data_6CK0
#
_model_server_result.job_id            mSyin6zr-j-f2dU4gRbv4w 
_model_server_result.datetime_utc      '2024-12-26 18:08:05' 
_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          6ck0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    6CK0 
#
_exptl.entry_id    6CK0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              735.492 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-O-[(S)-({5-[(2R,3aS,4S,6aR)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]adenosine" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         122.14 
_cell.angle_beta          94.73 
_cell.angle_gamma         107.85 
_cell.entry_id            6CK0 
_cell.length_a            52.89 
_cell.length_b            57.08 
_cell.length_c            57.03 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6CK0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_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,M 1 1 
B,F,G,H,I,J,K,L,N 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 F N N 
#
_chem_comp.formula           'C20 H32 N7 O15 P3 S' 
_chem_comp.formula_weight    735.492 
_chem_comp.id                F5D 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-O-[(S)-({5-[(2R,3aS,4S,6aR)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]adenosine" 
_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
C10 C02 F5D doub 92 n y 
C10 C06 F5D sing 93 n y 
C10 N09 F5D sing 94 n y 
C13 C14 F5D sing 95 n n 
C13 C43 F5D sing 96 n n 
C13 O12 F5D sing 97 n n 
C21 C22 F5D sing 98 n n 
C21 C19 F5D sing 99 n n 
C22 C23 F5D sing 100 n n 
C24 C23 F5D sing 101 n n 
C24 C25 F5D sing 102 n n 
C28 C27 F5D sing 103 n n 
C28 C33 F5D sing 104 n n 
C28 N29 F5D sing 105 n n 
C02 N01 F5D sing 106 n n 
C02 N03 F5D sing 107 n y 
C04 N03 F5D doub 108 n y 
C04 N05 F5D sing 109 n y 
C06 N05 F5D doub 110 n y 
C06 N07 F5D sing 111 n y 
C08 N07 F5D sing 112 n y 
C08 N09 F5D doub 113 n y 
C11 C45 F5D sing 114 n n 
C11 N07 F5D sing 115 n n 
C11 O12 F5D sing 116 n n 
C14 O15 F5D sing 117 n n 
C19 O18 F5D sing 118 n n 
C19 O20 F5D doub 119 n n 
C25 S26 F5D sing 120 n n 
C27 S26 F5D sing 121 n n 
C30 N29 F5D sing 122 n n 
C30 N32 F5D sing 123 n n 
C30 O31 F5D sing 124 n n 
C33 N32 F5D sing 125 n n 
C43 C45 F5D sing 126 n n 
C43 O44 F5D sing 127 n n 
C45 O46 F5D sing 128 n n 
O15 P16 F5D sing 129 n n 
O17 P16 F5D doub 130 n n 
O18 P16 F5D sing 131 n n 
O34 P16 F5D sing 132 n n 
O34 P35 F5D sing 133 n n 
O36 P35 F5D doub 134 n n 
O37 P35 F5D sing 135 n n 
O38 P35 F5D sing 136 n n 
O38 P39 F5D sing 137 n n 
O40 P39 F5D doub 138 n n 
O41 P39 F5D sing 139 n n 
O42 P39 F5D sing 140 n n 
C13 H1 F5D sing 141 n n 
C21 H2 F5D sing 142 n n 
C21 H3 F5D sing 143 n n 
C22 H4 F5D sing 144 n n 
C22 H5 F5D sing 145 n n 
C24 H6 F5D sing 146 n n 
C24 H7 F5D sing 147 n n 
C28 H8 F5D sing 148 n n 
C04 H9 F5D sing 149 n n 
C08 H10 F5D sing 150 n n 
C11 H11 F5D sing 151 n n 
C14 H12 F5D sing 152 n n 
C14 H13 F5D sing 153 n n 
C23 H14 F5D sing 154 n n 
C23 H15 F5D sing 155 n n 
C25 H16 F5D sing 156 n n 
C27 H18 F5D sing 157 n n 
C27 H19 F5D sing 158 n n 
C30 H20 F5D sing 159 n n 
C33 H21 F5D sing 160 n n 
C43 H23 F5D sing 161 n n 
C45 H24 F5D sing 162 n n 
N01 H25 F5D sing 163 n n 
N01 H26 F5D sing 164 n n 
N29 H27 F5D sing 165 n n 
N32 H29 F5D sing 166 n n 
O31 H31 F5D sing 167 n n 
O37 H32 F5D sing 168 n n 
O41 H33 F5D sing 169 n n 
O42 H34 F5D sing 170 n n 
O44 H35 F5D sing 171 n n 
O46 H36 F5D sing 172 n n 
C33 C25 F5D sing 173 n n 
#
_atom_sites.entry_id                     6CK0 
_atom_sites.fract_transf_matrix[1][1]    0.018907 
_atom_sites.fract_transf_matrix[1][2]    0.006089 
_atom_sites.fract_transf_matrix[1][3]    0.006354 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018405 
_atom_sites.fract_transf_matrix[2][3]    0.01336 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.021741 
_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 F5D A 1 301 300 F5D LIG . 
