data_6XUY
#
_model_server_result.job_id            gkUaLYa3aetMzhKl6etJ6Q 
_model_server_result.datetime_utc      '2024-11-18 18:46:51' 
_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          6xuy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    6XUY 
#
_exptl.entry_id    6XUY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_entity.pdbx_number_of_molecules    2 
_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         120 
_cell.entry_id            6XUY 
_cell.length_a            91.192 
_cell.length_b            91.192 
_cell.length_c            143.997 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XUY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
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 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,Q 1 1 
B,K,L,M,N,O,P,R 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 K N 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 135 A CYS 141 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 L ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc6 B SG CYS 160 B CYS 166 1_555 L ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc7 B SG CYS 171 B CYS 177 1_555 L ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                AR6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Adenosine-5-Diphosphoribose 
#
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
N1 C2 AR6 doub 13 n y 
N1 C6 AR6 sing 14 n y 
C2 N3 AR6 sing 15 n y 
N3 C4 AR6 doub 16 n y 
C4 C5 AR6 sing 17 n y 
C4 N9 AR6 sing 18 n y 
C5 C6 AR6 doub 19 n y 
C5 N7 AR6 sing 20 n y 
C6 N6 AR6 sing 21 n n 
N7 C8 AR6 doub 22 n y 
C8 N9 AR6 sing 23 n y 
N9 C1' AR6 sing 24 n n 
PA O1A AR6 sing 25 n n 
PA O2A AR6 doub 26 n n 
PA O3A AR6 sing 27 n n 
PA O5' AR6 sing 28 n n 
PB O1B AR6 sing 29 n n 
PB O2B AR6 doub 30 n n 
PB O3A AR6 sing 31 n n 
PB O5D AR6 sing 32 n n 
C1' C2' AR6 sing 33 n n 
C1' O4' AR6 sing 34 n n 
C1D O1D AR6 sing 35 n n 
C1D C2D AR6 sing 36 n n 
C1D O4D AR6 sing 37 n n 
C2' O2' AR6 sing 38 n n 
C2' C3' AR6 sing 39 n n 
C2D O2D AR6 sing 40 n n 
C2D C3D AR6 sing 41 n n 
C3' O3' AR6 sing 42 n n 
C3' C4' AR6 sing 43 n n 
C3D O3D AR6 sing 44 n n 
C3D C4D AR6 sing 45 n n 
C4' O4' AR6 sing 46 n n 
C4' C5' AR6 sing 47 n n 
C4D O4D AR6 sing 48 n n 
C4D C5D AR6 sing 49 n n 
C5' O5' AR6 sing 50 n n 
C5D O5D AR6 sing 51 n n 
C2 H2 AR6 sing 52 n n 
N6 HN6 AR6 sing 53 n n 
N6 HN6A AR6 sing 54 n n 
C8 H8 AR6 sing 55 n n 
C1' H1' AR6 sing 56 n n 
C1D H1D AR6 sing 57 n n 
C2' H2' AR6 sing 58 n n 
O2' HO2' AR6 sing 59 n n 
C2D H2D AR6 sing 60 n n 
O2D HO2D AR6 sing 61 n n 
C3' H3' AR6 sing 62 n n 
O3' HO3' AR6 sing 63 n n 
C3D H3D AR6 sing 64 n n 
O3D HO3D AR6 sing 65 n n 
C4' H4' AR6 sing 66 n n 
C4D H4D AR6 sing 67 n n 
C5' H5' AR6 sing 68 n n 
C5' "H5'A" AR6 sing 69 n n 
C5D H5D AR6 sing 70 n n 
C5D H5DA AR6 sing 71 n n 
O1A H1A AR6 sing 72 n n 
O1B H1B AR6 sing 73 n n 
O1D HD1 AR6 sing 74 n n 
#
_atom_sites.entry_id                     6XUY 
_atom_sites.fract_transf_matrix[1][1]    0.010966 
_atom_sites.fract_transf_matrix[1][2]    0.006331 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012662 
_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]    0.006945 
_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 2 AR6 A 1 401 500 AR6 AR6 . 
D 3 ZN A 1 402 501 ZN ZN . 
E 4 PGE A 1 403 601 PGE PGE . 
F 5 SO4 A 1 404 3 SO4 SO4 . 
G 5 SO4 A 1 405 5 SO4 SO4 . 
