data_3LL9
#
_model_server_result.job_id            ytucw0mo7RFa7WAlLeBSsA 
_model_server_result.datetime_utc      '2024-12-02 13:07:35' 
_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          3ll9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":268}' 
#
_entry.id    3LL9 
#
_exptl.entry_id    3LL9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          120.59 
_cell.angle_gamma         90 
_cell.entry_id            3LL9 
_cell.length_a            119.672 
_cell.length_b            96.36 
_cell.length_c            72.43 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LL9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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    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
? 2 C N N 
? 2 E 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 HIS 3 A HIS -1 1_555 A N MSE 4 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? 
covale ? covale2 A C MSE 4 A MSE 1 1_555 A N ILE 5 A ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale3 A C LEU 44 A LEU 41 1_555 A N MSE 45 A MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? 
covale ? covale4 A C MSE 45 A MSE 42 1_555 A N ILE 46 A ILE 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? 
covale ? covale5 A C SER 107 A SER 104 1_555 A N MSE 108 A MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale6 A C MSE 108 A MSE 105 1_555 A N GLN 109 A GLN 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale7 A C GLY 136 A GLY 133 1_555 A N MSE 137 A MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale8 A C MSE 137 A MSE 134 1_555 A N VAL 138 A VAL 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale9 A C LEU 171 A LEU 168 1_555 A N MSE 172 A MSE 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale10 A C MSE 172 A MSE 169 1_555 A N PRO 173 A PRO 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale11 A C GLY 222 A GLY 219 1_555 A N MSE 223 A MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale12 A C MSE 223 A MSE 220 1_555 A N VAL 224 A VAL 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? 
covale ? covale13 B C HIS 3 B HIS -1 1_555 B N MSE 4 B MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale14 B C MSE 4 B MSE 1 1_555 B N ILE 5 B ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale15 B C LEU 44 B LEU 41 1_555 B N MSE 45 B MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale16 B C MSE 45 B MSE 42 1_555 B N ILE 46 B ILE 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? 
covale ? covale17 B C SER 107 B SER 104 1_555 B N MSE 108 B MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? 
covale ? covale18 B C MSE 108 B MSE 105 1_555 B N GLN 109 B GLN 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale19 B C GLY 136 B GLY 133 1_555 B N MSE 137 B MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale20 B C MSE 137 B MSE 134 1_555 B N VAL 138 B VAL 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
covale ? covale21 B C LEU 171 B LEU 168 1_555 B N MSE 172 B MSE 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale22 B C MSE 172 B MSE 169 1_555 B N PRO 173 B PRO 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? 
covale ? covale23 B C GLY 222 B GLY 219 1_555 B N MSE 223 B MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale24 B C MSE 223 B MSE 220 1_555 B N VAL 224 B VAL 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
#
_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                     3LL9 
_atom_sites.fract_transf_matrix[1][1]    0.008356 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00494 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010378 
_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]    0.016038 
_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
C 2 ADP A 1 267 100 ADP ADP . 
D 3 GOL B 1 267 1 GOL GOL . 
E 2 ADP B 1 268 200 ADP ADP . 
F 4 HOH A 1 268 1 HOH HOH . 
F 4 HOH A 2 269 2 HOH HOH . 
F 4 HOH A 3 270 3 HOH HOH . 
F 4 HOH A 4 271 4 HOH HOH . 
F 4 HOH A 5 272 5 HOH HOH . 
F 4 HOH A 6 273 6 HOH HOH . 
F 4 HOH A 7 274 7 HOH HOH . 
F 4 HOH A 8 275 8 HOH HOH . 
F 4 HOH A 9 276 9 HOH HOH . 
F 4 HOH A 10 277 14 HOH HOH . 
F 4 HOH A 11 278 15 HOH HOH . 
F 4 HOH A 12 279 16 HOH HOH . 
F 4 HOH A 13 280 17 HOH HOH . 
F 4 HOH A 14 281 18 HOH HOH . 
F 4 HOH A 15 282 19 HOH HOH . 
F 4 HOH A 16 283 20 HOH HOH . 
F 4 HOH A 17 284 21 HOH HOH . 
F 4 HOH A 18 285 22 HOH HOH . 
F 4 HOH A 19 286 28 HOH HOH . 
F 4 HOH A 20 287 29 HOH HOH . 
F 4 HOH A 21 288 30 HOH HOH . 
