data_3R9I
#
_model_server_result.job_id            5Vn1-UPEgoUSi5eQ8XYUTQ 
_model_server_result.datetime_utc      '2025-03-05 21:03:27' 
_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          3r9i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":261}' 
#
_entry.id    3R9I 
#
_exptl.entry_id    3R9I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_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         102.64 
_cell.angle_beta          95.87 
_cell.angle_gamma         111.72 
_cell.entry_id            3R9I 
_cell.length_a            64.293 
_cell.length_b            71.796 
_cell.length_c            76.644 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3R9I 
_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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 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,I,J,M,N,Q,R 1 1 
C,D,G,H,K,L,O,P,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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N 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 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                     3R9I 
_atom_sites.fract_transf_matrix[1][1]    0.015554 
_atom_sites.fract_transf_matrix[1][2]    0.006197 
_atom_sites.fract_transf_matrix[1][3]    0.003458 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014993 
_atom_sites.fract_transf_matrix[2][3]    0.004336 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.013654 
_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 3 ADP A 1 261 1 ADP ADP . 
J 3 ADP B 1 261 2 ADP ADP . 
K 3 ADP C 1 261 3 ADP ADP . 
L 3 ADP D 1 261 4 ADP ADP . 
M 4 HOH A 1 262 2 HOH HOH . 
M 4 HOH A 2 263 5 HOH HOH . 
M 4 HOH A 3 264 14 HOH HOH . 
M 4 HOH A 4 265 20 HOH HOH . 
M 4 HOH A 5 266 31 HOH HOH . 
M 4 HOH A 6 267 34 HOH HOH . 
M 4 HOH A 7 268 35 HOH HOH . 
M 4 HOH A 8 269 39 HOH HOH . 
M 4 HOH A 9 270 40 HOH HOH . 
M 4 HOH A 10 271 43 HOH HOH . 
M 4 HOH A 11 272 45 HOH HOH . 
M 4 HOH A 12 273 47 HOH HOH . 
M 4 HOH A 13 274 49 HOH HOH . 
M 4 HOH A 14 275 52 HOH HOH . 
M 4 HOH A 15 276 56 HOH HOH . 
M 4 HOH A 16 277 61 HOH HOH . 
M 4 HOH A 17 278 63 HOH HOH . 
M 4 HOH A 18 279 70 HOH HOH . 
M 4 HOH A 19 280 73 HOH HOH . 
M 4 HOH A 20 281 77 HOH HOH . 
M 4 HOH A 21 282 79 HOH HOH . 
M 4 HOH A 22 283 80 HOH HOH . 
M 4 HOH A 23 284 83 HOH HOH . 
M 4 HOH A 24 285 96 HOH HOH . 
M 4 HOH A 25 286 97 HOH HOH . 
M 4 HOH A 26 287 99 HOH HOH . 
M 4 HOH A 27 288 101 HOH HOH . 
M 4 HOH A 28 289 103 HOH HOH . 
M 4 HOH A 29 290 107 HOH HOH . 
M 4 HOH A 30 291 114 HOH HOH . 
M 4 HOH A 31 292 116 HOH HOH . 
M 4 HOH A 32 293 117 HOH HOH . 
M 4 HOH A 33 294 122 HOH HOH . 
M 4 HOH A 34 295 124 HOH HOH . 
M 4 HOH A 35 296 125 HOH HOH . 
M 4 HOH A 36 297 129 HOH HOH . 
M 4 HOH A 37 298 137 HOH HOH . 
M 4 HOH A 38 299 140 HOH HOH . 
M 4 HOH A 39 300 143 HOH HOH . 
M 4 HOH A 40 301 144 HOH HOH . 
M 4 HOH A 41 302 145 HOH HOH . 
M 4 HOH A 42 303 150 HOH HOH . 
M 4 HOH A 43 304 153 HOH HOH . 
M 4 HOH A 44 305 155 HOH HOH . 
M 4 HOH A 45 306 156 HOH HOH . 
