data_3NIZ
#
_model_server_result.job_id            KDFmHKJSp2MzAwFom_2S4Q 
_model_server_result.datetime_utc      '2024-11-24 03:30:12' 
_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          3niz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":314}' 
#
_entry.id    3NIZ 
#
_exptl.entry_id    3NIZ 
_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    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            3NIZ 
_cell.length_a            64.337 
_cell.length_b            64.337 
_cell.length_c            200.039 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NIZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
PISA dimeric 2 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,C,D,E 1 1 
A,B,C,D,E 2 1,2 
#
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' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 200.039 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_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 OD1 ASN 149 A ASN 149 1_555 B MG MG . A MG 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc2 A OD1 ASP 162 A ASP 162 1_555 B MG MG . A MG 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc3 B MG MG . A MG 312 1_555 D O1A ADP . A ADP 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc4 B MG MG . A MG 312 1_555 D O1B ADP . A ADP 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? 
metalc ? metalc5 C MG MG . A MG 313 1_555 D O3B ADP . A ADP 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc6 C MG MG . A MG 313 1_555 E O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc7 C MG MG . A MG 313 1_555 E O HOH . A HOH 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
#
_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                     3NIZ 
_atom_sites.fract_transf_matrix[1][1]    0.015543 
_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]    0.015543 
_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]    0.004999 
_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 MG A 1 312 1 MG MG . 
C 2 MG A 1 313 1 MG MG . 
D 3 ADP A 1 314 1 ADP ADP . 
E 4 HOH A 1 315 1 HOH HOH . 
E 4 HOH A 2 316 2 HOH HOH . 
E 4 HOH A 3 317 3 HOH HOH . 
E 4 HOH A 4 318 4 HOH HOH . 
E 4 HOH A 5 319 5 HOH HOH . 
E 4 HOH A 6 320 8 HOH HOH . 
E 4 HOH A 7 321 9 HOH HOH . 
E 4 HOH A 8 322 10 HOH HOH . 
E 4 HOH A 9 323 11 HOH HOH . 
E 4 HOH A 10 324 12 HOH HOH . 
E 4 HOH A 11 325 13 HOH HOH . 
E 4 HOH A 12 326 14 HOH HOH . 
E 4 HOH A 13 327 18 HOH HOH . 
E 4 HOH A 14 328 19 HOH HOH . 
E 4 HOH A 15 329 23 HOH HOH . 
E 4 HOH A 16 330 24 HOH HOH . 
E 4 HOH A 17 331 25 HOH HOH . 
E 4 HOH A 18 332 27 HOH HOH . 
E 4 HOH A 19 333 28 HOH HOH . 
E 4 HOH A 20 334 29 HOH HOH . 
E 4 HOH A 21 335 30 HOH HOH . 
E 4 HOH A 22 336 31 HOH HOH . 
E 4 HOH A 23 337 33 HOH HOH . 
E 4 HOH A 24 338 35 HOH HOH . 
E 4 HOH A 25 339 36 HOH HOH . 
E 4 HOH A 26 340 39 HOH HOH . 
E 4 HOH A 27 341 40 HOH HOH . 
E 4 HOH A 28 342 41 HOH HOH . 
E 4 HOH A 29 343 42 HOH HOH . 
E 4 HOH A 30 344 43 HOH HOH . 
E 4 HOH A 31 345 44 HOH HOH . 
E 4 HOH A 32 346 47 HOH HOH . 
E 4 HOH A 33 347 48 HOH HOH . 
E 4 HOH A 34 348 51 HOH HOH . 
E 4 HOH A 35 349 58 HOH HOH . 
E 4 HOH A 36 350 61 HOH HOH . 
E 4 HOH A 37 351 62 HOH HOH . 
E 4 HOH A 38 352 66 HOH HOH . 
E 4 HOH A 39 353 67 HOH HOH . 
E 4 HOH A 40 354 68 HOH HOH . 
E 4 HOH A 41 355 75 HOH HOH . 
E 4 HOH A 42 356 76 HOH HOH . 
E 4 HOH A 43 357 80 HOH HOH . 
E 4 HOH A 44 358 87 HOH HOH . 
E 4 HOH A 45 359 91 HOH HOH . 
E 4 HOH A 46 360 101 HOH HOH . 
E 4 HOH A 47 361 127 HOH HOH . 
E 4 HOH A 48 362 130 HOH HOH . 
E 4 HOH A 49 363 131 HOH HOH . 
E 4 HOH A 50 364 132 HOH HOH . 
E 4 HOH A 51 365 135 HOH HOH . 
E 4 HOH A 52 366 136 HOH HOH . 