H 5 SO4 A 1 406 7 SO4 SO4 . 
I 5 SO4 A 1 407 8 SO4 SO4 . 
J 5 SO4 A 1 408 9 SO4 SO4 . 
K 2 AR6 B 1 401 500 AR6 AR6 . 
L 3 ZN B 1 402 501 ZN ZN . 
M 5 SO4 B 1 403 1 SO4 SO4 . 
N 5 SO4 B 1 404 2 SO4 SO4 . 
O 5 SO4 B 1 405 4 SO4 SO4 . 
P 5 SO4 B 1 406 6 SO4 SO4 . 
Q 6 HOH A 1 501 49 HOH HOH . 
Q 6 HOH A 2 502 18 HOH HOH . 
Q 6 HOH A 3 503 32 HOH HOH . 
Q 6 HOH A 4 504 19 HOH HOH . 
Q 6 HOH A 5 505 34 HOH HOH . 
Q 6 HOH A 6 506 17 HOH HOH . 
Q 6 HOH A 7 507 2 HOH HOH . 
Q 6 HOH A 8 508 11 HOH HOH . 
Q 6 HOH A 9 509 29 HOH HOH . 
Q 6 HOH A 10 510 3 HOH HOH . 
Q 6 HOH A 11 511 46 HOH HOH . 
Q 6 HOH A 12 512 41 HOH HOH . 
Q 6 HOH A 13 513 25 HOH HOH . 
Q 6 HOH A 14 514 36 HOH HOH . 
Q 6 HOH A 15 515 24 HOH HOH . 
Q 6 HOH A 16 516 27 HOH HOH . 
Q 6 HOH A 17 517 10 HOH HOH . 
Q 6 HOH A 18 518 35 HOH HOH . 
Q 6 HOH A 19 519 21 HOH HOH . 
Q 6 HOH A 20 520 16 HOH HOH . 
Q 6 HOH A 21 521 8 HOH HOH . 
Q 6 HOH A 22 522 43 HOH HOH . 
Q 6 HOH A 23 523 48 HOH HOH . 
Q 6 HOH A 24 524 5 HOH HOH . 
Q 6 HOH A 25 525 4 HOH HOH . 
Q 6 HOH A 26 526 38 HOH HOH . 
Q 6 HOH A 27 527 1 HOH HOH . 
Q 6 HOH A 28 528 31 HOH HOH . 
Q 6 HOH A 29 529 12 HOH HOH . 
Q 6 HOH A 30 530 13 HOH HOH . 
Q 6 HOH A 31 531 15 HOH HOH . 
R 6 HOH B 1 501 42 HOH HOH . 
R 6 HOH B 2 502 40 HOH HOH . 
R 6 HOH B 3 503 23 HOH HOH . 
R 6 HOH B 4 504 44 HOH HOH . 
R 6 HOH B 5 505 28 HOH HOH . 
R 6 HOH B 6 506 30 HOH HOH . 
R 6 HOH B 7 507 39 HOH HOH . 
R 6 HOH B 8 508 47 HOH HOH . 
R 6 HOH B 9 509 37 HOH HOH . 
R 6 HOH B 10 510 14 HOH HOH . 
R 6 HOH B 11 511 9 HOH HOH . 
R 6 HOH B 12 512 33 HOH HOH . 
R 6 HOH B 13 513 45 HOH HOH . 
R 6 HOH B 14 514 6 HOH HOH . 
R 6 HOH B 15 515 22 HOH HOH . 
R 6 HOH B 16 516 7 HOH HOH . 
R 6 HOH B 17 517 20 HOH HOH . 