F 4 HOH A 22 289 31 HOH HOH . 
F 4 HOH A 23 290 32 HOH HOH . 
F 4 HOH A 24 291 41 HOH HOH . 
F 4 HOH A 25 292 42 HOH HOH . 
F 4 HOH A 26 293 44 HOH HOH . 
F 4 HOH A 27 294 45 HOH HOH . 
F 4 HOH A 28 295 47 HOH HOH . 
F 4 HOH A 29 296 48 HOH HOH . 
F 4 HOH A 30 297 49 HOH HOH . 
F 4 HOH A 31 298 51 HOH HOH . 
F 4 HOH A 32 299 54 HOH HOH . 
F 4 HOH A 33 300 55 HOH HOH . 
F 4 HOH A 34 301 56 HOH HOH . 
F 4 HOH A 35 302 57 HOH HOH . 
F 4 HOH A 36 303 59 HOH HOH . 
F 4 HOH A 37 304 65 HOH HOH . 
F 4 HOH A 38 305 66 HOH HOH . 
F 4 HOH A 39 306 68 HOH HOH . 
F 4 HOH A 40 307 74 HOH HOH . 
F 4 HOH A 41 308 76 HOH HOH . 
F 4 HOH A 42 309 78 HOH HOH . 
F 4 HOH A 43 310 81 HOH HOH . 
F 4 HOH A 44 311 82 HOH HOH . 
F 4 HOH A 45 312 83 HOH HOH . 
F 4 HOH A 46 313 84 HOH HOH . 
F 4 HOH A 47 314 85 HOH HOH . 
F 4 HOH A 48 315 88 HOH HOH . 
F 4 HOH A 49 316 92 HOH HOH . 
F 4 HOH A 50 317 94 HOH HOH . 
F 4 HOH A 51 318 97 HOH HOH . 
F 4 HOH A 52 319 100 HOH HOH . 
F 4 HOH A 53 320 103 HOH HOH . 
F 4 HOH A 54 321 108 HOH HOH . 
F 4 HOH A 55 322 111 HOH HOH . 
F 4 HOH A 56 323 113 HOH HOH . 
G 4 HOH B 1 269 10 HOH HOH . 
G 4 HOH B 2 270 11 HOH HOH . 
G 4 HOH B 3 271 12 HOH HOH . 
G 4 HOH B 4 272 13 HOH HOH . 
G 4 HOH B 5 273 23 HOH HOH . 
G 4 HOH B 6 274 24 HOH HOH . 
G 4 HOH B 7 275 25 HOH HOH . 
G 4 HOH B 8 276 26 HOH HOH . 
G 4 HOH B 9 277 27 HOH HOH . 
G 4 HOH B 10 278 33 HOH HOH . 
G 4 HOH B 11 279 34 HOH HOH . 
G 4 HOH B 12 280 35 HOH HOH . 
G 4 HOH B 13 281 36 HOH HOH . 
G 4 HOH B 14 282 37 HOH HOH . 
G 4 HOH B 15 283 38 HOH HOH . 
G 4 HOH B 16 284 39 HOH HOH . 
G 4 HOH B 17 285 40 HOH HOH . 
G 4 HOH B 18 286 43 HOH HOH . 
G 4 HOH B 19 287 46 HOH HOH . 
G 4 HOH B 20 288 50 HOH HOH . 
G 4 HOH B 21 289 52 HOH HOH . 
G 4 HOH B 22 290 53 HOH HOH . 
G 4 HOH B 23 291 58 HOH HOH . 
G 4 HOH B 24 292 61 HOH HOH . 
G 4 HOH B 25 293 62 HOH HOH . 
G 4 HOH B 26 294 63 HOH HOH . 
G 4 HOH B 27 295 64 HOH HOH . 
G 4 HOH B 28 296 67 HOH HOH . 
G 4 HOH B 29 297 69 HOH HOH . 
G 4 HOH B 30 298 70 HOH HOH . 
G 4 HOH B 31 299 71 HOH HOH . 
G 4 HOH B 32 300 72 HOH HOH . 
G 4 HOH B 33 301 73 HOH HOH . 
G 4 HOH B 34 302 77 HOH HOH . 
G 4 HOH B 35 303 79 HOH HOH . 
G 4 HOH B 36 304 80 HOH HOH . 
G 4 HOH B 37 305 86 HOH HOH . 
G 4 HOH B 38 306 90 HOH HOH . 
G 4 HOH B 39 307 91 HOH HOH . 