E 4 HOH A 53 367 138 HOH HOH . 
E 4 HOH A 54 368 139 HOH HOH . 
E 4 HOH A 55 369 140 HOH HOH . 
E 4 HOH A 56 370 142 HOH HOH . 
E 4 HOH A 57 371 143 HOH HOH . 
E 4 HOH A 58 372 144 HOH HOH . 
E 4 HOH A 59 373 145 HOH HOH . 
E 4 HOH A 60 374 146 HOH HOH . 
E 4 HOH A 61 375 147 HOH HOH . 
E 4 HOH A 62 376 148 HOH HOH . 
E 4 HOH A 63 377 149 HOH HOH . 
E 4 HOH A 64 378 150 HOH HOH . 
E 4 HOH A 65 379 151 HOH HOH . 
E 4 HOH A 66 380 13 HOH HOH . 
E 4 HOH A 67 381 93 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 . . . D 3 -0.919 13.109 86.706 1 70.3 ? PB ADP 314 A 1 
HETATM 2 O O1B ADP . . . D 3 -1.512 13.178 85.241 1 70.83 ? O1B ADP 314 A 1 
HETATM 3 O O2B ADP . . . D 3 -1.971 13.383 87.738 1 72.02 ? O2B ADP 314 A 1 
HETATM 4 O O3B ADP . . . D 3 -0.398 11.725 87.134 1 70.9 ? O3B ADP 314 A 1 
HETATM 5 P PA ADP . . . D 3 0.918 15.028 85.82 1 71.09 ? PA ADP 314 A 1 
HETATM 6 O O1A ADP . . . D 3 0.967 14.531 84.311 1 71.27 ? O1A ADP 314 A 1 
HETATM 7 O O2A ADP . . . D 3 2.39 15.478 86.04 1 72.21 ? O2A ADP 314 A 1 
HETATM 8 O O3A ADP . . . D 3 0.371 13.992 86.803 1 71.06 ? O3A ADP 314 A 1 
HETATM 9 O O5' ADP . . . D 3 -0.283 16.025 85.98 1 72.56 ? O5' ADP 314 A 1 
HETATM 10 C C5' ADP . . . D 3 0.17 17.318 86.115 1 71.18 ? C5' ADP 314 A 1 
HETATM 11 C C4' ADP . . . D 3 -0.599 18.289 85.246 1 70.81 ? C4' ADP 314 A 1 
HETATM 12 O O4' ADP . . . D 3 -0.366 19.519 85.99 1 71 ? O4' ADP 314 A 1 
HETATM 13 C C3' ADP . . . D 3 0.143 18.448 83.917 1 71.6 ? C3' ADP 314 A 1 
HETATM 14 O O3' ADP . . . D 3 -0.405 17.721 82.783 1 73.36 ? O3' ADP 314 A 1 
HETATM 15 C C2' ADP . . . D 3 0.315 19.99 83.812 1 71.58 ? C2' ADP 314 A 1 
HETATM 16 O O2' ADP . . . D 3 -0.969 20.588 83.326 1 74.02 ? O2' ADP 314 A 1 
HETATM 17 C C1' ADP . . . D 3 0.614 20.364 85.303 1 70.73 ? C1' ADP 314 A 1 
HETATM 18 N N9 ADP . . . D 3 2.057 20.228 85.636 1 69.22 ? N9 ADP 314 A 1 
HETATM 19 C C8 ADP . . . D 3 2.803 19.072 85.841 1 69.24 ? C8 ADP 314 A 1 
HETATM 20 N N7 ADP . . . D 3 4.098 19.313 86.049 1 67.6 ? N7 ADP 314 A 1 
HETATM 21 C C5 ADP . . . D 3 4.259 20.669 85.991 1 67.43 ? C5 ADP 314 A 1 
HETATM 22 C C6 ADP . . . D 3 5.403 21.545 86.123 1 67.3 ? C6 ADP 314 A 1 
HETATM 23 N N6 ADP . . . D 3 6.693 21.125 86.339 1 67.05 ? N6 ADP 314 A 1 
HETATM 24 N N1 ADP . . . D 3 5.195 22.925 85.964 1 67.5 ? N1 ADP 314 A 1 
HETATM 25 C C2 ADP . . . D 3 3.905 23.338 85.767 1 68.16 ? C2 ADP 314 A 1 
HETATM 26 N N3 ADP . . . D 3 2.772 22.6 85.618 1 67.8 ? N3 ADP 314 A 1 
HETATM 27 C C4 ADP . . . D 3 2.99 21.277 85.731 1 67.77 ? C4 ADP 314 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#