data_5VDQ
#
_model_server_result.job_id            rvLpCZMotzkOuceQu42Xtw 
_model_server_result.datetime_utc      '2024-10-15 12:17:41' 
_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          5vdq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    5VDQ 
#
_exptl.entry_id    5VDQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              692.427 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2',5'-GpAp" 
_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          110.05 
_cell.angle_gamma         90 
_cell.entry_id            5VDQ 
_cell.length_a            215.211 
_cell.length_b            47.632 
_cell.length_c            88.365 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VDQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 1 1 
B,E,F 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
? 3 D N N 
? 3 F 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 NE2 HIS 231 A HIS 390 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc2 A SG CYS 237 A CYS 396 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc3 A SG CYS 238 A CYS 397 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc4 A SG CYS 245 A CYS 404 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc5 B NE2 HIS 231 B HIS 390 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc6 B SG CYS 237 B CYS 396 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? 
metalc ? metalc7 B SG CYS 238 B CYS 397 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc8 B SG CYS 245 B CYS 404 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
#
_chem_comp.formula           'C20 H26 N10 O14 P2' 
_chem_comp.formula_weight    692.427 
_chem_comp.id                9BG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2',5'-GpAp" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate' 
#
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
O18 C17 9BG sing 1 n n 
C15 C14 9BG sing 2 n n 
C15 O16 9BG sing 3 n n 
C14 C17 9BG sing 4 n n 
C14 O13 9BG sing 5 n n 
C17 C19 9BG sing 6 n n 
O13 C12 9BG sing 7 n n 
C19 O20 9BG sing 8 n n 
C19 C12 9BG sing 9 n n 
O20 P21 9BG sing 10 n n 
C12 N11 9BG sing 11 n n 
O45 P21 9BG doub 12 n n 
P21 O46 9BG sing 13 n n 
P21 O22 9BG sing 14 n n 
N11 C10 9BG sing 15 n y 
N11 C07 9BG sing 16 n y 
C10 N09 9BG doub 17 n y 
O22 C23 9BG sing 18 n n 
N06 C07 9BG sing 19 n n 
N06 C04 9BG sing 20 n n 
C07 C08 9BG doub 21 n y 
C23 C24 9BG sing 22 n n 
N05 C04 9BG sing 23 n n 
N09 C08 9BG sing 24 n y 
C04 N03 9BG doub 25 n n 
C08 C02 9BG sing 26 n n 
O28 P27 9BG doub 27 n n 
C24 O44 9BG sing 28 n n 
C24 C25 9BG sing 29 n n 
O44 C33 9BG sing 30 n n 
C43 N42 9BG doub 31 n y 
C43 N34 9BG sing 32 n y 
N03 C02 9BG sing 33 n n 
N42 C41 9BG sing 34 n y 
O30 P27 9BG sing 35 n n 
C02 O01 9BG doub 36 n n 
P27 O29 9BG sing 37 n n 
P27 O26 9BG sing 38 n n 
C25 O26 9BG sing 39 n n 
C25 C31 9BG sing 40 n n 
N34 C33 9BG sing 41 n n 
N34 C35 9BG sing 42 n y 
C33 C31 9BG sing 43 n n 
C41 C35 9BG doub 44 n y 
C41 C39 9BG sing 45 n y 
N40 C39 9BG sing 46 n n 
C31 O32 9BG sing 47 n n 
C35 N36 9BG sing 48 n y 
C39 N38 9BG doub 49 n y 
N36 C37 9BG doub 50 n y 
N38 C37 9BG sing 51 n y 
C10 H1 9BG sing 52 n n 
C17 H2 9BG sing 53 n n 
C24 H3 9BG sing 54 n n 
C12 H4 9BG sing 55 n n 
C14 H5 9BG sing 56 n n 
C19 H6 9BG sing 57 n n 
C23 H7 9BG sing 58 n n 
C23 H8 9BG sing 59 n n 
C25 H9 9BG sing 60 n n 
N05 H10 9BG sing 61 n n 
N05 H11 9BG sing 62 n n 
N06 H12 9BG sing 63 n n 
C15 H13 9BG sing 64 n n 
C15 H14 9BG sing 65 n n 
O16 H15 9BG sing 66 n n 
O18 H16 9BG sing 67 n n 
O29 H17 9BG sing 68 n n 
O30 H18 9BG sing 69 n n 
C31 H19 9BG sing 70 n n 
O32 H20 9BG sing 71 n n 
C33 H21 9BG sing 72 n n 
C37 H22 9BG sing 73 n n 
N40 H23 9BG sing 74 n n 
N40 H24 9BG sing 75 n n 
C43 H25 9BG sing 76 n n 
O46 H26 9BG sing 77 n n 
#
_atom_sites.entry_id                     5VDQ 
_atom_sites.fract_transf_matrix[1][1]    0.004647 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001696 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020994 
_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]    0.012047 
_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 ZN A 1 601 601 ZN ZN . 
