data_5NP9
#
_model_server_result.job_id            IG-ACD7gMM2OvMB5GdgzEA 
_model_server_result.datetime_utc      '2024-11-05 01:17:58' 
_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          5np9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    5NP9 
#
_exptl.entry_id    5NP9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  nat 
_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                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            5NP9 
_cell.length_a            84.03 
_cell.length_b            111.77 
_cell.length_c            35.68 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NP9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 A OG1 THR 42 A THR 42 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc2 A OE1 GLU 106 A GLU 106 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc3 B O2B ADP . A ADP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc4 C MG MG . A MG 202 1_555 D O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc5 C MG MG . A MG 202 1_555 D O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc6 C MG MG . A MG 202 1_555 D O HOH . A HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
#
_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                     5NP9 
_atom_sites.fract_transf_matrix[1][1]    0.011901 
_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]    0.008947 
_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]    0.028027 
_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
B 2 ADP A 1 201 560 ADP ADP . 
C 3 MG A 1 202 561 MG MG . 
D 4 HOH A 1 301 9 HOH HOH . 
D 4 HOH A 2 302 71 HOH HOH . 
D 4 HOH A 3 303 18 HOH HOH . 
D 4 HOH A 4 304 34 HOH HOH . 
D 4 HOH A 5 305 36 HOH HOH . 
D 4 HOH A 6 306 1 HOH HOH . 
D 4 HOH A 7 307 50 HOH HOH . 
D 4 HOH A 8 308 12 HOH HOH . 
D 4 HOH A 9 309 44 HOH HOH . 
D 4 HOH A 10 310 23 HOH HOH . 
D 4 HOH A 11 311 10 HOH HOH . 
D 4 HOH A 12 312 79 HOH HOH . 
D 4 HOH A 13 313 40 HOH HOH . 
D 4 HOH A 14 314 51 HOH HOH . 
D 4 HOH A 15 315 45 HOH HOH . 
D 4 HOH A 16 316 3 HOH HOH . 
D 4 HOH A 17 317 26 HOH HOH . 
D 4 HOH A 18 318 29 HOH HOH . 
D 4 HOH A 19 319 35 HOH HOH . 
D 4 HOH A 20 320 7 HOH HOH . 
D 4 HOH A 21 321 47 HOH HOH . 
D 4 HOH A 22 322 27 HOH HOH . 
D 4 HOH A 23 323 31 HOH HOH . 
D 4 HOH A 24 324 5 HOH HOH . 
D 4 HOH A 25 325 19 HOH HOH . 
D 4 HOH A 26 326 30 HOH HOH . 
D 4 HOH A 27 327 77 HOH HOH . 
D 4 HOH A 28 328 4 HOH HOH . 
D 4 HOH A 29 329 15 HOH HOH . 
D 4 HOH A 30 330 37 HOH HOH . 
D 4 HOH A 31 331 43 HOH HOH . 
D 4 HOH A 32 332 13 HOH HOH . 
D 4 HOH A 33 333 63 HOH HOH . 
D 4 HOH A 34 334 38 HOH HOH . 
D 4 HOH A 35 335 80 HOH HOH . 
D 4 HOH A 36 336 16 HOH HOH . 
D 4 HOH A 37 337 57 HOH HOH . 
D 4 HOH A 38 338 28 HOH HOH . 
D 4 HOH A 39 339 6 HOH HOH . 
D 4 HOH A 40 340 22 HOH HOH . 
D 4 HOH A 41 341 21 HOH HOH . 
D 4 HOH A 42 342 53 HOH HOH . 
D 4 HOH A 43 343 85 HOH HOH . 
D 4 HOH A 44 344 41 HOH HOH . 
D 4 HOH A 45 345 56 HOH HOH . 
D 4 HOH A 46 346 2 HOH HOH . 
D 4 HOH A 47 347 54 HOH HOH . 
D 4 HOH A 48 348 42 HOH HOH . 
D 4 HOH A 49 349 24 HOH HOH . 
D 4 HOH A 50 350 14 HOH HOH . 
D 4 HOH A 51 351 11 HOH HOH . 
D 4 HOH A 52 352 65 HOH HOH . 
D 4 HOH A 53 353 8 HOH HOH . 
D 4 HOH A 54 354 55 HOH HOH . 
D 4 HOH A 55 355 48 HOH HOH . 
D 4 HOH A 56 356 20 HOH HOH . 
D 4 HOH A 57 357 76 HOH HOH . 
D 4 HOH A 58 358 49 HOH HOH . 
D 4 HOH A 59 359 58 HOH HOH . 
D 4 HOH A 60 360 46 HOH HOH . 
D 4 HOH A 61 361 52 HOH HOH . 
D 4 HOH A 62 362 25 HOH HOH . 
D 4 HOH A 63 363 33 HOH HOH . 
D 4 HOH A 64 364 82 HOH HOH . 
D 4 HOH A 65 365 62 HOH HOH . 
