data_4BVG
#
_model_server_result.job_id            59JiqhGXNSSDNzRBQBPpeQ 
_model_server_result.datetime_utc      '2024-11-13 19:02:15' 
_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          4bvg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":1000}' 
#
_entry.id    4BVG 
#
_exptl.entry_id    4BVG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              601.352 
_entity.id                          8 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE' 
_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            4BVG 
_cell.length_a            78.023 
_cell.length_b            131.329 
_cell.length_c            76.508 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4BVG 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,H,I,J,K,L,M,N,O,P,Q,R 
_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                      8 
_struct_asym.id                             Q 
_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
covale ? covale1 B NZ LYS 5 B LYS 0 1_555 Q CH XYQ . B XYQ 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? 
metalc ? metalc1 A SG CYS 141 A CYS 256 1_555 P ZN ZN . A ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc2 A SG CYS 144 A CYS 259 1_555 P ZN ZN . A ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc3 A SG CYS 165 A CYS 280 1_555 P ZN ZN . A ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc4 A SG CYS 168 A CYS 283 1_555 P ZN ZN . A ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
#
_chem_comp.formula           'C17 H25 N5 O15 P2' 
_chem_comp.formula_weight    601.352 
_chem_comp.id                XYQ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ACETYL-RIBOSYL-ADP 
#
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
O5 CH XYQ doub 418 n n 
CH CH3 XYQ sing 419 n n 
CH OH XYQ sing 420 n n 
CH3 HH31 XYQ sing 421 n n 
CH3 HH32 XYQ sing 422 n n 
CH3 HH33 XYQ sing 423 n n 
OH C1N XYQ sing 424 n n 
C1N C2N XYQ sing 425 n n 
C1N O4N XYQ sing 426 n n 
C1N H1N XYQ sing 427 n n 
C2N C3N XYQ sing 428 n n 
C2N O2N XYQ sing 429 n n 
C2N H2N XYQ sing 430 n n 
C3N O3N XYQ sing 431 n n 
C3N C4N XYQ sing 432 n n 
C3N H3N XYQ sing 433 n n 
O3N HO3N XYQ sing 434 n n 
O2N HO2N XYQ sing 435 n n 
O4N C4N XYQ sing 436 n n 
C4N C5N XYQ sing 437 n n 
C4N H4N XYQ sing 438 n n 
C5N O5N XYQ sing 439 n n 
C5N H5N1 XYQ sing 440 n n 
C5N H5N2 XYQ sing 441 n n 
O5N PN XYQ sing 442 n n 
PN ON2 XYQ sing 443 n n 
PN ON1 XYQ doub 444 n n 
PN ON3 XYQ sing 445 n n 
ON2 HON2 XYQ sing 446 n n 
ON3 PA XYQ sing 447 n n 
PA OA2 XYQ sing 448 n n 
PA O5A XYQ sing 449 n n 
PA OA1 XYQ doub 450 n n 
OA2 HOA2 XYQ sing 451 n n 
O5A C5A XYQ sing 452 n n 
C5A C4A XYQ sing 453 n n 
C5A H5A1 XYQ sing 454 n n 
C5A H5A2 XYQ sing 455 n n 
C4A O4A XYQ sing 456 n n 
C4A C3A XYQ sing 457 n n 
C4A H4A XYQ sing 458 n n 
O4A C1A XYQ sing 459 n n 
C1A N9 XYQ sing 460 n n 
C1A C2A XYQ sing 461 n n 
C1A H1A XYQ sing 462 n n 
N9 C8 XYQ sing 463 n y 
N9 C4 XYQ sing 464 n y 
C8 N7 XYQ doub 465 n y 
C8 H8 XYQ sing 466 n n 
N7 C5 XYQ sing 467 n y 
C5 C4 XYQ sing 468 n y 
C5 C6 XYQ doub 469 n y 
C4 N3 XYQ doub 470 n y 
N3 C2 XYQ sing 471 n y 
C2 N1 XYQ doub 472 n y 
C2 H2 XYQ sing 473 n n 
N1 C6 XYQ sing 474 n y 
C6 N6 XYQ sing 475 n n 
N6 HN61 XYQ sing 476 n n 
N6 HN62 XYQ sing 477 n n 
C2A C3A XYQ sing 478 n n 
C2A O2A XYQ sing 479 n n 
C2A H2A XYQ sing 480 n n 
C3A O3A XYQ sing 481 n n 
C3A H3A XYQ sing 482 n n 
O3A HO3A XYQ sing 483 n n 
O2A HO2A XYQ sing 484 n n 
#
_atom_sites.entry_id                     4BVG 
_atom_sites.fract_transf_matrix[1][1]    0.012817 
_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]    0.007614 
_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]    0.013071 
_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 3 EDO A 1 1396 1396 EDO EDO . 
D 3 EDO A 1 1397 1397 EDO EDO . 
E 3 EDO A 1 1398 1398 EDO EDO . 
F 3 EDO A 1 1399 1399 EDO EDO . 
G 4 GOL A 1 1400 1400 GOL GOL . 
