data_5KQ4
#
_model_server_result.job_id            s4HGA8WsZPfAtiQ0TyrZFQ 
_model_server_result.datetime_utc      '2024-10-19 03:37:31' 
_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          5kq4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":301}' 
#
_entry.id    5KQ4 
#
_exptl.entry_id    5KQ4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              930.586 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-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          97.9 
_cell.angle_gamma         90 
_cell.entry_id            5KQ4 
_cell.length_a            43.067 
_cell.length_b            120.752 
_cell.length_c            91.849 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KQ4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_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
? 4 G N N 
? 4 H N N 
#
_chem_comp.formula           'C22 H34 N10 O19 P4 S2 2' 
_chem_comp.formula_weight    930.586 
_chem_comp.id                6VQ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate' 
_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
N53 C52 6VQ sing 1 n n 
C52 N54 6VQ doub 2 n n 
C52 N51 6VQ sing 3 n n 
N54 C55 6VQ sing 4 n n 
N51 C50 6VQ sing 5 n n 
C55 O56 6VQ doub 6 n n 
C55 C57 6VQ sing 7 n n 
C50 C57 6VQ doub 8 n y 
C50 N04 6VQ sing 9 n y 
C57 N02 6VQ sing 10 n y 
N04 C05 6VQ sing 11 n n 
N04 C03 6VQ sing 12 n y 
N02 C03 6VQ doub 13 n y 
N02 C01 6VQ sing 14 n n 
C05 C48 6VQ sing 15 n n 
C05 O06 6VQ sing 16 n n 
O49 C48 6VQ sing 17 n n 
C48 C46 6VQ sing 18 n n 
O06 C07 6VQ sing 19 n n 
C46 C07 6VQ sing 20 n n 
C46 O47 6VQ sing 21 n n 
C07 C08 6VQ sing 22 n n 
O09 C08 6VQ sing 23 n n 
O09 P10 6VQ sing 24 n n 
O11 P10 6VQ doub 25 n n 
S12 P10 6VQ sing 26 n n 
P10 O13 6VQ sing 27 n n 
O45 C44 6VQ sing 28 n n 
O43 C42 6VQ sing 29 n n 
O13 P14 6VQ sing 30 n n 
C44 C42 6VQ sing 31 n n 
C44 C27 6VQ sing 32 n n 
C42 C29 6VQ sing 33 n n 
O15 P14 6VQ doub 34 n n 
C27 O28 6VQ sing 35 n n 
C27 C26 6VQ sing 36 n n 
P14 O17 6VQ sing 37 n n 
P14 O16 6VQ sing 38 n n 
C29 O28 6VQ sing 39 n n 
C29 N30 6VQ sing 40 n n 
O19 P18 6VQ doub 41 n n 
C26 O25 6VQ sing 42 n n 
O17 P18 6VQ sing 43 n n 
N30 C31 6VQ sing 44 n y 
N30 C41 6VQ sing 45 n y 
O25 P22 6VQ sing 46 n n 
P18 O20 6VQ sing 47 n n 
P18 O21 6VQ sing 48 n n 
N40 C41 6VQ sing 49 n n 
