data_6ZU4
#
_model_server_result.job_id            ElpNhSP8o2VSNKjim5R31A 
_model_server_result.datetime_utc      '2025-01-10 10:40:11' 
_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          6zu4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":401}' 
#
_entry.id    6ZU4 
#
_exptl.entry_id    6ZU4 
_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            6ZU4 
_cell.length_a            91.407 
_cell.length_b            91.407 
_cell.length_c            144.277 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6ZU4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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,S,T 
_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 
#
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 J 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 K ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 K ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 K ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 K ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? 
#
_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 71 n y 
N1 C6 AR6 sing 72 n y 
C2 N3 AR6 sing 73 n y 
N3 C4 AR6 doub 74 n y 
C4 C5 AR6 sing 75 n y 
C4 N9 AR6 sing 76 n y 
C5 C6 AR6 doub 77 n y 
C5 N7 AR6 sing 78 n y 
C6 N6 AR6 sing 79 n n 
N7 C8 AR6 doub 80 n y 
C8 N9 AR6 sing 81 n y 
N9 C1' AR6 sing 82 n n 
PA O1A AR6 sing 83 n n 
PA O2A AR6 doub 84 n n 
PA O3A AR6 sing 85 n n 
PA O5' AR6 sing 86 n n 
PB O1B AR6 sing 87 n n 
PB O2B AR6 doub 88 n n 
PB O3A AR6 sing 89 n n 
PB O5D AR6 sing 90 n n 
C1' C2' AR6 sing 91 n n 
C1' O4' AR6 sing 92 n n 
C1D O1D AR6 sing 93 n n 
C1D C2D AR6 sing 94 n n 
C1D O4D AR6 sing 95 n n 
C2' O2' AR6 sing 96 n n 
C2' C3' AR6 sing 97 n n 
C2D O2D AR6 sing 98 n n 
C2D C3D AR6 sing 99 n n 
C3' O3' AR6 sing 100 n n 
C3' C4' AR6 sing 101 n n 
C3D O3D AR6 sing 102 n n 
C3D C4D AR6 sing 103 n n 
C4' O4' AR6 sing 104 n n 
C4' C5' AR6 sing 105 n n 
C4D O4D AR6 sing 106 n n 
C4D C5D AR6 sing 107 n n 
C5' O5' AR6 sing 108 n n 
C5D O5D AR6 sing 109 n n 
C2 H2 AR6 sing 110 n n 
N6 HN6 AR6 sing 111 n n 
N6 HN6A AR6 sing 112 n n 
C8 H8 AR6 sing 113 n n 
C1' H1' AR6 sing 114 n n 
C1D H1D AR6 sing 115 n n 
C2' H2' AR6 sing 116 n n 
O2' HO2' AR6 sing 117 n n 
C2D H2D AR6 sing 118 n n 
O2D HO2D AR6 sing 119 n n 
C3' H3' AR6 sing 120 n n 
O3' HO3' AR6 sing 121 n n 
C3D H3D AR6 sing 122 n n 
O3D HO3D AR6 sing 123 n n 
C4' H4' AR6 sing 124 n n 
C4D H4D AR6 sing 125 n n 
C5' H5' AR6 sing 126 n n 
C5' "H5'A" AR6 sing 127 n n 
C5D H5D AR6 sing 128 n n 
C5D H5DA AR6 sing 129 n n 
O1A H1A AR6 sing 130 n n 
O1B H1B AR6 sing 131 n n 
O1D HD1 AR6 sing 132 n n 
#
_atom_sites.entry_id                     6ZU4 
_atom_sites.fract_transf_matrix[1][1]    0.01094 
_atom_sites.fract_transf_matrix[1][2]    0.006316 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012633 
_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]    0.006931 
_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 GOL A 1 403 701 GOL GOL . 
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 2 AR6 B 1 401 500 AR6 AR6 . 
K 3 ZN B 1 402 501 ZN ZN . 
L 6 115 B 1 403 601 115 115 . 
M 4 GOL B 1 404 701 GOL GOL . 
N 5 SO4 B 1 405 1 SO4 SO4 . 
O 5 SO4 B 1 406 2 SO4 SO4 . 
P 5 SO4 B 1 407 4 SO4 SO4 . 
Q 5 SO4 B 1 408 6 SO4 SO4 . 
R 5 SO4 B 1 409 9 SO4 SO4 . 
S 7 HOH A 1 501 6 HOH HOH . 
S 7 HOH A 2 502 3 HOH HOH . 
S 7 HOH A 3 503 12 HOH HOH . 
S 7 HOH A 4 504 5 HOH HOH . 
S 7 HOH A 5 505 13 HOH HOH . 
S 7 HOH A 6 506 2 HOH HOH . 
S 7 HOH A 7 507 1 HOH HOH . 
S 7 HOH A 8 508 7 HOH HOH . 
S 7 HOH A 9 509 16 HOH HOH . 
S 7 HOH A 10 510 10 HOH HOH . 
S 7 HOH A 11 511 18 HOH HOH . 
T 7 HOH B 1 501 11 HOH HOH . 
T 7 HOH B 2 502 15 HOH HOH . 
T 7 HOH B 3 503 8 HOH HOH . 
T 7 HOH B 4 504 14 HOH HOH . 