H 4 GOL A 1 1401 1401 GOL GOL . 
I 4 GOL A 1 1402 1402 GOL GOL . 
J 3 EDO A 1 1403 1403 EDO EDO . 
K 3 EDO A 1 1404 1404 EDO EDO . 
L 5 SO4 A 1 1405 1405 SO4 SO4 . 
M 5 SO4 A 1 1406 1406 SO4 SO4 . 
N 3 EDO A 1 1407 1407 EDO EDO . 
O 6 PEG A 1 1408 1408 PEG PEG . 
P 7 ZN A 1 1409 1409 ZN ZN . 
Q 8 XYQ B 1 1000 1000 XYQ OAD . 
R 9 HOH A 1 2001 2001 HOH HOH . 
R 9 HOH A 2 2002 2002 HOH HOH . 
R 9 HOH A 3 2003 2003 HOH HOH . 
R 9 HOH A 4 2004 2004 HOH HOH . 
R 9 HOH A 5 2005 2005 HOH HOH . 
R 9 HOH A 6 2006 2006 HOH HOH . 
R 9 HOH A 7 2007 2007 HOH HOH . 
R 9 HOH A 8 2008 2008 HOH HOH . 
R 9 HOH A 9 2009 2009 HOH HOH . 
R 9 HOH A 10 2010 2010 HOH HOH . 
R 9 HOH A 11 2011 2011 HOH HOH . 
R 9 HOH A 12 2012 2012 HOH HOH . 
R 9 HOH A 13 2013 2013 HOH HOH . 
R 9 HOH A 14 2014 2014 HOH HOH . 
R 9 HOH A 15 2015 2015 HOH HOH . 
R 9 HOH A 16 2016 2016 HOH HOH . 
R 9 HOH A 17 2017 2017 HOH HOH . 
R 9 HOH A 18 2018 2018 HOH HOH . 
R 9 HOH A 19 2019 2019 HOH HOH . 
R 9 HOH A 20 2020 2020 HOH HOH . 
R 9 HOH A 21 2021 2021 HOH HOH . 
R 9 HOH A 22 2022 2022 HOH HOH . 
R 9 HOH A 23 2023 2023 HOH HOH . 
R 9 HOH A 24 2024 2024 HOH HOH . 
R 9 HOH A 25 2025 2025 HOH HOH . 
R 9 HOH A 26 2026 2026 HOH HOH . 
R 9 HOH A 27 2027 2027 HOH HOH . 
R 9 HOH A 28 2028 2028 HOH HOH . 
R 9 HOH A 29 2029 2029 HOH HOH . 
R 9 HOH A 30 2030 2030 HOH HOH . 
R 9 HOH A 31 2031 2031 HOH HOH . 
R 9 HOH A 32 2032 2032 HOH HOH . 
R 9 HOH A 33 2033 2033 HOH HOH . 
R 9 HOH A 34 2034 2034 HOH HOH . 
R 9 HOH A 35 2035 2035 HOH HOH . 
R 9 HOH A 36 2036 2036 HOH HOH . 
R 9 HOH A 37 2037 2037 HOH HOH . 
R 9 HOH A 38 2038 2038 HOH HOH . 
R 9 HOH A 39 2039 2039 HOH HOH . 
R 9 HOH A 40 2040 2040 HOH HOH . 
R 9 HOH A 41 2041 2041 HOH HOH . 
R 9 HOH A 42 2042 2042 HOH HOH . 
R 9 HOH A 43 2043 2043 HOH HOH . 
R 9 HOH A 44 2044 2044 HOH HOH . 
R 9 HOH A 45 2045 2045 HOH HOH . 
R 9 HOH A 46 2046 2046 HOH HOH . 
R 9 HOH A 47 2047 2047 HOH HOH . 
R 9 HOH A 48 2048 2048 HOH HOH . 
R 9 HOH A 49 2049 2049 HOH HOH . 
R 9 HOH A 50 2050 2050 HOH HOH . 
R 9 HOH A 51 2051 2051 HOH HOH . 
R 9 HOH A 52 2052 2052 HOH HOH . 
R 9 HOH A 53 2053 2053 HOH HOH . 
R 9 HOH A 54 2054 2054 HOH HOH . 
R 9 HOH A 55 2055 2055 HOH HOH . 