N40 C38 6VQ sing 50 n n 
C31 N32 6VQ doub 51 n y 
C41 C34 6VQ doub 52 n y 
N39 C38 6VQ sing 53 n n 
O21 P22 6VQ sing 54 n n 
C38 N37 6VQ doub 55 n n 
N32 C34 6VQ sing 56 n y 
N32 C33 6VQ sing 57 n n 
C34 C35 6VQ sing 58 n n 
P22 O23 6VQ doub 59 n n 
P22 S24 6VQ sing 60 n n 
N37 C35 6VQ sing 61 n n 
C35 O36 6VQ doub 62 n n 
C01 H1 6VQ sing 63 n n 
C01 H2 6VQ sing 64 n n 
C01 H3 6VQ sing 65 n n 
C03 H4 6VQ sing 66 n n 
C05 H5 6VQ sing 67 n n 
C07 H6 6VQ sing 68 n n 
C08 H7 6VQ sing 69 n n 
C08 H8 6VQ sing 70 n n 
S12 H9 6VQ sing 71 n n 
O16 H10 6VQ sing 72 n n 
O20 H11 6VQ sing 73 n n 
S24 H12 6VQ sing 74 n n 
C26 H13 6VQ sing 75 n n 
C26 H14 6VQ sing 76 n n 
C27 H15 6VQ sing 77 n n 
C29 H16 6VQ sing 78 n n 
C31 H17 6VQ sing 79 n n 
C33 H18 6VQ sing 80 n n 
C33 H19 6VQ sing 81 n n 
C33 H20 6VQ sing 82 n n 
N39 H21 6VQ sing 83 n n 
N39 H22 6VQ sing 84 n n 
N40 H23 6VQ sing 85 n n 
C42 H24 6VQ sing 86 n n 
O43 H25 6VQ sing 87 n n 
C44 H26 6VQ sing 88 n n 
O45 H27 6VQ sing 89 n n 
C46 H28 6VQ sing 90 n n 
O47 H29 6VQ sing 91 n n 
C48 H30 6VQ sing 92 n n 
O49 H31 6VQ sing 93 n n 
N51 H32 6VQ sing 94 n n 
N53 H33 6VQ sing 95 n n 
N53 H34 6VQ sing 96 n n 
#
_atom_sites.entry_id                     5KQ4 
_atom_sites.fract_transf_matrix[1][1]    0.02322 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003222 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008281 
_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]    0.010992 
_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
G 4 6VQ E 1 301 2 6VQ ZD3 . 
H 4 6VQ B 1 301 1 6VQ ZD3 . 
I 5 HOH D 1 201 22 HOH HOH . 
I 5 HOH D 2 202 27 HOH HOH . 
J 5 HOH F 1 201 3 HOH HOH . 
K 5 HOH E 1 401 18 HOH HOH . 
K 5 HOH E 2 402 24 HOH HOH . 
K 5 HOH E 3 403 21 HOH HOH . 
K 5 HOH E 4 404 15 HOH HOH . 
K 5 HOH E 5 405 12 HOH HOH . 
K 5 HOH E 6 406 5 HOH HOH . 
K 5 HOH E 7 407 7 HOH HOH . 
K 5 HOH E 8 408 2 HOH HOH . 
K 5 HOH E 9 409 1 HOH HOH . 
K 5 HOH E 10 410 4 HOH HOH . 
K 5 HOH E 11 411 10 HOH HOH . 
K 5 HOH E 12 412 6 HOH HOH . 
K 5 HOH E 13 413 17 HOH HOH . 
K 5 HOH E 14 414 26 HOH HOH . 
L 5 HOH A 1 201 19 HOH HOH . 
M 5 HOH B 1 401 8 HOH HOH . 
M 5 HOH B 2 402 13 HOH HOH . 
M 5 HOH B 3 403 11 HOH HOH . 
M 5 HOH B 4 404 9 HOH HOH . 
M 5 HOH B 5 405 14 HOH HOH . 
M 5 HOH B 6 406 25 HOH HOH . 
M 5 HOH B 7 407 16 HOH HOH . 
M 5 HOH B 8 408 23 HOH HOH . 