D 4 HOH A 66 366 66 HOH HOH . 
D 4 HOH A 67 367 73 HOH HOH . 
D 4 HOH A 68 368 78 HOH HOH . 
D 4 HOH A 69 369 61 HOH HOH . 
D 4 HOH A 70 370 84 HOH HOH . 
D 4 HOH A 71 371 74 HOH HOH . 
D 4 HOH A 72 372 67 HOH HOH . 
D 4 HOH A 73 373 64 HOH HOH . 
D 4 HOH A 74 374 83 HOH HOH . 
D 4 HOH A 75 375 68 HOH HOH . 
D 4 HOH A 76 376 70 HOH HOH . 
D 4 HOH A 77 377 39 HOH HOH . 
D 4 HOH A 78 378 81 HOH HOH . 
D 4 HOH A 79 379 72 HOH HOH . 
D 4 HOH A 80 380 32 HOH HOH . 
D 4 HOH A 81 381 60 HOH HOH . 
D 4 HOH A 82 382 75 HOH HOH . 
D 4 HOH A 83 383 69 HOH HOH . 
D 4 HOH A 84 384 17 HOH HOH . 
D 4 HOH A 85 385 86 HOH HOH . 
D 4 HOH A 86 386 59 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 . . . B 2 16.945 22.802 -1.54 1 31.48 ? PB ADP 201 A 1 
HETATM 2 O O1B ADP . . . B 2 16.912 22.047 -2.87 1 27.9 ? O1B ADP 201 A 1 
HETATM 3 O O2B ADP . . . B 2 18.203 22.522 -0.778 1 23.33 ? O2B ADP 201 A 1 
HETATM 4 O O3B ADP . . . B 2 16.565 24.263 -1.673 1 33.08 ? O3B ADP 201 A 1 
HETATM 5 P PA ADP . . . B 2 15.781 21.635 0.831 1 30.33 ? PA ADP 201 A 1 
HETATM 6 O O1A ADP . . . B 2 16.369 20.25 0.792 1 28.51 ? O1A ADP 201 A 1 
HETATM 7 O O2A ADP . . . B 2 16.42 22.659 1.751 1 28.57 ? O2A ADP 201 A 1 
HETATM 8 O O3A ADP . . . B 2 15.73 22.184 -0.692 1 31.4 ? O3A ADP 201 A 1 
HETATM 9 O O5' ADP . . . B 2 14.224 21.505 1.161 1 33.79 ? O5' ADP 201 A 1 
HETATM 10 C C5' ADP . . . B 2 13.363 20.649 0.409 1 28.99 ? C5' ADP 201 A 1 
HETATM 11 C C4' ADP . . . B 2 11.989 20.676 1.08 1 35.55 ? C4' ADP 201 A 1 
HETATM 12 O O4' ADP . . . B 2 11.029 19.877 0.367 1 36 ? O4' ADP 201 A 1 
HETATM 13 C C3' ADP . . . B 2 12.057 20.126 2.486 1 37.04 ? C3' ADP 201 A 1 
HETATM 14 O O3' ADP . . . B 2 11.164 20.911 3.279 1 44.44 ? O3' ADP 201 A 1 
HETATM 15 C C2' ADP . . . B 2 11.478 18.731 2.376 1 37.27 ? C2' ADP 201 A 1 
HETATM 16 O O2' ADP . . . B 2 10.817 18.377 3.596 1 43.67 ? O2' ADP 201 A 1 
HETATM 17 C C1' ADP . . . B 2 10.474 18.879 1.236 1 39.51 ? C1' ADP 201 A 1 
HETATM 18 N N9 ADP . . . B 2 10.224 17.638 0.446 1 39.99 ? N9 ADP 201 A 1 
HETATM 19 C C8 ADP . . . B 2 9.002 17.128 0.166 1 43.27 ? C8 ADP 201 A 1 
HETATM 20 N N7 ADP . . . B 2 9.103 15.994 -0.586 1 44.2 ? N7 ADP 201 A 1 
HETATM 21 C C5 ADP . . . B 2 10.412 15.776 -0.802 1 36.77 ? C5 ADP 201 A 1 
HETATM 22 C C6 ADP . . . B 2 11.205 14.749 -1.52 1 41.39 ? C6 ADP 201 A 1 
HETATM 23 N N6 ADP . . . B 2 10.59 13.728 -2.169 1 39.12 ? N6 ADP 201 A 1 
HETATM 24 N N1 ADP . . . B 2 12.549 14.878 -1.508 1 40.12 ? N1 ADP 201 A 1 
HETATM 25 C C2 ADP . . . B 2 13.157 15.903 -0.87 1 39.36 ? C2 ADP 201 A 1 
HETATM 26 N N3 ADP . . . B 2 12.502 16.87 -0.191 1 39.35 ? N3 ADP 201 A 1 
HETATM 27 C C4 ADP . . . B 2 11.147 16.854 -0.117 1 31.97 ? C4 ADP 201 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           228 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#