R 6 HOH B 18 518 26 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 N N1 AR6 . . . C 2 -29.68 9.761 24.469 1 25.12 ? N1 AR6 401 A 1 
HETATM 2 C C2 AR6 . . . C 2 -30.559 9.51 23.458 1 21.91 ? C2 AR6 401 A 1 
HETATM 3 N N3 AR6 . . . C 2 -31.234 10.394 22.695 1 31.25 ? N3 AR6 401 A 1 
HETATM 4 C C4 AR6 . . . C 2 -30.925 11.665 23.041 1 23.74 ? C4 AR6 401 A 1 
HETATM 5 C C5 AR6 . . . C 2 -30.097 12.063 24.085 1 19.63 ? C5 AR6 401 A 1 
HETATM 6 C C6 AR6 . . . C 2 -29.45 11.05 24.843 1 25.8 ? C6 AR6 401 A 1 
HETATM 7 N N6 AR6 . . . C 2 -28.585 11.279 25.859 1 33.46 ? N6 AR6 401 A 1 
HETATM 8 N N7 AR6 . . . C 2 -30.029 13.461 24.121 1 23.96 ? N7 AR6 401 A 1 
HETATM 9 C C8 AR6 . . . C 2 -30.779 13.898 23.15 1 21.44 ? C8 AR6 401 A 1 
HETATM 10 N N9 AR6 . . . C 2 -31.336 12.825 22.427 1 22.55 ? N9 AR6 401 A 1 
HETATM 11 P PA AR6 . . . C 2 -31.691 17.269 17.237 1 30.4 ? PA AR6 401 A 1 
HETATM 12 P PB AR6 . . . C 2 -29.882 16.77 15.038 1 23.7 ? PB AR6 401 A 1 
HETATM 13 C C1' AR6 . . . C 2 -32.192 12.981 21.276 1 20.36 ? C1' AR6 401 A 1 
HETATM 14 O O1A AR6 . . . C 2 -32.724 17.676 16.228 1 33.36 ? O1A AR6 401 A 1 
HETATM 15 O O1B AR6 . . . C 2 -28.462 16.294 15.223 1 23.83 ? O1B AR6 401 A 1 
HETATM 16 C C1D AR6 . . . C 2 -29.822 21.549 13.428 1 38.63 ? C1D AR6 401 A 1 
HETATM 17 O O1D AR6 . . . C 2 -30.297 22.713 12.878 1 35.8 ? O1D AR6 401 A 1 
HETATM 18 C C2' AR6 . . . C 2 -33.217 14.09 21.37 1 15.49 ? C2' AR6 401 A 1 
HETATM 19 O O2' AR6 . . . C 2 -34.423 13.442 21.7 1 10.92 ? O2' AR6 401 A 1 
HETATM 20 O O2A AR6 . . . C 2 -31.648 17.977 18.578 1 30.44 ? O2A AR6 401 A 1 
HETATM 21 O O2B AR6 . . . C 2 -30.845 15.609 14.736 1 18.73 ? O2B AR6 401 A 1 
HETATM 22 C C2D AR6 . . . C 2 -28.288 21.471 13.383 1 37.68 ? C2D AR6 401 A 1 
HETATM 23 O O2D AR6 . . . C 2 -27.82 21.917 12.148 1 26.02 ? O2D AR6 401 A 1 
HETATM 24 C C3' AR6 . . . C 2 -33.375 14.555 19.908 1 18.7 ? C3' AR6 401 A 1 
HETATM 25 O O3' AR6 . . . C 2 -34.374 13.86 19.205 1 15.5 ? O3' AR6 401 A 1 
HETATM 26 O O3A AR6 . . . C 2 -30.226 17.262 16.557 1 26.82 ? O3A AR6 401 A 1 
HETATM 27 C C3D AR6 . . . C 2 -28.025 19.972 13.456 1 35.2 ? C3D AR6 401 A 1 
HETATM 28 O O3D AR6 . . . C 2 -26.746 19.632 12.903 1 32.75 ? O3D AR6 401 A 1 
HETATM 29 C C4' AR6 . . . C 2 -32.123 14.057 19.218 1 20.24 ? C4' AR6 401 A 1 
HETATM 30 O O4' AR6 . . . C 2 -31.373 13.403 20.244 1 25.03 ? O4' AR6 401 A 1 
HETATM 31 C C4D AR6 . . . C 2 -29.162 19.457 12.567 1 34.17 ? C4D AR6 401 A 1 
HETATM 32 O O4D AR6 . . . C 2 -30.24 20.41 12.645 1 33.77 ? O4D AR6 401 A 1 
HETATM 33 C C5' AR6 . . . C 2 -31.236 15.154 18.682 1 27.66 ? C5' AR6 401 A 1 
HETATM 34 O O5' AR6 . . . C 2 -31.882 15.706 17.453 1 26.68 ? O5' AR6 401 A 1 
HETATM 35 C C5D AR6 . . . C 2 -29.723 18.098 12.838 1 38.9 ? C5D AR6 401 A 1 
HETATM 36 O O5D AR6 . . . C 2 -30.001 18.085 14.213 1 33.82 ? O5D AR6 401 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#