data_7NUB
#
_model_server_result.job_id            dKvvSkRlR67MshadNGmH1g 
_model_server_result.datetime_utc      '2024-11-19 10:32:01' 
_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          7nub 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":901}' 
#
_entry.id    7NUB 
#
_exptl.entry_id    7NUB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              460.379 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate' 
_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            7NUB 
_cell.length_a            49.309 
_cell.length_b            81.748 
_cell.length_c            217.95 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7NUB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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 SG CYS 450 A CYS 449 1_555 C ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? 
metalc ? metalc2 A SG CYS 453 A CYS 452 1_555 C ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? 
metalc ? metalc3 A SG CYS 491 A CYS 490 1_555 C ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc4 A SG CYS 494 A CYS 493 1_555 C ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
#
_chem_comp.formula           'C16 H25 N6 O8 P' 
_chem_comp.formula_weight    460.379 
_chem_comp.id                USB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate' 
_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
CD2 CG USB sing 358 n n 
O3' C3' USB sing 359 n n 
CG CB USB sing 360 n n 
CG CD1 USB sing 361 n n 
C4' C3' USB sing 362 n n 
C4' O4' USB sing 363 n n 
C4' C5' USB sing 364 n n 
C3' C2' USB sing 365 n n 
CB CA USB sing 366 n n 
O4' C1' USB sing 367 n n 
C5' O5' USB sing 368 n n 
C1' C2' USB sing 369 n n 
C1' N9 USB sing 370 n n 
O2' C2' USB sing 371 n n 
N3 C2 USB doub 372 n y 
N3 C4 USB sing 373 n y 
C2 N1 USB sing 374 n y 
N CA USB sing 375 n n 
CA C USB sing 376 n n 
N9 C4 USB sing 377 n y 
N9 C8 USB sing 378 n y 
C4 C5 USB doub 379 n y 
C O USB doub 380 n n 
C OPP USB sing 381 n n 
O5' P USB sing 382 n n 
OPP P USB sing 383 n n 
N1 C6 USB doub 384 n y 
P O1P USB doub 385 n n 
P O2P USB sing 386 n n 
C8 N7 USB doub 387 n y 
C5 C6 USB sing 388 n y 
C5 N7 USB sing 389 n y 
C6 N6 USB sing 390 n n 
C2 H1 USB sing 391 n n 
C8 H2 USB sing 392 n n 
N H3 USB sing 393 n n 
N H4 USB sing 394 n n 
CA H6 USB sing 395 n n 
CB H7 USB sing 396 n n 
CB H8 USB sing 397 n n 
CG H9 USB sing 398 n n 
CD1 H10 USB sing 399 n n 
CD1 H11 USB sing 400 n n 
CD1 H12 USB sing 401 n n 
CD2 H13 USB sing 402 n n 
CD2 H14 USB sing 403 n n 
CD2 H15 USB sing 404 n n 
C1' H16 USB sing 405 n n 
C2' H17 USB sing 406 n n 
C3' H18 USB sing 407 n n 
C4' H19 USB sing 408 n n 
C5' H20 USB sing 409 n n 
C5' H21 USB sing 410 n n 
N6 H22 USB sing 411 n n 
N6 H23 USB sing 412 n n 
O2' H24 USB sing 413 n n 
O2P H25 USB sing 414 n n 
O3' H26 USB sing 415 n n 
#
_atom_sites.entry_id                     7NUB 
_atom_sites.fract_transf_matrix[1][1]    0.02028 
_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]    0.012233 
_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]    0.004588 
_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 USB A 1 901 1402 USB LPA . 
C 3 ZN A 1 902 1 ZN ZN . 
D 4 MG A 1 903 1 MG MG . 
E 5 HOH A 1 1001 28 HOH HOH . 
E 5 HOH A 2 1002 39 HOH HOH . 
E 5 HOH A 3 1003 31 HOH HOH . 
E 5 HOH A 4 1004 5 HOH HOH . 
E 5 HOH A 5 1005 27 HOH HOH . 
E 5 HOH A 6 1006 2 HOH HOH . 
E 5 HOH A 7 1007 19 HOH HOH . 
E 5 HOH A 8 1008 29 HOH HOH . 
E 5 HOH A 9 1009 12 HOH HOH . 
E 5 HOH A 10 1010 7 HOH HOH . 
E 5 HOH A 11 1011 24 HOH HOH . 
E 5 HOH A 12 1012 4 HOH HOH . 
E 5 HOH A 13 1013 8 HOH HOH . 
E 5 HOH A 14 1014 18 HOH HOH . 
E 5 HOH A 15 1015 32 HOH HOH . 
E 5 HOH A 16 1016 1 HOH HOH . 
E 5 HOH A 17 1017 3 HOH HOH . 