R 9 HOH A 56 2056 2056 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 CH XYQ . . . Q 8 27.195 29.884 -14.471 1 36.42 ? CH XYQ 1000 B 1 
HETATM 2 C CH3 XYQ . . . Q 8 27.878 30.481 -13.234 1 33.83 ? CH3 XYQ 1000 B 1 
HETATM 3 O OH XYQ . . . Q 8 25.786 29.855 -14.439 1 45.28 ? OH XYQ 1000 B 1 
HETATM 4 C C1N XYQ . . . Q 8 24.595 29.089 -15.25 1 50.47 ? C1N XYQ 1000 B 1 
HETATM 5 C C2N XYQ . . . Q 8 23.991 29.879 -16.424 1 48.89 ? C2N XYQ 1000 B 1 
HETATM 6 C C3N XYQ . . . Q 8 22.651 29.185 -16.758 1 48.1 ? C3N XYQ 1000 B 1 
HETATM 7 O O3N XYQ . . . Q 8 21.721 30.19 -17.13 1 47.87 ? O3N XYQ 1000 B 1 
HETATM 8 O O2N XYQ . . . Q 8 23.631 31.198 -16.095 1 50.57 ? O2N XYQ 1000 B 1 
HETATM 9 O O4N XYQ . . . Q 8 23.307 28.532 -14.538 1 41.87 ? O4N XYQ 1000 B 1 
HETATM 10 C C4N XYQ . . . Q 8 22.169 28.527 -15.512 1 44.54 ? C4N XYQ 1000 B 1 
HETATM 11 C C5N XYQ . . . Q 8 21.523 27.194 -15.987 1 39.32 ? C5N XYQ 1000 B 1 
HETATM 12 O O5N XYQ . . . Q 8 20.087 27.335 -15.984 1 38.47 ? O5N XYQ 1000 B 1 
HETATM 13 P PN XYQ . . . Q 8 18.993 26.905 -14.778 1 32 ? PN XYQ 1000 B 1 
HETATM 14 O ON2 XYQ . . . Q 8 19.762 26.537 -13.429 1 30.63 ? ON2 XYQ 1000 B 1 
HETATM 15 O ON1 XYQ . . . Q 8 18.166 25.783 -15.278 1 35.74 ? ON1 XYQ 1000 B 1 
HETATM 16 O ON3 XYQ . . . Q 8 18.086 28.172 -14.459 1 36.98 ? ON3 XYQ 1000 B 1 
HETATM 17 P PA XYQ . . . Q 8 16.671 28.547 -15.232 1 33.77 ? PA XYQ 1000 B 1 
HETATM 18 O OA2 XYQ . . . Q 8 16.217 29.855 -14.467 1 30.47 ? OA2 XYQ 1000 B 1 
HETATM 19 O O5A XYQ . . . Q 8 15.67 27.328 -14.976 1 35.09 ? O5A XYQ 1000 B 1 
HETATM 20 C C5A XYQ . . . Q 8 14.942 27.259 -13.721 1 35.15 ? C5A XYQ 1000 B 1 
HETATM 21 C C4A XYQ . . . Q 8 13.867 26.174 -13.894 1 35.8 ? C4A XYQ 1000 B 1 
HETATM 22 O O4A XYQ . . . Q 8 13.202 25.718 -12.667 1 34.46 ? O4A XYQ 1000 B 1 
HETATM 23 C C1A XYQ . . . Q 8 11.796 26.147 -12.707 1 37.09 ? C1A XYQ 1000 B 1 
HETATM 24 N N9 XYQ . . . Q 8 11.424 26.609 -11.284 1 35.66 ? N9 XYQ 1000 B 1 
HETATM 25 C C8 XYQ . . . Q 8 11.77 27.68 -10.549 1 33.15 ? C8 XYQ 1000 B 1 
HETATM 26 N N7 XYQ . . . Q 8 11.176 27.545 -9.333 1 35.55 ? N7 XYQ 1000 B 1 
HETATM 27 C C5 XYQ . . . Q 8 10.481 26.385 -9.313 1 33.67 ? C5 XYQ 1000 B 1 
HETATM 28 C C4 XYQ . . . Q 8 10.629 25.813 -10.524 1 34.48 ? C4 XYQ 1000 B 1 
HETATM 29 N N3 XYQ . . . Q 8 10.041 24.628 -10.808 1 34.36 ? N3 XYQ 1000 B 1 
HETATM 30 C C2 XYQ . . . Q 8 9.255 23.958 -9.879 1 31.86 ? C2 XYQ 1000 B 1 
HETATM 31 N N1 XYQ . . . Q 8 9.105 24.6 -8.662 1 33.62 ? N1 XYQ 1000 B 1 
HETATM 32 C C6 XYQ . . . Q 8 9.724 25.764 -8.393 1 33.77 ? C6 XYQ 1000 B 1 
HETATM 33 N N6 XYQ . . . Q 8 9.583 26.334 -7.186 1 29.64 ? N6 XYQ 1000 B 1 
HETATM 34 C C2A XYQ . . . Q 8 11.681 27.15 -13.837 1 36.51 ? C2A XYQ 1000 B 1 
HETATM 35 C C3A XYQ . . . Q 8 12.808 26.715 -14.801 1 34.38 ? C3A XYQ 1000 B 1 
HETATM 36 O O3A XYQ . . . Q 8 12.469 25.581 -15.59 1 35.09 ? O3A XYQ 1000 B 1 
HETATM 37 O O2A XYQ . . . Q 8 10.383 26.944 -14.394 1 38.46 ? O2A XYQ 1000 B 1 
HETATM 38 O OA1 XYQ . . . Q 8 16.845 28.771 -16.704 1 38.92 ? OA1 XYQ 1000 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           38 
#