M 4 HOH A 46 307 159 HOH HOH . 
M 4 HOH A 47 308 163 HOH HOH . 
M 4 HOH A 48 309 168 HOH HOH . 
M 4 HOH A 49 310 170 HOH HOH . 
M 4 HOH A 50 311 171 HOH HOH . 
M 4 HOH A 51 312 172 HOH HOH . 
M 4 HOH A 52 313 173 HOH HOH . 
M 4 HOH A 53 314 176 HOH HOH . 
N 4 HOH B 1 262 9 HOH HOH . 
N 4 HOH B 2 263 10 HOH HOH . 
N 4 HOH B 3 264 13 HOH HOH . 
N 4 HOH B 4 265 15 HOH HOH . 
N 4 HOH B 5 266 16 HOH HOH . 
N 4 HOH B 6 267 17 HOH HOH . 
N 4 HOH B 7 268 18 HOH HOH . 
N 4 HOH B 8 269 29 HOH HOH . 
N 4 HOH B 9 270 30 HOH HOH . 
N 4 HOH B 10 271 33 HOH HOH . 
N 4 HOH B 11 272 38 HOH HOH . 
N 4 HOH B 12 273 46 HOH HOH . 
N 4 HOH B 13 274 48 HOH HOH . 
N 4 HOH B 14 275 51 HOH HOH . 
N 4 HOH B 15 276 53 HOH HOH . 
N 4 HOH B 16 277 54 HOH HOH . 
N 4 HOH B 17 278 55 HOH HOH . 
N 4 HOH B 18 279 66 HOH HOH . 
N 4 HOH B 19 280 68 HOH HOH . 
N 4 HOH B 20 281 69 HOH HOH . 
N 4 HOH B 21 282 71 HOH HOH . 
N 4 HOH B 22 283 74 HOH HOH . 
N 4 HOH B 23 284 87 HOH HOH . 
N 4 HOH B 24 285 94 HOH HOH . 
N 4 HOH B 25 286 108 HOH HOH . 
N 4 HOH B 26 287 110 HOH HOH . 
N 4 HOH B 27 288 111 HOH HOH . 
N 4 HOH B 28 289 112 HOH HOH . 
N 4 HOH B 29 290 118 HOH HOH . 
N 4 HOH B 30 291 121 HOH HOH . 
N 4 HOH B 31 292 126 HOH HOH . 
N 4 HOH B 32 293 131 HOH HOH . 
N 4 HOH B 33 294 132 HOH HOH . 
N 4 HOH B 34 295 134 HOH HOH . 
N 4 HOH B 35 296 136 HOH HOH . 
N 4 HOH B 36 297 139 HOH HOH . 
N 4 HOH B 37 298 141 HOH HOH . 
N 4 HOH B 38 299 147 HOH HOH . 
N 4 HOH B 39 300 157 HOH HOH . 
N 4 HOH B 40 301 158 HOH HOH . 
N 4 HOH B 41 302 161 HOH HOH . 
N 4 HOH B 42 303 162 HOH HOH . 
N 4 HOH B 43 304 164 HOH HOH . 
N 4 HOH B 44 305 167 HOH HOH . 
N 4 HOH B 45 306 169 HOH HOH . 
N 4 HOH B 46 307 174 HOH HOH . 
O 4 HOH C 1 262 4 HOH HOH . 
O 4 HOH C 2 263 6 HOH HOH . 
O 4 HOH C 3 264 19 HOH HOH . 
O 4 HOH C 4 265 23 HOH HOH . 
O 4 HOH C 5 266 25 HOH HOH . 
O 4 HOH C 6 267 27 HOH HOH . 
O 4 HOH C 7 268 28 HOH HOH . 
O 4 HOH C 8 269 32 HOH HOH . 
O 4 HOH C 9 270 37 HOH HOH . 
O 4 HOH C 10 271 42 HOH HOH . 
O 4 HOH C 11 272 50 HOH HOH . 
