data_1NDP
#
_model_server_result.job_id            OFkRNwmGwHSNQUtPMEa7DQ 
_model_server_result.datetime_utc      '2025-03-02 22:29:38' 
_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          1ndp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":160}' 
#
_entry.id    1NDP 
#
_exptl.entry_id    1NDP 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            1NDP 
_cell.length_a            73.18 
_cell.length_b            73.18 
_cell.length_c            158.45 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1NDP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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
metalc ? metalc1 E O1B ADP . B ADP 160 1_555 D MG MG . B MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc2 E O1A ADP . B ADP 160 1_555 D MG MG . B MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc3 D MG MG . B MG 161 1_555 G O HOH . B HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
metalc ? metalc4 D MG MG . B MG 161 1_555 G O HOH . B HOH 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc5 D MG MG . B MG 161 1_555 G O HOH . B HOH 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc6 D MG MG . B MG 161 1_555 G O HOH . B HOH 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
#
_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                     1NDP 
_atom_sites.fract_transf_matrix[1][1]    0.013665 
_atom_sites.fract_transf_matrix[1][2]    0.007889 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015779 
_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]    0.006311 
_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 1 160 160 ADP ADP . 
D 3 MG B 1 161 161 MG MG . 
E 2 ADP B 1 160 160 ADP ADP . 
F 4 HOH A 1 161 257 HOH HOH . 
F 4 HOH A 2 162 262 HOH HOH . 
F 4 HOH A 3 163 161 HOH HOH . 
F 4 HOH A 4 164 200 HOH HOH . 
F 4 HOH A 5 165 201 HOH HOH . 
F 4 HOH A 6 166 202 HOH HOH . 
F 4 HOH A 7 167 203 HOH HOH . 
F 4 HOH A 8 168 204 HOH HOH . 
F 4 HOH A 9 169 205 HOH HOH . 
F 4 HOH A 10 170 206 HOH HOH . 
F 4 HOH A 11 171 207 HOH HOH . 
F 4 HOH A 12 172 208 HOH HOH . 
F 4 HOH A 13 173 209 HOH HOH . 
F 4 HOH A 14 174 210 HOH HOH . 
F 4 HOH A 15 175 211 HOH HOH . 
F 4 HOH A 16 176 212 HOH HOH . 
F 4 HOH A 17 177 213 HOH HOH . 
F 4 HOH A 18 178 214 HOH HOH . 
F 4 HOH A 19 179 215 HOH HOH . 
F 4 HOH A 20 180 216 HOH HOH . 
F 4 HOH A 21 181 217 HOH HOH . 
F 4 HOH A 22 182 218 HOH HOH . 
F 4 HOH A 23 183 219 HOH HOH . 
F 4 HOH A 24 184 220 HOH HOH . 
F 4 HOH A 25 185 221 HOH HOH . 
F 4 HOH A 26 186 222 HOH HOH . 
F 4 HOH A 27 187 223 HOH HOH . 
F 4 HOH A 28 188 224 HOH HOH . 
F 4 HOH A 29 189 225 HOH HOH . 
F 4 HOH A 30 190 226 HOH HOH . 
F 4 HOH A 31 191 227 HOH HOH . 
F 4 HOH A 32 192 228 HOH HOH . 
F 4 HOH A 33 193 229 HOH HOH . 
F 4 HOH A 34 194 230 HOH HOH . 
F 4 HOH A 35 195 231 HOH HOH . 
F 4 HOH A 36 196 232 HOH HOH . 
F 4 HOH A 37 197 233 HOH HOH . 
F 4 HOH A 38 198 234 HOH HOH . 
F 4 HOH A 39 199 235 HOH HOH . 
F 4 HOH A 40 200 236 HOH HOH . 
F 4 HOH A 41 201 237 HOH HOH . 
F 4 HOH A 42 202 238 HOH HOH . 
F 4 HOH A 43 203 239 HOH HOH . 
F 4 HOH A 44 204 240 HOH HOH . 
F 4 HOH A 45 205 241 HOH HOH . 
F 4 HOH A 46 206 242 HOH HOH . 
F 4 HOH A 47 207 243 HOH HOH . 
F 4 HOH A 48 208 244 HOH HOH . 
F 4 HOH A 49 209 245 HOH HOH . 
F 4 HOH A 50 210 246 HOH HOH . 
F 4 HOH A 51 211 247 HOH HOH . 
F 4 HOH A 52 212 248 HOH HOH . 
F 4 HOH A 53 213 249 HOH HOH . 
F 4 HOH A 54 214 250 HOH HOH . 
F 4 HOH A 55 215 251 HOH HOH . 
F 4 HOH A 56 216 253 HOH HOH . 
F 4 HOH A 57 217 254 HOH HOH . 
F 4 HOH A 58 218 255 HOH HOH . 
F 4 HOH A 59 219 256 HOH HOH . 
F 4 HOH A 60 220 258 HOH HOH . 