D 3 SO4 A 1 302 1 SO4 SO4 . 
E 4 EDO A 1 303 4 EDO EDO . 
F 2 F5D B 1 301 300 F5D LIG . 
G 3 SO4 B 1 302 2 SO4 SO4 . 
H 3 SO4 B 1 303 3 SO4 SO4 . 
I 3 SO4 B 1 304 4 SO4 SO4 . 
J 4 EDO B 1 305 1 EDO EDO . 
K 4 EDO B 1 306 2 EDO EDO . 
L 4 EDO B 1 307 3 EDO EDO . 
M 5 HOH A 1 401 101 HOH HOH . 
M 5 HOH A 2 402 114 HOH HOH . 
M 5 HOH A 3 403 47 HOH HOH . 
M 5 HOH A 4 404 89 HOH HOH . 
M 5 HOH A 5 405 66 HOH HOH . 
M 5 HOH A 6 406 13 HOH HOH . 
M 5 HOH A 7 407 8 HOH HOH . 
M 5 HOH A 8 408 30 HOH HOH . 
M 5 HOH A 9 409 52 HOH HOH . 
M 5 HOH A 10 410 23 HOH HOH . 
M 5 HOH A 11 411 31 HOH HOH . 
M 5 HOH A 12 412 98 HOH HOH . 
M 5 HOH A 13 413 49 HOH HOH . 
M 5 HOH A 14 414 5 HOH HOH . 
M 5 HOH A 15 415 46 HOH HOH . 
M 5 HOH A 16 416 2 HOH HOH . 
M 5 HOH A 17 417 53 HOH HOH . 
M 5 HOH A 18 418 85 HOH HOH . 
M 5 HOH A 19 419 34 HOH HOH . 
M 5 HOH A 20 420 54 HOH HOH . 
M 5 HOH A 21 421 99 HOH HOH . 
M 5 HOH A 22 422 33 HOH HOH . 
M 5 HOH A 23 423 32 HOH HOH . 
M 5 HOH A 24 424 78 HOH HOH . 
M 5 HOH A 25 425 51 HOH HOH . 
M 5 HOH A 26 426 93 HOH HOH . 
M 5 HOH A 27 427 79 HOH HOH . 
M 5 HOH A 28 428 26 HOH HOH . 
M 5 HOH A 29 429 100 HOH HOH . 
M 5 HOH A 30 430 24 HOH HOH . 
M 5 HOH A 31 431 90 HOH HOH . 
M 5 HOH A 32 432 35 HOH HOH . 
M 5 HOH A 33 433 76 HOH HOH . 
M 5 HOH A 34 434 38 HOH HOH . 
M 5 HOH A 35 435 73 HOH HOH . 
M 5 HOH A 36 436 27 HOH HOH . 
M 5 HOH A 37 437 67 HOH HOH . 
M 5 HOH A 38 438 56 HOH HOH . 
M 5 HOH A 39 439 69 HOH HOH . 
M 5 HOH A 40 440 42 HOH HOH . 
M 5 HOH A 41 441 68 HOH HOH . 
M 5 HOH A 42 442 92 HOH HOH . 
M 5 HOH A 43 443 71 HOH HOH . 
M 5 HOH A 44 444 91 HOH HOH . 
M 5 HOH A 45 445 55 HOH HOH . 
M 5 HOH A 46 446 44 HOH HOH . 
M 5 HOH A 47 447 50 HOH HOH . 
M 5 HOH A 48 448 58 HOH HOH . 
M 5 HOH A 49 449 7 HOH HOH . 
M 5 HOH A 50 450 72 HOH HOH . 
M 5 HOH A 51 451 96 HOH HOH . 
M 5 HOH A 52 452 48 HOH HOH . 
M 5 HOH A 53 453 94 HOH HOH . 
N 5 HOH B 1 401 105 HOH HOH . 
N 5 HOH B 2 402 115 HOH HOH . 
N 5 HOH B 3 403 102 HOH HOH . 
N 5 HOH B 4 404 41 HOH HOH . 
N 5 HOH B 5 405 103 HOH HOH . 
N 5 HOH B 6 406 43 HOH HOH . 
N 5 HOH B 7 407 75 HOH HOH . 
N 5 HOH B 8 408 15 HOH HOH . 
N 5 HOH B 9 409 19 HOH HOH . 
N 5 HOH B 10 410 113 HOH HOH . 
N 5 HOH B 11 411 25 HOH HOH . 