E 5 HOH A 18 1018 9 HOH HOH . 
E 5 HOH A 19 1019 14 HOH HOH . 
E 5 HOH A 20 1020 10 HOH HOH . 
E 5 HOH A 21 1021 33 HOH HOH . 
E 5 HOH A 22 1022 22 HOH HOH . 
E 5 HOH A 23 1023 13 HOH HOH . 
E 5 HOH A 24 1024 25 HOH HOH . 
E 5 HOH A 25 1025 6 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 C C2 USB . . . B 2 -12.449 -7.903 -27.386 1 45.8 ? C2 USB 901 A 1 
HETATM 2 C C4 USB . . . B 2 -10.394 -7.669 -26.627 1 41.67 ? C4 USB 901 A 1 
HETATM 3 C C5 USB . . . B 2 -10.742 -8.147 -25.375 1 42.3 ? C5 USB 901 A 1 
HETATM 4 C C6 USB . . . B 2 -12.089 -8.514 -25.185 1 45.32 ? C6 USB 901 A 1 
HETATM 5 C C8 USB . . . B 2 -8.671 -7.696 -25.281 1 43.64 ? C8 USB 901 A 1 
HETATM 6 N N USB . . . B 2 -0.597 -4.555 -26.835 1 33.65 ? N USB 901 A 1 
HETATM 7 C CA USB . . . B 2 -1.758 -3.653 -26.794 1 37.73 ? CA USB 901 A 1 
HETATM 8 C C USB . . . B 2 -3.028 -4.326 -26.273 1 49.32 ? C USB 901 A 1 
HETATM 9 O O USB . . . B 2 -4.041 -3.716 -26.071 1 61.8 ? O USB 901 A 1 
HETATM 10 C CB USB . . . B 2 -2.009 -3.08 -28.191 1 34.68 ? CB USB 901 A 1 
HETATM 11 C CG USB . . . B 2 -0.954 -2.057 -28.597 1 28.69 ? CG USB 901 A 1 
HETATM 12 C CD1 USB . . . B 2 -1.178 -1.583 -30.022 1 21.11 ? CD1 USB 901 A 1 
HETATM 13 C CD2 USB . . . B 2 -0.941 -0.88 -27.637 1 32.97 ? CD2 USB 901 A 1 
HETATM 14 C C1' USB . . . B 2 -8.223 -6.807 -27.613 1 29.22 ? C1' USB 901 A 1 
HETATM 15 C C2' USB . . . B 2 -7.595 -5.464 -27.258 1 37.72 ? C2' USB 901 A 1 
HETATM 16 C C3' USB . . . B 2 -6.388 -5.437 -28.202 1 40.21 ? C3' USB 901 A 1 
HETATM 17 C C4' USB . . . B 2 -6.009 -6.917 -28.333 1 50.1 ? C4' USB 901 A 1 
HETATM 18 C C5' USB . . . B 2 -4.758 -7.334 -27.6 1 60.42 ? C5' USB 901 A 1 
HETATM 19 N N1 USB . . . B 2 -12.93 -8.377 -26.233 1 47.99 ? N1 USB 901 A 1 
HETATM 20 N N3 USB . . . B 2 -11.204 -7.524 -27.681 1 42.09 ? N3 USB 901 A 1 
HETATM 21 N N6 USB . . . B 2 -12.576 -8.984 -24.031 1 47.13 ? N6 USB 901 A 1 
HETATM 22 N N7 USB . . . B 2 -9.641 -8.161 -24.531 1 45.44 ? N7 USB 901 A 1 
HETATM 23 N N9 USB . . . B 2 -9.054 -7.375 -26.557 1 31.48 ? N9 USB 901 A 1 
HETATM 24 O O1P USB . . . B 2 -4.231 -6.217 -23.996 1 76.33 ? O1P USB 901 A 1 
HETATM 25 O O2' USB . . . B 2 -8.507 -4.407 -27.534 1 42.78 ? O2' USB 901 A 1 
HETATM 26 O O2P USB . . . B 2 -2.812 -7.979 -25.179 1 53.33 ? O2P USB 901 A 1 
HETATM 27 O O3' USB . . . B 2 -6.719 -4.876 -29.467 1 41.52 ? O3' USB 901 A 1 
HETATM 28 O O4' USB . . . B 2 -7.138 -7.681 -27.852 1 47.55 ? O4' USB 901 A 1 
HETATM 29 O O5' USB . . . B 2 -4.952 -7.125 -26.186 1 61.18 ? O5' USB 901 A 1 
HETATM 30 O OPP USB . . . B 2 -2.938 -5.629 -26.055 1 48.11 ? OPP USB 901 A 1 
HETATM 31 P P USB . . . B 2 -3.702 -6.797 -25.25 1 57.82 ? P USB 901 A 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           361 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           31 
#