F 4 HOH A 61 221 259 HOH HOH . 
F 4 HOH A 62 222 260 HOH HOH . 
F 4 HOH A 63 223 261 HOH HOH . 
F 4 HOH A 64 224 263 HOH HOH . 
F 4 HOH A 65 225 264 HOH HOH . 
F 4 HOH A 66 226 265 HOH HOH . 
F 4 HOH A 67 227 242 HOH HOH . 
F 4 HOH A 68 228 243 HOH HOH . 
F 4 HOH A 69 229 244 HOH HOH . 
F 4 HOH A 70 230 247 HOH HOH . 
F 4 HOH A 71 231 249 HOH HOH . 
F 4 HOH A 72 232 251 HOH HOH . 
F 4 HOH A 73 233 252 HOH HOH . 
G 4 HOH B 1 162 252 HOH HOH . 
G 4 HOH B 2 163 200 HOH HOH . 
G 4 HOH B 3 164 201 HOH HOH . 
G 4 HOH B 4 165 202 HOH HOH . 
G 4 HOH B 5 166 203 HOH HOH . 
G 4 HOH B 6 167 204 HOH HOH . 
G 4 HOH B 7 168 205 HOH HOH . 
G 4 HOH B 8 169 206 HOH HOH . 
G 4 HOH B 9 170 207 HOH HOH . 
G 4 HOH B 10 171 208 HOH HOH . 
G 4 HOH B 11 172 209 HOH HOH . 
G 4 HOH B 12 173 210 HOH HOH . 
G 4 HOH B 13 174 211 HOH HOH . 
G 4 HOH B 14 175 212 HOH HOH . 
G 4 HOH B 15 176 213 HOH HOH . 
G 4 HOH B 16 177 214 HOH HOH . 
G 4 HOH B 17 178 215 HOH HOH . 
G 4 HOH B 18 179 216 HOH HOH . 
G 4 HOH B 19 180 217 HOH HOH . 
G 4 HOH B 20 181 218 HOH HOH . 
G 4 HOH B 21 182 219 HOH HOH . 
G 4 HOH B 22 183 220 HOH HOH . 
G 4 HOH B 23 184 221 HOH HOH . 
G 4 HOH B 24 185 222 HOH HOH . 
G 4 HOH B 25 186 223 HOH HOH . 
G 4 HOH B 26 187 224 HOH HOH . 
G 4 HOH B 27 188 225 HOH HOH . 
G 4 HOH B 28 189 226 HOH HOH . 
G 4 HOH B 29 190 227 HOH HOH . 
G 4 HOH B 30 191 228 HOH HOH . 
G 4 HOH B 31 192 229 HOH HOH . 
G 4 HOH B 32 193 230 HOH HOH . 
G 4 HOH B 33 194 231 HOH HOH . 
G 4 HOH B 34 195 232 HOH HOH . 
G 4 HOH B 35 196 233 HOH HOH . 
G 4 HOH B 36 197 234 HOH HOH . 
G 4 HOH B 37 198 235 HOH HOH . 
G 4 HOH B 38 199 236 HOH HOH . 
G 4 HOH B 39 200 237 HOH HOH . 
G 4 HOH B 40 201 238 HOH HOH . 
G 4 HOH B 41 202 239 HOH HOH . 
G 4 HOH B 42 203 240 HOH HOH . 
G 4 HOH B 43 204 241 HOH HOH . 
G 4 HOH B 44 205 245 HOH HOH . 
G 4 HOH B 45 206 246 HOH HOH . 
G 4 HOH B 46 207 248 HOH HOH . 
G 4 HOH B 47 208 250 HOH HOH . 
G 4 HOH B 48 209 253 HOH HOH . 
G 4 HOH B 49 210 254 HOH HOH . 
G 4 HOH B 50 211 255 HOH HOH . 
G 4 HOH B 51 212 256 HOH HOH . 
G 4 HOH B 52 213 257 HOH HOH . 
G 4 HOH B 53 214 258 HOH HOH . 
G 4 HOH B 54 215 259 HOH HOH . 
G 4 HOH B 55 216 260 HOH HOH . 
G 4 HOH B 56 217 261 HOH HOH . 
G 4 HOH B 57 218 262 HOH HOH . 
G 4 HOH B 58 219 263 HOH HOH . 
G 4 HOH B 59 220 264 HOH HOH . 
G 4 HOH B 60 221 265 HOH HOH . 
G 4 HOH B 61 222 266 HOH HOH . 
G 4 HOH B 62 223 267 HOH HOH . 
G 4 HOH B 63 224 268 HOH HOH . 
G 4 HOH B 64 225 269 HOH HOH . 
G 4 HOH B 65 226 270 HOH HOH . 
G 4 HOH B 66 227 271 HOH HOH . 
G 4 HOH B 67 228 272 HOH HOH . 
G 4 HOH B 68 229 273 HOH HOH . 