T 7 HOH B 5 505 9 HOH HOH . 
T 7 HOH B 6 506 4 HOH HOH . 
T 7 HOH B 7 507 17 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 . . . J 2 -19.56 24.695 36.932 1 44.7 ? N1 AR6 401 B 1 
HETATM 2 C C2 AR6 . . . J 2 -19.657 25.499 38.007 1 40.65 ? C2 AR6 401 B 1 
HETATM 3 N N3 AR6 . . . J 2 -20.698 25.739 38.792 1 35.52 ? N3 AR6 401 B 1 
HETATM 4 C C4 AR6 . . . J 2 -21.766 25.043 38.35 1 41.08 ? C4 AR6 401 B 1 
HETATM 5 C C5 AR6 . . . J 2 -21.825 24.213 37.254 1 40.13 ? C5 AR6 401 B 1 
HETATM 6 C C6 AR6 . . . J 2 -20.654 24.027 36.507 1 39.34 ? C6 AR6 401 B 1 
HETATM 7 N N6 AR6 . . . J 2 -20.58 23.224 35.443 1 34.69 ? N6 AR6 401 B 1 
HETATM 8 N N7 AR6 . . . J 2 -23.104 23.705 37.104 1 48.72 ? N7 AR6 401 B 1 
HETATM 9 C C8 AR6 . . . J 2 -23.784 24.225 38.097 1 44.65 ? C8 AR6 401 B 1 
HETATM 10 N N9 AR6 . . . J 2 -23.033 25.036 38.872 1 38.69 ? N9 AR6 401 B 1 
HETATM 11 P PA AR6 . . . J 2 -27.48 23.832 44.073 1 53.5 ? PA AR6 401 B 1 
HETATM 12 P PB AR6 . . . J 2 -26.219 22.237 46.076 1 40.66 ? PB AR6 401 B 1 
HETATM 13 C C1' AR6 . . . J 2 -23.468 25.729 40.068 1 40.01 ? C1' AR6 401 B 1 
HETATM 14 O O1A AR6 . . . J 2 -28.045 24.502 45.283 1 55.26 ? O1A AR6 401 B 1 
HETATM 15 O O1B AR6 . . . J 2 -25.503 20.924 46.023 1 36.68 ? O1B AR6 401 B 1 
HETATM 16 C C1D AR6 . . . J 2 -30.91 20.546 47.728 1 50.54 ? C1D AR6 401 B 1 
HETATM 17 O O1D AR6 . . . J 2 -32.094 20.6 48.431 1 57.63 ? O1D AR6 401 B 1 
HETATM 18 C C2' AR6 . . . J 2 -24.774 26.512 39.992 1 36.69 ? C2' AR6 401 B 1 
HETATM 19 O O2' AR6 . . . J 2 -24.514 27.843 39.572 1 39.25 ? O2' AR6 401 B 1 
HETATM 20 O O2A AR6 . . . J 2 -28.313 23.405 42.912 1 55.63 ? O2A AR6 401 B 1 
HETATM 21 O O2B AR6 . . . J 2 -25.482 23.475 46.474 1 38.67 ? O2B AR6 401 B 1 
HETATM 22 C C2D AR6 . . . J 2 -30.359 19.138 47.893 1 44.42 ? C2D AR6 401 B 1 
HETATM 23 O O2D AR6 . . . J 2 -30.55 18.664 49.199 1 49.31 ? O2D AR6 401 B 1 
HETATM 24 C C3' AR6 . . . J 2 -25.308 26.426 41.441 1 40.27 ? C3' AR6 401 B 1 
HETATM 25 O O3' AR6 . . . J 2 -25.182 27.546 42.328 1 41.63 ? O3' AR6 401 B 1 
HETATM 26 O O3A AR6 . . . J 2 -26.729 22.525 44.595 1 46.29 ? O3A AR6 401 B 1 
HETATM 27 C C3D AR6 . . . J 2 -28.866 19.342 47.743 1 45.12 ? C3D AR6 401 B 1 
HETATM 28 O O3D AR6 . . . J 2 -28.249 18.186 48.303 1 44.21 ? O3D AR6 401 B 1 
HETATM 29 C C4' AR6 . . . J 2 -24.549 25.248 42.056 1 36.72 ? C4' AR6 401 B 1 
HETATM 30 O O4' AR6 . . . J 2 -23.669 24.732 41.034 1 42.24 ? O4' AR6 401 B 1 
HETATM 31 C C4D AR6 . . . J 2 -28.693 20.639 48.551 1 44.19 ? C4D AR6 401 B 1 
HETATM 32 O O4D AR6 . . . J 2 -29.91 21.402 48.317 1 46.73 ? O4D AR6 401 B 1 
HETATM 33 C C5' AR6 . . . J 2 -25.443 24.141 42.542 1 42.49 ? C5' AR6 401 B 1 
HETATM 34 O O5' AR6 . . . J 2 -26.282 24.71 43.549 1 45.57 ? O5' AR6 401 B 1 
HETATM 35 C C5D AR6 . . . J 2 -27.474 21.487 48.253 1 39.75 ? C5D AR6 401 B 1 
HETATM 36 O O5D AR6 . . . J 2 -27.564 22.069 46.925 1 41.99 ? O5D AR6 401 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           357 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           36 
#