data_4XJT
#
_model_server_result.job_id            FaFncTCu5pDmXXafM_Fnug 
_model_server_result.datetime_utc      '2024-12-26 22:10:07' 
_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          4xjt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    4XJT 
#
_exptl.entry_id    4XJT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              623.296 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN 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            4XJT 
_cell.length_a            51.017 
_cell.length_b            63.95 
_cell.length_c            72.308 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XJT 
_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 
_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                      3 
_struct_asym.id                             C 
_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
disulf ? disulf1 A SG CYS 29 A CYS 67 1_555 A SG CYS 44 A CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf2 A SG CYS 61 A CYS 99 1_555 A SG CYS 142 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf3 A SG CYS 81 A CYS 119 1_555 A SG CYS 163 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 A SG CYS 122 A CYS 160 1_555 A SG CYS 135 A CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf5 A SG CYS 216 A CYS 254 1_555 A SG CYS 237 A CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
covale ? covale1 A NE2 GLN 188 A GLN 226 1_555 C C1D NA7 . A NA7 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? 
#
_chem_comp.formula           'C15 H24 N5 O16 P3' 
_chem_comp.formula_weight    623.296 
_chem_comp.id                NA7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN 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
PA O5B NA7 sing 284 n n 
PA O2A NA7 doub 285 n n 
PA O1A NA7 sing 286 n n 
PA O3 NA7 sing 287 n n 
O1A HAO1 NA7 sing 288 n n 
O5B C5B NA7 sing 289 n n 
C5B C4B NA7 sing 290 n n 
C5B "H5'1" NA7 sing 291 n n 
C5B "H5'2" NA7 sing 292 n n 
C4B C3B NA7 sing 293 n n 
C4B O4B NA7 sing 294 n n 
C4B HC4' NA7 sing 295 n n 
O4B C1B NA7 sing 296 n n 
C3B O3B NA7 sing 297 n n 
C3B C2B NA7 sing 298 n n 
C3B HC3' NA7 sing 299 n n 
O3B HO3' NA7 sing 300 n n 
C2B O2B NA7 sing 301 n n 
C2B C1B NA7 sing 302 n n 
C2B HC2' NA7 sing 303 n n 
O2B P2B NA7 sing 304 n n 
C1B N9A NA7 sing 305 n n 
C1B HC1' NA7 sing 306 n n 
N9A C4A NA7 sing 307 n y 
N9A C8A NA7 sing 308 n y 
C8A N7A NA7 doub 309 n y 
C8A HC8 NA7 sing 310 n n 
N7A C5A NA7 sing 311 n y 
C5A C4A NA7 doub 312 n y 
C5A C6A NA7 sing 313 n y 
C6A N1A NA7 doub 314 n y 
C6A N6A NA7 sing 315 n n 
N6A HN61 NA7 sing 316 n n 
N6A HN62 NA7 sing 317 n n 
N1A C2A NA7 sing 318 n y 
C2A N3A NA7 doub 319 n y 
C2A HC2 NA7 sing 320 n n 
N3A C4A NA7 sing 321 n y 
O3 PN NA7 sing 322 n n 
PN O5D NA7 sing 323 n n 
PN O1N NA7 doub 324 n n 
PN O2N NA7 sing 325 n n 
O2N HNO2 NA7 sing 326 n n 
O5D C5D NA7 sing 327 n n 
C5D C4D NA7 sing 328 n n 
C5D H51' NA7 sing 329 n n 
C5D H52' NA7 sing 330 n n 
C4D O4D NA7 sing 331 n n 
C4D C3D NA7 sing 332 n n 
C4D HN4' NA7 sing 333 n n 
O4D C1D NA7 sing 334 n n 
C3D C2D NA7 sing 335 n n 
C3D O3D NA7 sing 336 n n 
C3D HN3' NA7 sing 337 n n 
O3D HN5' NA7 sing 338 n n 
C2D O2D NA7 sing 339 n n 
C2D C1D NA7 sing 340 n n 
C2D HN6' NA7 sing 341 n n 
O2D HN7' NA7 sing 342 n n 
C1D "H1'1" NA7 sing 343 n n 
C1D "H1'2" NA7 sing 344 n n 
P2B O3X NA7 doub 345 n n 
P2B O2X NA7 sing 346 n n 
P2B O1X NA7 sing 347 n n 
O1X HOP1 NA7 sing 348 n n 
O2X HOP2 NA7 sing 349 n n 
#
_atom_sites.entry_id                     4XJT 
_atom_sites.fract_transf_matrix[1][1]    0.019601 
_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]    0.015637 
_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]    0.01383 
_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 41Z A 1 401 1 41Z LIG . 