G 4 HOH B 69 230 274 HOH HOH . 
G 4 HOH B 70 231 275 HOH HOH . 
G 4 HOH B 71 232 276 HOH HOH . 
G 4 HOH B 72 233 277 HOH HOH . 
G 4 HOH B 73 234 278 HOH HOH . 
G 4 HOH B 74 235 279 HOH HOH . 
G 4 HOH B 75 236 280 HOH HOH . 
G 4 HOH B 76 237 281 HOH HOH . 
G 4 HOH B 77 238 282 HOH HOH . 
G 4 HOH B 78 239 283 HOH HOH . 
G 4 HOH B 79 240 284 HOH HOH . 
G 4 HOH B 80 241 285 HOH HOH . 
G 4 HOH B 81 242 286 HOH HOH . 
G 4 HOH B 82 243 287 HOH HOH . 
G 4 HOH B 83 244 288 HOH HOH . 
G 4 HOH B 84 245 289 HOH HOH . 
G 4 HOH B 85 246 290 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 . . . C 2 -13.718 -11.722 -20.152 1 21.99 ? PB ADP 160 A 1 
HETATM 2 O O1B ADP . . . C 2 -14.71 -10.853 -20.821 1 32.19 ? O1B ADP 160 A 1 
HETATM 3 O O2B ADP . . . C 2 -12.361 -11.118 -20.195 1 32.26 ? O2B ADP 160 A 1 
HETATM 4 O O3B ADP . . . C 2 -14.043 -12.118 -18.791 1 25.9 ? O3B ADP 160 A 1 
HETATM 5 P PA ADP . . . C 2 -14.796 -13.822 -21.966 1 26.44 ? PA ADP 160 A 1 
HETATM 6 O O1A ADP . . . C 2 -15.713 -12.892 -22.667 1 31.52 ? O1A ADP 160 A 1 
HETATM 7 O O2A ADP . . . C 2 -14.102 -14.72 -22.873 1 31.48 ? O2A ADP 160 A 1 
HETATM 8 O O3A ADP . . . C 2 -13.695 -13.042 -21.046 1 32.77 ? O3A ADP 160 A 1 
HETATM 9 O O5' ADP . . . C 2 -15.566 -14.446 -20.731 1 30.25 ? O5' ADP 160 A 1 
HETATM 10 C C5' ADP . . . C 2 -15.373 -15.745 -20.256 1 20.51 ? C5' ADP 160 A 1 
HETATM 11 C C4' ADP . . . C 2 -14.662 -16.024 -18.982 1 22.69 ? C4' ADP 160 A 1 
HETATM 12 O O4' ADP . . . C 2 -14.63 -17.477 -19.044 1 24.11 ? O4' ADP 160 A 1 
HETATM 13 C C3' ADP . . . C 2 -13.192 -15.626 -18.792 1 21.94 ? C3' ADP 160 A 1 
HETATM 14 O O3' ADP . . . C 2 -13.025 -14.453 -18.032 1 24.09 ? O3' ADP 160 A 1 
HETATM 15 C C2' ADP . . . C 2 -12.599 -16.835 -18.061 1 21.51 ? C2' ADP 160 A 1 
HETATM 16 O O2' ADP . . . C 2 -12.917 -17.029 -16.687 1 21.81 ? O2' ADP 160 A 1 
HETATM 17 C C1' ADP . . . C 2 -13.305 -17.932 -18.875 1 24.7 ? C1' ADP 160 A 1 
HETATM 18 N N9 ADP . . . C 2 -12.75 -18.199 -20.201 1 25.49 ? N9 ADP 160 A 1 
HETATM 19 C C8 ADP . . . C 2 -12.847 -17.606 -21.407 1 25.37 ? C8 ADP 160 A 1 
HETATM 20 N N7 ADP . . . C 2 -12.154 -18.197 -22.357 1 24.48 ? N7 ADP 160 A 1 
HETATM 21 C C5 ADP . . . C 2 -11.589 -19.251 -21.696 1 28.56 ? C5 ADP 160 A 1 
HETATM 22 C C6 ADP . . . C 2 -10.735 -20.27 -22.168 1 32.57 ? C6 ADP 160 A 1 
HETATM 23 N N6 ADP . . . C 2 -10.378 -20.275 -23.469 1 39.14 ? N6 ADP 160 A 1 
HETATM 24 N N1 ADP . . . C 2 -10.339 -21.19 -21.252 1 32.24 ? N1 ADP 160 A 1 
HETATM 25 C C2 ADP . . . C 2 -10.767 -21.1 -19.957 1 29.17 ? C2 ADP 160 A 1 
HETATM 26 N N3 ADP . . . C 2 -11.554 -20.205 -19.433 1 30.77 ? N3 ADP 160 A 1 
HETATM 27 C C4 ADP . . . C 2 -11.926 -19.295 -20.375 1 28.04 ? C4 ADP 160 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           27 
#