N 5 HOH B 12 412 16 HOH HOH . 
N 5 HOH B 13 413 22 HOH HOH . 
N 5 HOH B 14 414 6 HOH HOH . 
N 5 HOH B 15 415 108 HOH HOH . 
N 5 HOH B 16 416 109 HOH HOH . 
N 5 HOH B 17 417 70 HOH HOH . 
N 5 HOH B 18 418 1 HOH HOH . 
N 5 HOH B 19 419 9 HOH HOH . 
N 5 HOH B 20 420 3 HOH HOH . 
N 5 HOH B 21 421 106 HOH HOH . 
N 5 HOH B 22 422 37 HOH HOH . 
N 5 HOH B 23 423 57 HOH HOH . 
N 5 HOH B 24 424 11 HOH HOH . 
N 5 HOH B 25 425 40 HOH HOH . 
N 5 HOH B 26 426 112 HOH HOH . 
N 5 HOH B 27 427 4 HOH HOH . 
N 5 HOH B 28 428 77 HOH HOH . 
N 5 HOH B 29 429 28 HOH HOH . 
N 5 HOH B 30 430 36 HOH HOH . 
N 5 HOH B 31 431 64 HOH HOH . 
N 5 HOH B 32 432 61 HOH HOH . 
N 5 HOH B 33 433 12 HOH HOH . 
N 5 HOH B 34 434 10 HOH HOH . 
N 5 HOH B 35 435 74 HOH HOH . 
N 5 HOH B 36 436 17 HOH HOH . 
N 5 HOH B 37 437 87 HOH HOH . 
N 5 HOH B 38 438 88 HOH HOH . 
N 5 HOH B 39 439 95 HOH HOH . 
N 5 HOH B 40 440 80 HOH HOH . 
N 5 HOH B 41 441 21 HOH HOH . 
N 5 HOH B 42 442 82 HOH HOH . 
N 5 HOH B 43 443 97 HOH HOH . 
N 5 HOH B 44 444 83 HOH HOH . 
N 5 HOH B 45 445 14 HOH HOH . 
N 5 HOH B 46 446 59 HOH HOH . 
N 5 HOH B 47 447 60 HOH HOH . 
N 5 HOH B 48 448 63 HOH HOH . 
N 5 HOH B 49 449 81 HOH HOH . 
N 5 HOH B 50 450 45 HOH HOH . 
N 5 HOH B 51 451 84 HOH HOH . 
N 5 HOH B 52 452 110 HOH HOH . 
N 5 HOH B 53 453 39 HOH HOH . 
N 5 HOH B 54 454 62 HOH HOH . 
N 5 HOH B 55 455 86 HOH HOH . 
N 5 HOH B 56 456 29 HOH HOH . 
N 5 HOH B 57 457 18 HOH HOH . 
N 5 HOH B 58 458 111 HOH HOH . 
N 5 HOH B 59 459 104 HOH HOH . 
N 5 HOH B 60 460 65 HOH HOH . 
N 5 HOH B 61 461 107 HOH HOH . 
N 5 HOH B 62 462 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 C C10 F5D . . . C 2 -4.791 11.224 54.504 1 45.8 ? C10 F5D 301 A 1 
HETATM 2 C C13 F5D . . . C 2 -1.245 7.243 55.56 1 76.85 ? C13 F5D 301 A 1 
HETATM 3 C C21 F5D . . . C 2 3.344 12.038 52.592 1 44.01 ? C21 F5D 301 A 1 
HETATM 4 C C22 F5D . . . C 2 2.252 13.08 52.217 1 36.87 ? C22 F5D 301 A 1 
HETATM 5 C C24 F5D . . . C 2 1.452 14.575 50.22 1 24.83 ? C24 F5D 301 A 1 
HETATM 6 C C28 F5D . . . C 2 2.256 16.547 47.017 1 20.74 ? C28 F5D 301 A 1 
HETATM 7 C C02 F5D . . . C 2 -5.109 12.531 54.877 1 40.49 ? C02 F5D 301 A 1 
HETATM 8 C C04 F5D . . . C 2 -4.543 12.073 57.069 1 42.81 ? C04 F5D 301 A 1 
HETATM 9 C C06 F5D . . . C 2 -4.351 10.387 55.493 1 45.16 ? C06 F5D 301 A 1 
HETATM 10 C C08 F5D . . . C 2 -4.391 9.278 53.656 1 46.75 ? C08 F5D 301 A 1 
HETATM 11 C C11 F5D . . . C 2 -3.608 8.087 55.715 1 68.81 ? C11 F5D 301 A 1 
HETATM 12 C C14 F5D . . . C 2 -0.464 7.451 54.24 1 73.77 ? C14 F5D 301 A 1 
HETATM 13 C C19 F5D . . . C 2 2.968 11.019 53.694 1 44.16 ? C19 F5D 301 A 1 