D 3 9BG A 1 602 1 9BG 25G . 
E 2 ZN B 1 601 601 ZN ZN . 
F 3 9BG B 1 602 1 9BG 25G . 
#
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 C10 9BG . . . D 3 -25.527 -7.298 -27.175 1 93.65 ? C10 9BG 602 A 1 
HETATM 2 C C17 9BG . . . D 3 -27.287 -8.434 -30.657 1 112.08 ? C17 9BG 602 A 1 
HETATM 3 C C24 9BG . . . D 3 -28.466 -12.209 -24.787 1 103.17 ? C24 9BG 602 A 1 
HETATM 4 C C02 9BG . . . D 3 -24.68 -9.655 -24.423 1 89.58 ? C02 9BG 602 A 1 
HETATM 5 C C04 9BG . . . D 3 -24.621 -11.715 -25.838 1 92.85 ? C04 9BG 602 A 1 
HETATM 6 C C07 9BG . . . D 3 -25.155 -9.448 -26.911 1 91.21 ? C07 9BG 602 A 1 
HETATM 7 C C08 9BG . . . D 3 -25.027 -8.831 -25.67 1 89.96 ? C08 9BG 602 A 1 
HETATM 8 C C12 9BG . . . D 3 -25.657 -8.688 -29.113 1 103.74 ? C12 9BG 602 A 1 
HETATM 9 C C14 9BG . . . D 3 -26.06 -7.313 -30.914 1 106.19 ? C14 9BG 602 A 1 
HETATM 10 C C19 9BG . . . D 3 -27.157 -8.871 -29.441 1 108.84 ? C19 9BG 602 A 1 
HETATM 11 C C23 9BG . . . D 3 -28.976 -12.397 -26.204 1 101.5 ? C23 9BG 602 A 1 
HETATM 12 C C25 9BG . . . D 3 -29.751 -12.026 -23.731 1 116.05 ? C25 9BG 602 A 1 
HETATM 13 N N34 9BG . . . D 3 -28.401 -9.162 -23.588 1 80.71 ? N34 9BG 602 A 1 
HETATM 14 O O01 9BG . . . D 3 -24.571 -9.122 -23.363 1 89.15 ? O01 9BG 602 A 1 
HETATM 15 N N03 9BG . . . D 3 -24.487 -11.072 -24.538 1 92.99 ? N03 9BG 602 A 1 
HETATM 16 N N05 9BG . . . D 3 -24.432 -13.116 -25.964 1 93.09 ? N05 9BG 602 A 1 
HETATM 17 N N06 9BG . . . D 3 -24.955 -10.911 -27.03 1 90.69 ? N06 9BG 602 A 1 
HETATM 18 N N09 9BG . . . D 3 -25.257 -7.517 -25.843 1 90.24 ? N09 9BG 602 A 1 
HETATM 19 N N11 9BG . . . D 3 -25.463 -8.497 -27.817 1 96.58 ? N11 9BG 602 A 1 
HETATM 20 O O13 9BG . . . D 3 -25.239 -7.396 -29.942 1 103.76 ? O13 9BG 602 A 1 
HETATM 21 C C15 9BG . . . D 3 -26.628 -5.915 -30.982 1 104.81 ? C15 9BG 602 A 1 
HETATM 22 O O16 9BG . . . D 3 -26.431 -5.282 -29.691 1 100.94 ? O16 9BG 602 A 1 
HETATM 23 O O18 9BG . . . D 3 -27.162 -9.516 -31.58 1 114.86 ? O18 9BG 602 A 1 