C 3 NA7 A 1 402 1 NA7 NAP . 
D 4 HOH A 1 501 4 HOH HOH . 
D 4 HOH A 2 502 33 HOH HOH . 
D 4 HOH A 3 503 38 HOH HOH . 
D 4 HOH A 4 504 43 HOH HOH . 
D 4 HOH A 5 505 29 HOH HOH . 
D 4 HOH A 6 506 32 HOH HOH . 
D 4 HOH A 7 507 46 HOH HOH . 
D 4 HOH A 8 508 47 HOH HOH . 
D 4 HOH A 9 509 25 HOH HOH . 
D 4 HOH A 10 510 34 HOH HOH . 
D 4 HOH A 11 511 35 HOH HOH . 
D 4 HOH A 12 512 1 HOH HOH . 
D 4 HOH A 13 513 2 HOH HOH . 
D 4 HOH A 14 514 3 HOH HOH . 
D 4 HOH A 15 515 5 HOH HOH . 
D 4 HOH A 16 516 6 HOH HOH . 
D 4 HOH A 17 517 7 HOH HOH . 
D 4 HOH A 18 518 8 HOH HOH . 
D 4 HOH A 19 519 9 HOH HOH . 
D 4 HOH A 20 520 10 HOH HOH . 
D 4 HOH A 21 521 11 HOH HOH . 
D 4 HOH A 22 522 12 HOH HOH . 
D 4 HOH A 23 523 13 HOH HOH . 
D 4 HOH A 24 524 14 HOH HOH . 
D 4 HOH A 25 525 15 HOH HOH . 
D 4 HOH A 26 526 16 HOH HOH . 
D 4 HOH A 27 527 17 HOH HOH . 
D 4 HOH A 28 528 18 HOH HOH . 
D 4 HOH A 29 529 19 HOH HOH . 
D 4 HOH A 30 530 20 HOH HOH . 
D 4 HOH A 31 531 21 HOH HOH . 
D 4 HOH A 32 532 22 HOH HOH . 
D 4 HOH A 33 533 23 HOH HOH . 
D 4 HOH A 34 534 24 HOH HOH . 
D 4 HOH A 35 535 26 HOH HOH . 
D 4 HOH A 36 536 27 HOH HOH . 
D 4 HOH A 37 537 28 HOH HOH . 
D 4 HOH A 38 538 30 HOH HOH . 
D 4 HOH A 39 539 31 HOH HOH . 
D 4 HOH A 40 540 36 HOH HOH . 
D 4 HOH A 41 541 37 HOH HOH . 
D 4 HOH A 42 542 39 HOH HOH . 
D 4 HOH A 43 543 40 HOH HOH . 
D 4 HOH A 44 544 41 HOH HOH . 
D 4 HOH A 45 545 42 HOH HOH . 
D 4 HOH A 46 546 44 HOH HOH . 
D 4 HOH A 47 547 45 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 PA NA7 . . . C 3 -10.611 -23.48 16.014 1 97.97 ? PA NA7 402 A 1 
HETATM 2 O O1A NA7 . . . C 3 -9.81 -24.487 16.802 1 86.12 ? O1A NA7 402 A 1 
HETATM 3 O O2A NA7 . . . C 3 -12.123 -23.51 16.083 1 101.7 ? O2A NA7 402 A 1 
HETATM 4 O O5B NA7 . . . C 3 -10.195 -23.612 14.422 1 100.17 ? O5B NA7 402 A 1 
HETATM 5 C C5B NA7 . . . C 3 -8.946 -23.115 13.946 1 96.42 ? C5B NA7 402 A 1 
HETATM 6 C C4B NA7 . . . C 3 -8.414 -23.907 12.759 1 96.96 ? C4B NA7 402 A 1 
HETATM 7 O O4B NA7 . . . C 3 -7.086 -24.36 13.043 1 103.25 ? O4B NA7 402 A 1 
HETATM 8 C C3B NA7 . . . C 3 -9.21 -25.139 12.462 1 97.09 ? C3B NA7 402 A 1 
HETATM 9 O O3B NA7 . . . C 3 -9.128 -25.331 11.059 1 98.62 ? O3B NA7 402 A 1 
HETATM 10 C C2B NA7 . . . C 3 -8.464 -26.235 13.168 1 98.31 ? C2B NA7 402 A 1 
HETATM 11 O O2B NA7 . . . C 3 -8.546 -27.401 12.385 1 97.41 ? O2B NA7 402 A 1 