O 4 HOH C 12 273 58 HOH HOH . 
O 4 HOH C 13 274 60 HOH HOH . 
O 4 HOH C 14 275 62 HOH HOH . 
O 4 HOH C 15 276 64 HOH HOH . 
O 4 HOH C 16 277 67 HOH HOH . 
O 4 HOH C 17 278 81 HOH HOH . 
O 4 HOH C 18 279 82 HOH HOH . 
O 4 HOH C 19 280 88 HOH HOH . 
O 4 HOH C 20 281 90 HOH HOH . 
O 4 HOH C 21 282 95 HOH HOH . 
O 4 HOH C 22 283 98 HOH HOH . 
O 4 HOH C 23 284 100 HOH HOH . 
O 4 HOH C 24 285 106 HOH HOH . 
O 4 HOH C 25 286 109 HOH HOH . 
O 4 HOH C 26 287 115 HOH HOH . 
O 4 HOH C 27 288 119 HOH HOH . 
O 4 HOH C 28 289 127 HOH HOH . 
O 4 HOH C 29 290 146 HOH HOH . 
O 4 HOH C 30 291 148 HOH HOH . 
O 4 HOH C 31 292 149 HOH HOH . 
O 4 HOH C 32 293 151 HOH HOH . 
O 4 HOH C 33 294 160 HOH HOH . 
O 4 HOH C 34 295 166 HOH HOH . 
O 4 HOH C 35 296 177 HOH HOH . 
P 4 HOH D 1 262 1 HOH HOH . 
P 4 HOH D 2 263 3 HOH HOH . 
P 4 HOH D 3 264 7 HOH HOH . 
P 4 HOH D 4 265 8 HOH HOH . 
P 4 HOH D 5 266 11 HOH HOH . 
P 4 HOH D 6 267 12 HOH HOH . 
P 4 HOH D 7 268 21 HOH HOH . 
P 4 HOH D 8 269 22 HOH HOH . 
P 4 HOH D 9 270 24 HOH HOH . 
P 4 HOH D 10 271 26 HOH HOH . 
P 4 HOH D 11 272 36 HOH HOH . 
P 4 HOH D 12 273 41 HOH HOH . 
P 4 HOH D 13 274 44 HOH HOH . 
P 4 HOH D 14 275 57 HOH HOH . 
P 4 HOH D 15 276 59 HOH HOH . 
P 4 HOH D 16 277 65 HOH HOH . 
P 4 HOH D 17 278 72 HOH HOH . 
P 4 HOH D 18 279 75 HOH HOH . 
P 4 HOH D 19 280 84 HOH HOH . 
P 4 HOH D 20 281 85 HOH HOH . 
P 4 HOH D 21 282 86 HOH HOH . 
P 4 HOH D 22 283 89 HOH HOH . 
P 4 HOH D 23 284 91 HOH HOH . 
P 4 HOH D 24 285 92 HOH HOH . 
P 4 HOH D 25 286 93 HOH HOH . 
P 4 HOH D 26 287 102 HOH HOH . 
P 4 HOH D 27 288 104 HOH HOH . 
P 4 HOH D 28 289 105 HOH HOH . 
P 4 HOH D 29 290 113 HOH HOH . 
P 4 HOH D 30 291 120 HOH HOH . 
P 4 HOH D 31 292 128 HOH HOH . 
P 4 HOH D 32 293 130 HOH HOH . 
P 4 HOH D 33 294 133 HOH HOH . 
P 4 HOH D 34 295 135 HOH HOH . 
P 4 HOH D 35 296 138 HOH HOH . 
P 4 HOH D 36 297 152 HOH HOH . 
P 4 HOH D 37 298 154 HOH HOH . 
P 4 HOH D 38 299 165 HOH HOH . 
P 4 HOH D 39 300 175 HOH HOH . 
Q 4 HOH E 1 123 123 HOH HOH . 
R 4 HOH F 1 76 76 HOH HOH . 