M 5 HOH B 9 409 20 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 P10 6VQ . . . H 4 -3.93 -12.88 -43.21 1 98.65 ? P10 6VQ 301 B 1 
HETATM 2 P P14 6VQ . . . H 4 -4.298 -12.317 -40.139 1 94.43 ? P14 6VQ 301 B 1 
HETATM 3 P P18 6VQ . . . H 4 -6.577 -13.769 -38.796 1 86.21 ? P18 6VQ 301 B 1 
HETATM 4 P P22 6VQ . . . H 4 -8.095 -11.421 -37.411 1 79.95 ? P22 6VQ 301 B 1 
HETATM 5 C C01 6VQ . . . H 4 -1.602 -8.462 -46.04 1 105.52 ? C01 6VQ 301 B 1 
HETATM 6 N N02 6VQ . . . H 4 -1.264 -9.722 -46.761 1 105.09 ? N02 6VQ 301 B 1 
HETATM 7 C C03 6VQ . . . H 4 -0.83 -10.908 -46.184 1 105.15 ? C03 6VQ 301 B 1 
HETATM 8 N N04 6VQ . . . H 4 -0.61 -11.879 -47.196 1 103.39 ? N04 6VQ 301 B 1 
HETATM 9 C C05 6VQ . . . H 4 -0.092 -13.341 -46.751 1 103.66 ? C05 6VQ 301 B 1 
HETATM 10 O O06 6VQ . . . H 4 -0.689 -14.209 -45.817 1 104.94 ? O06 6VQ 301 B 1 
HETATM 11 C C07 6VQ . . . H 4 -0.151 -14.041 -44.465 1 104.67 ? C07 6VQ 301 B 1 
HETATM 12 C C08 6VQ . . . H 4 -1.236 -13.568 -43.403 1 101.13 ? C08 6VQ 301 B 1 
HETATM 13 O O09 6VQ . . . H 4 -2.416 -13.399 -44.009 1 97.5 ? O09 6VQ 301 B 1 
HETATM 14 O O11 6VQ . . . H 4 -4.151 -11.622 -43.98 1 106.78 ? O11 6VQ 301 B 1 
HETATM 15 S S12 6VQ . . . H 4 -5.264 -14.258 -43.495 1 92.15 ? S12 6VQ 301 B 1 
HETATM 16 O O13 6VQ . . . H 4 -3.474 -12.659 -41.741 1 98.27 ? O13 6VQ 301 B 1 
HETATM 17 O O15 6VQ . . . H 4 -5.39 -11.46 -40.684 1 98.65 ? O15 6VQ 301 B 1 
HETATM 18 O O16 6VQ . . . H 4 -3.217 -11.687 -39.334 1 95.32 ? O16 6VQ 301 B 1 
HETATM 19 O O17 6VQ . . . H 4 -5.036 -13.576 -39.381 1 88.8 ? O17 6VQ 301 B 1 
HETATM 20 O O19 6VQ . . . H 4 -7.583 -13.598 -39.887 1 81.23 ? O19 6VQ 301 B 1 
HETATM 21 O O20 6VQ . . . H 4 -6.781 -14.95 -37.898 1 89.39 ? O20 6VQ 301 B 1 
HETATM 22 O O21 6VQ . . . H 4 -6.846 -12.272 -37.788 1 88.4 ? O21 6VQ 301 B 1 
HETATM 23 O O23 6VQ . . . H 4 -7.67 -10.078 -36.945 1 79.62 ? O23 6VQ 301 B 1 
HETATM 24 S S24 6VQ . . . H 4 -9.394 -12.288 -36.258 1 83.41 ? S24 6VQ 301 B 1 
HETATM 25 O O25 6VQ . . . H 4 -8.997 -10.863 -38.923 1 74.43 ? O25 6VQ 301 B 1 
HETATM 26 C C26 6VQ . . . H 4 -10.096 -11.463 -39.452 1 72.81 ? C26 6VQ 301 B 1 
HETATM 27 C C27 6VQ . . . H 4 -11.002 -10.472 -40.35 1 75.04 ? C27 6VQ 301 B 1 
HETATM 28 O O28 6VQ . . . H 4 -11.335 -9.229 -39.684 1 72.61 ? O28 6VQ 301 B 1 
HETATM 29 C C29 6VQ . . . H 4 -10.525 -8.161 -40.116 1 68.89 ? C29 6VQ 301 B 1 