HETATM 12 C C1B NA7 . . . C 3 -7.03 -25.785 13.18 1 101.51 ? C1B NA7 402 A 1 
HETATM 13 N N9A NA7 . . . C 3 -6.259 -26.062 14.395 1 103.98 ? N9A NA7 402 A 1 
HETATM 14 C C8A NA7 . . . C 3 -4.917 -25.815 14.478 1 105 ? C8A NA7 402 A 1 
HETATM 15 N N7A NA7 . . . C 3 -4.412 -26.119 15.653 1 104.62 ? N7A NA7 402 A 1 
HETATM 16 C C5A NA7 . . . C 3 -5.489 -26.587 16.36 1 109.68 ? C5A NA7 402 A 1 
HETATM 17 C C6A NA7 . . . C 3 -5.555 -27.046 17.66 1 112.75 ? C6A NA7 402 A 1 
HETATM 18 N N6A NA7 . . . C 3 -4.397 -27.084 18.446 1 108.4 ? N6A NA7 402 A 1 
HETATM 19 N N1A NA7 . . . C 3 -6.755 -27.445 18.109 1 117.6 ? N1A NA7 402 A 1 
HETATM 20 C C2A NA7 . . . C 3 -7.804 -27.372 17.279 1 114.66 ? C2A NA7 402 A 1 
HETATM 21 N N3A NA7 . . . C 3 -7.857 -26.948 16.012 1 111.05 ? N3A NA7 402 A 1 
HETATM 22 C C4A NA7 . . . C 3 -6.646 -26.563 15.607 1 106.6 ? C4A NA7 402 A 1 
HETATM 23 O O3 NA7 . . . C 3 -10.154 -21.938 16.399 1 84.74 ? O3 NA7 402 A 1 
HETATM 24 P PN NA7 . . . C 3 -11.036 -20.71 17.022 1 68.86 ? PN NA7 402 A 1 
HETATM 25 O O1N NA7 . . . C 3 -12.2 -20.445 16.098 1 68.9 ? O1N NA7 402 A 1 
HETATM 26 O O2N NA7 . . . C 3 -11.224 -21.031 18.483 1 72.86 ? O2N NA7 402 A 1 
HETATM 27 O O5D NA7 . . . C 3 -9.968 -19.479 16.877 1 61.59 ? O5D NA7 402 A 1 
HETATM 28 C C5D NA7 . . . C 3 -10.495 -18.163 16.92 1 56.64 ? C5D NA7 402 A 1 
HETATM 29 C C4D NA7 . . . C 3 -9.954 -17.392 18.105 1 57.44 ? C4D NA7 402 A 1 
HETATM 30 O O4D NA7 . . . C 3 -8.541 -17.257 17.97 1 56.5 ? O4D NA7 402 A 1 
HETATM 31 C C3D NA7 . . . C 3 -10.542 -15.991 18.11 1 60.55 ? C3D NA7 402 A 1 
HETATM 32 O O3D NA7 . . . C 3 -10.964 -15.615 19.422 1 57.72 ? O3D NA7 402 A 1 
HETATM 33 C C2D NA7 . . . C 3 -9.417 -15.082 17.717 1 61.4 ? C2D NA7 402 A 1 
HETATM 34 O O2D NA7 . . . C 3 -9.562 -13.82 18.375 1 56.87 ? O2D NA7 402 A 1 
HETATM 35 C C1D NA7 . . . C 3 -8.211 -15.878 18.196 1 61.27 ? C1D NA7 402 A 1 
HETATM 36 P P2B NA7 . . . C 3 -9.653 -28.491 12.854 1 94.6 ? P2B NA7 402 A 1 
HETATM 37 O O1X NA7 . . . C 3 -10.082 -29.019 11.503 1 95.53 ? O1X NA7 402 A 1 
HETATM 38 O O2X NA7 . . . C 3 -8.835 -29.405 13.74 1 88.64 ? O2X NA7 402 A 1 
HETATM 39 O O3X NA7 . . . C 3 -10.738 -27.734 13.588 1 93.25 ? O3X NA7 402 A 1 
#
_model_server_stats.io_time_ms              58 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#