R 4 HOH F 2 142 142 HOH HOH . 
S 4 HOH G 1 78 78 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 . . . L 3 -32.576 40.364 -36.328 1 17.62 ? PB ADP 261 D 1 
HETATM 2 O O1B ADP . . . L 3 -32.808 39.238 -37.244 1 18.88 ? O1B ADP 261 D 1 
HETATM 3 O O2B ADP . . . L 3 -31.63 41.439 -36.758 1 17.36 ? O2B ADP 261 D 1 
HETATM 4 O O3B ADP . . . L 3 -33.82 40.907 -35.733 1 14.42 ? O3B ADP 261 D 1 
HETATM 5 P PA ADP . . . L 3 -30.558 40.061 -34.308 1 19.98 ? PA ADP 261 D 1 
HETATM 6 O O1A ADP . . . L 3 -30.91 41.377 -33.631 1 20.37 ? O1A ADP 261 D 1 
HETATM 7 O O2A ADP . . . L 3 -29.3 39.913 -35.153 1 17.86 ? O2A ADP 261 D 1 
HETATM 8 O O3A ADP . . . L 3 -31.829 39.566 -35.176 1 17.51 ? O3A ADP 261 D 1 
HETATM 9 O O5' ADP . . . L 3 -30.502 38.973 -33.127 1 19.15 ? O5' ADP 261 D 1 
HETATM 10 C C5' ADP . . . L 3 -31.621 38.353 -32.498 1 24.93 ? C5' ADP 261 D 1 
HETATM 11 C C4' ADP . . . L 3 -31.182 37.865 -31.104 1 21.82 ? C4' ADP 261 D 1 
HETATM 12 O O4' ADP . . . L 3 -30.446 36.649 -31.196 1 16.96 ? O4' ADP 261 D 1 
HETATM 13 C C3' ADP . . . L 3 -30.257 38.88 -30.459 1 27.34 ? C3' ADP 261 D 1 
HETATM 14 O O3' ADP . . . L 3 -30.661 39.12 -29.107 1 30.81 ? O3' ADP 261 D 1 
HETATM 15 C C2' ADP . . . L 3 -28.881 38.228 -30.492 1 24.27 ? C2' ADP 261 D 1 
HETATM 16 O O2' ADP . . . L 3 -28.08 38.732 -29.406 1 24.47 ? O2' ADP 261 D 1 
HETATM 17 C C1' ADP . . . L 3 -29.188 36.727 -30.538 1 19.68 ? C1' ADP 261 D 1 
HETATM 18 N N9 ADP . . . L 3 -28.251 35.954 -31.379 1 22.54 ? N9 ADP 261 D 1 
HETATM 19 C C8 ADP . . . L 3 -28.076 36.164 -32.689 1 25.14 ? C8 ADP 261 D 1 
HETATM 20 N N7 ADP . . . L 3 -27.157 35.318 -33.214 1 27.34 ? N7 ADP 261 D 1 
HETATM 21 C C5 ADP . . . L 3 -26.733 34.538 -32.227 1 26.3 ? C5 ADP 261 D 1 
HETATM 22 C C6 ADP . . . L 3 -25.758 33.45 -32.12 1 23.87 ? C6 ADP 261 D 1 
HETATM 23 N N6 ADP . . . L 3 -25.06 33.002 -33.186 1 21.25 ? N6 ADP 261 D 1 
HETATM 24 N N1 ADP . . . L 3 -25.601 32.919 -30.902 1 30.72 ? N1 ADP 261 D 1 
HETATM 25 C C2 ADP . . . L 3 -26.291 33.326 -29.828 1 25.19 ? C2 ADP 261 D 1 
HETATM 26 N N3 ADP . . . L 3 -27.194 34.317 -29.866 1 28.29 ? N3 ADP 261 D 1 
HETATM 27 C C4 ADP . . . L 3 -27.453 34.958 -31.019 1 25.55 ? C4 ADP 261 D 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#