HETATM 14 C C23 F5D . . . C 2 2.619 14.065 51.088 1 30.68 ? C23 F5D 301 A 1 
HETATM 15 C C25 F5D . . . C 2 1.7 15.871 49.413 1 22.36 ? C25 F5D 301 A 1 
HETATM 16 C C27 F5D . . . C 2 1.198 17.583 47.836 1 25.52 ? C27 F5D 301 A 1 
HETATM 17 C C30 F5D . . . C 2 1.17 14.595 46.366 1 23.34 ? C30 F5D 301 A 1 
HETATM 18 C C33 F5D . . . C 2 2.645 15.568 47.977 1 25.93 ? C33 F5D 301 A 1 
HETATM 19 C C43 F5D . . . C 2 -2.142 6.264 55.532 1 78.63 ? C43 F5D 301 A 1 
HETATM 20 C C45 F5D . . . C 2 -3.573 6.961 55.042 1 75.74 ? C45 F5D 301 A 1 
HETATM 21 N N01 F5D . . . C 2 -5.579 13.469 53.879 1 38.89 ? N01 F5D 301 A 1 
HETATM 22 N N03 F5D . . . C 2 -4.97 12.912 56.142 1 40.86 ? N03 F5D 301 A 1 
HETATM 23 N N05 F5D . . . C 2 -4.239 10.827 56.751 1 43.86 ? N05 F5D 301 A 1 
HETATM 24 N N07 F5D . . . C 2 -4.13 9.2 54.95 1 51.78 ? N07 F5D 301 A 1 
HETATM 25 N N09 F5D . . . C 2 -4.804 10.5 53.371 1 49.76 ? N09 F5D 301 A 1 
HETATM 26 N N29 F5D . . . C 2 1.54 15.772 45.851 1 24.71 ? N29 F5D 301 A 1 
HETATM 27 N N32 F5D . . . C 2 2.372 14.227 47.346 1 26.74 ? N32 F5D 301 A 1 
HETATM 28 O O12 F5D . . . C 2 -2.089 8.502 55.963 1 68.91 ? O12 F5D 301 A 1 
HETATM 29 O O15 F5D . . . C 2 0.427 8.547 54.367 1 72.83 ? O15 F5D 301 A 1 
HETATM 30 O O17 F5D . . . C 2 2.313 7.137 53.547 1 78.86 ? O17 F5D 301 A 1 
HETATM 31 O O18 F5D . . . C 2 2.9 9.594 53.491 1 56.53 ? O18 F5D 301 A 1 
HETATM 32 O O20 F5D . . . C 2 2.763 11.502 54.744 1 45.73 ? O20 F5D 301 A 1 
HETATM 33 O O31 F5D . . . C 2 0.898 13.629 45.41 1 28.53 ? O31 F5D 301 A 1 
HETATM 34 O O34 F5D . . . C 2 2.619 8.032 55.89 1 67.19 ? O34 F5D 301 A 1 
HETATM 35 O O36 F5D . . . C 2 0.777 6.737 57.264 1 58.47 -1 O36 F5D 301 A 1 
HETATM 36 O O37 F5D . . . C 2 2.596 5.413 56.241 1 61.19 ? O37 F5D 301 A 1 
HETATM 37 O O38 F5D . . . C 2 2.911 6.744 58.401 1 49.96 ? O38 F5D 301 A 1 
HETATM 38 O O40 F5D . . . C 2 4.366 6.563 60.407 1 35.01 -1 O40 F5D 301 A 1 
HETATM 39 O O41 F5D . . . C 2 5.378 7.516 58.347 1 31.2 -1 O41 F5D 301 A 1 
HETATM 40 O O42 F5D . . . C 2 4.958 5.117 58.469 1 32.6 ? O42 F5D 301 A 1 
HETATM 41 O O44 F5D . . . C 2 -2.328 5.768 56.864 1 76.89 ? O44 F5D 301 A 1 
HETATM 42 O O46 F5D . . . C 2 -4.708 6.125 55.359 1 71.72 ? O46 F5D 301 A 1 
HETATM 43 P P16 F5D . . . C 2 2.084 8.353 54.321 1 68.52 ? P16 F5D 301 A 1 
HETATM 44 P P35 F5D . . . C 2 2.246 6.723 56.897 1 58.01 ? P35 F5D 301 A 1 
HETATM 45 P P39 F5D . . . C 2 4.452 6.471 58.907 1 36.31 ? P39 F5D 301 A 1 
HETATM 46 S S26 F5D . . . C 2 0.481 16.552 48.918 1 29.75 ? S26 F5D 301 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           645 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           46 
#