HETATM 30 N N30 6VQ . . . H 4 -9.805 -7.34 -39.003 1 63.44 ? N30 6VQ 301 B 1 
HETATM 31 C C31 6VQ . . . H 4 -8.532 -7.554 -38.484 1 60.99 ? C31 6VQ 301 B 1 
HETATM 32 N N32 6VQ . . . H 4 -8.23 -6.611 -37.511 1 57.72 ? N32 6VQ 301 B 1 
HETATM 33 C C33 6VQ . . . H 4 -6.963 -6.526 -36.733 1 62.29 ? C33 6VQ 301 B 1 
HETATM 34 C C34 6VQ . . . H 4 -9.36 -5.771 -37.415 1 55.91 ? C34 6VQ 301 B 1 
HETATM 35 C C35 6VQ . . . H 4 -9.65 -4.602 -36.572 1 59.05 ? C35 6VQ 301 B 1 
HETATM 36 O O36 6VQ . . . H 4 -8.868 -4.156 -35.757 1 64.09 ? O36 6VQ 301 B 1 
HETATM 37 N N37 6VQ . . . H 4 -10.925 -4.009 -36.771 1 59.14 ? N37 6VQ 301 B 1 
HETATM 38 C C38 6VQ . . . H 4 -11.831 -4.488 -37.683 1 56.86 ? C38 6VQ 301 B 1 
HETATM 39 N N39 6VQ . . . H 4 -13.091 -3.822 -37.809 1 52.42 ? N39 6VQ 301 B 1 
HETATM 40 N N40 6VQ . . . H 4 -11.593 -5.603 -38.509 1 62.73 ? N40 6VQ 301 B 1 
HETATM 41 C C41 6VQ . . . H 4 -10.355 -6.19 -38.327 1 61.12 ? C41 6VQ 301 B 1 
HETATM 42 C C42 6VQ . . . H 4 -9.454 -8.742 -41.081 1 69.96 ? C42 6VQ 301 B 1 
HETATM 43 O O43 6VQ . . . H 4 -9.17 -7.895 -42.157 1 69.5 ? O43 6VQ 301 B 1 
HETATM 44 C C44 6VQ . . . H 4 -10.219 -9.952 -41.615 1 74.52 ? C44 6VQ 301 B 1 
HETATM 45 O O45 6VQ . . . H 4 -11.053 -9.406 -42.592 1 80 ? O45 6VQ 301 B 1 
HETATM 46 C C46 6VQ . . . H 4 0.974 -12.967 -44.584 1 106.06 ? C46 6VQ 301 B 1 
HETATM 47 O O47 6VQ . . . H 4 2.102 -13.338 -43.864 1 110.53 ? O47 6VQ 301 B 1 
HETATM 48 C C48 6VQ . . . H 4 1.262 -12.957 -46.084 1 103.1 ? C48 6VQ 301 B 1 
HETATM 49 O O49 6VQ . . . H 4 2.261 -13.87 -46.445 1 100.26 ? O49 6VQ 301 B 1 
HETATM 50 C C50 6VQ . . . H 4 -0.912 -11.289 -48.447 1 102.66 ? C50 6VQ 301 B 1 
HETATM 51 N N51 6VQ . . . H 4 -0.833 -11.881 -49.677 1 99.4 ? N51 6VQ 301 B 1 
HETATM 52 C C52 6VQ . . . H 4 -1.201 -11.046 -50.75 1 98.47 ? C52 6VQ 301 B 1 
HETATM 53 N N53 6VQ . . . H 4 -1.149 -11.58 -52.063 1 98.84 ? N53 6VQ 301 B 1 
HETATM 54 N N54 6VQ . . . H 4 -1.608 -9.736 -50.589 1 100.82 ? N54 6VQ 301 B 1 
HETATM 55 C C55 6VQ . . . H 4 -1.691 -9.116 -49.313 1 103.01 ? C55 6VQ 301 B 1 
HETATM 56 O O56 6VQ . . . H 4 -2.052 -7.963 -49.203 1 103.17 ? O56 6VQ 301 B 1 
HETATM 57 C C57 6VQ . . . H 4 -1.317 -9.954 -48.158 1 103.97 ? C57 6VQ 301 B 1 
#
_model_server_stats.io_time_ms              101 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    49 
_model_server_stats.query_time_ms           338 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           57 
#