G 4 HOH B 40 308 93 HOH HOH . 
G 4 HOH B 41 309 98 HOH HOH . 
G 4 HOH B 42 310 99 HOH HOH . 
G 4 HOH B 43 311 101 HOH HOH . 
G 4 HOH B 44 312 102 HOH HOH . 
G 4 HOH B 45 313 105 HOH HOH . 
G 4 HOH B 46 314 107 HOH HOH . 
G 4 HOH B 47 315 110 HOH HOH . 
G 4 HOH B 48 316 112 HOH HOH . 
G 4 HOH B 49 317 114 HOH HOH . 
G 4 HOH B 50 318 115 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 . . . E 2 22.953 -30.749 6.023 1 70.33 ? PB ADP 268 B 1 
HETATM 2 O O1B ADP . . . E 2 23.452 -30.344 4.642 1 69.11 ? O1B ADP 268 B 1 
HETATM 3 O O2B ADP . . . E 2 23.667 -30.01 7.176 1 66.74 ? O2B ADP 268 B 1 
HETATM 4 O O3B ADP . . . E 2 21.441 -30.82 6.131 1 63.78 ? O3B ADP 268 B 1 
HETATM 5 P PA ADP . . . E 2 22.825 -33.414 7.191 1 75.77 ? PA ADP 268 B 1 
HETATM 6 O O1A ADP . . . E 2 21.352 -33.196 7.412 1 82.46 ? O1A ADP 268 B 1 
HETATM 7 O O2A ADP . . . E 2 23.718 -33.577 8.39 1 73.99 ? O2A ADP 268 B 1 
HETATM 8 O O3A ADP . . . E 2 23.442 -32.29 6.169 1 73.95 ? O3A ADP 268 B 1 
HETATM 9 O O5' ADP . . . E 2 22.978 -34.656 6.176 1 76.6 ? O5' ADP 268 B 1 
HETATM 10 C C5' ADP . . . E 2 24.287 -34.986 5.702 1 71.07 ? C5' ADP 268 B 1 
HETATM 11 C C4' ADP . . . E 2 24.774 -36.221 6.454 1 68.36 ? C4' ADP 268 B 1 
HETATM 12 O O4' ADP . . . E 2 23.967 -37.393 6.242 1 71.91 ? O4' ADP 268 B 1 
HETATM 13 C C3' ADP . . . E 2 26.142 -36.632 5.976 1 68.73 ? C3' ADP 268 B 1 
HETATM 14 O O3' ADP . . . E 2 27.118 -35.977 6.766 1 73.03 ? O3' ADP 268 B 1 
HETATM 15 C C2' ADP . . . E 2 26.197 -38.137 6.199 1 73.75 ? C2' ADP 268 B 1 
HETATM 16 O O2' ADP . . . E 2 26.946 -38.397 7.382 1 70.82 ? O2' ADP 268 B 1 
HETATM 17 C C1' ADP . . . E 2 24.774 -38.591 6.452 1 70.08 ? C1' ADP 268 B 1 
HETATM 18 N N9 ADP . . . E 2 24.276 -39.639 5.527 1 60.99 ? N9 ADP 268 B 1 
HETATM 19 C C8 ADP . . . E 2 23.466 -40.631 5.93 1 54.15 ? C8 ADP 268 B 1 
HETATM 20 N N7 ADP . . . E 2 23.131 -41.392 4.865 1 66.19 ? N7 ADP 268 B 1 
HETATM 21 C C5 ADP . . . E 2 23.729 -40.852 3.774 1 57.88 ? C5 ADP 268 B 1 
HETATM 22 C C6 ADP . . . E 2 23.786 -41.236 2.366 1 53.44 ? C6 ADP 268 B 1 
HETATM 23 N N6 ADP . . . E 2 23.06 -42.321 2.013 1 53.58 ? N6 ADP 268 B 1 
HETATM 24 N N1 ADP . . . E 2 24.55 -40.517 1.524 1 49.95 ? N1 ADP 268 B 1 
HETATM 25 C C2 ADP . . . E 2 25.221 -39.398 1.946 1 57.22 ? C2 ADP 268 B 1 
HETATM 26 N N3 ADP . . . E 2 25.245 -39.019 3.249 1 60.5 ? N3 ADP 268 B 1 
HETATM 27 C C4 ADP . . . E 2 24.514 -39.714 4.194 1 53.66 ? C4 ADP 268 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#