HETATM 24 O O20 9BG . . . D 3 -27.516 -10.353 -29.368 1 108.15 ? O20 9BG 602 A 1 
HETATM 25 P P21 9BG . . . D 3 -28.715 -10.794 -28.3 1 103.32 ? P21 9BG 602 A 1 
HETATM 26 O O22 9BG . . . D 3 -28.081 -11.798 -27.119 1 101.91 ? O22 9BG 602 A 1 
HETATM 27 O O26 9BG . . . D 3 -30.135 -13.328 -23.127 1 131.69 ? O26 9BG 602 A 1 
HETATM 28 P P27 9BG . . . D 3 -30.583 -14.666 -24.129 1 139.04 ? P27 9BG 602 A 1 
HETATM 29 O O28 9BG . . . D 3 -31.279 -14.177 -25.371 1 141.15 -1 O28 9BG 602 A 1 
HETATM 30 O O29 9BG . . . D 3 -31.504 -15.554 -23.37 1 141.43 -1 O29 9BG 602 A 1 
HETATM 31 O O30 9BG . . . D 3 -29.332 -15.455 -24.528 1 133.87 ? O30 9BG 602 A 1 
HETATM 32 C C31 9BG . . . D 3 -29.381 -11.217 -22.815 1 106.07 ? C31 9BG 602 A 1 
HETATM 33 O O32 9BG . . . D 3 -28.999 -11.969 -21.556 1 106.05 ? O32 9BG 602 A 1 
HETATM 34 C C33 9BG . . . D 3 -28.123 -10.448 -23.376 1 91.78 ? C33 9BG 602 A 1 
HETATM 35 C C35 9BG . . . D 3 -28.253 -8.129 -22.664 1 75.5 ? C35 9BG 602 A 1 
HETATM 36 N N36 9BG . . . D 3 -27.826 -8.091 -21.351 1 73.13 ? N36 9BG 602 A 1 
HETATM 37 C C37 9BG . . . D 3 -27.792 -6.959 -20.719 1 72.1 ? C37 9BG 602 A 1 
HETATM 38 N N38 9BG . . . D 3 -28.155 -5.832 -21.29 1 71.06 ? N38 9BG 602 A 1 
HETATM 39 C C39 9BG . . . D 3 -28.579 -5.797 -22.558 1 70.65 ? C39 9BG 602 A 1 
HETATM 40 N N40 9BG . . . D 3 -28.98 -4.532 -23.179 1 68.61 ? N40 9BG 602 A 1 
HETATM 41 C C41 9BG . . . D 3 -28.632 -6.994 -23.28 1 72.63 ? C41 9BG 602 A 1 
HETATM 42 N N42 9BG . . . D 3 -28.995 -7.312 -24.529 1 74.18 ? N42 9BG 602 A 1 
HETATM 43 C C43 9BG . . . D 3 -28.84 -8.661 -24.691 1 77.07 ? C43 9BG 602 A 1 
HETATM 44 O O44 9BG . . . D 3 -27.76 -11.134 -24.718 1 95.24 ? O44 9BG 602 A 1 
HETATM 45 O O45 9BG . . . D 3 -29.779 -11.486 -29.03 1 106.55 -1 O45 9BG 602 A 1 
HETATM 46 O O46 9BG . . . D 3 -29.292 -9.506 -27.625 1 106.15 ? O46 9BG 602 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           46 
#