 1 
HETATM 22 C C6 ADP . . . N 5 57.499 134.365 28.495 1 121.75 ? C6 ADP 3304 D 1 
HETATM 23 N N6 ADP . . . N 5 58.553 134.148 29.31 1 121.75 ? N6 ADP 3304 D 1 
HETATM 24 N N1 ADP . . . N 5 57.671 134.875 27.261 1 121.75 ? N1 ADP 3304 D 1 
HETATM 25 C C2 ADP . . . N 5 56.634 135.094 26.436 1 121.75 ? C2 ADP 3304 D 1 
HETATM 26 N N3 ADP . . . N 5 55.362 134.833 26.759 1 121.75 ? N3 ADP 3304 D 1 
HETATM 27 C C4 ADP . . . N 5 55.043 134.318 27.967 1 121.75 ? C4 ADP 3304 D 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           349 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
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