data_6BYU
#
_model_server_result.job_id            fcCCUC2SrNyt_FzcLaiLlA 
_model_server_result.datetime_utc      '2025-09-04 01:07:52' 
_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          6byu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":1501}' 
#
_entry.id    6BYU 
#
_exptl.entry_id    6BYU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              583.129 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate' 
_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         90 
_cell.entry_id            6BYU 
_cell.length_a            186.254 
_cell.length_b            203.656 
_cell.length_c            308.322 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BYU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 hexameric 6 author_and_software_defined_assembly 1 
PISA hexameric 6 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,B,C,D,E,F,M,N,O,P 1 1 
G,H,I,J,K,L,Q,R,S,T 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
? 6 M N N 
? 6 Q 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
disulf ? disulf1 D SG CYS 814 D CYS 814 1_555 D SG CYS 895 D CYS 895 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? 
disulf ? disulf2 D SG CYS 888 D CYS 888 1_555 D SG CYS 895 D CYS 895 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? 
metalc ? metalc1 D SG CYS 70 D CYS 70 1_555 O ZN ZN . D ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc2 D SG CYS 72 D CYS 72 1_555 O ZN ZN . D ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc3 D SG CYS 85 D CYS 85 1_555 O ZN ZN . D ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc4 D SG CYS 88 D CYS 88 1_555 O ZN ZN . D ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
metalc ? metalc5 D OD1 ASP 460 D ASP 460 1_555 N MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc6 D OD1 ASP 462 D ASP 462 1_555 N MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc7 D OD2 ASP 462 D ASP 462 1_555 N MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc8 D OD1 ASP 464 D ASP 464 1_555 N MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? 
metalc ? metalc9 D OD2 ASP 464 D ASP 464 1_555 N MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc10 D SG CYS 814 D CYS 814 1_555 P ZN ZN . D ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc11 D SG CYS 888 D CYS 888 1_555 P ZN ZN . D ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc12 D SG CYS 895 D CYS 895 1_555 P ZN ZN . D ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc13 D SG CYS 898 D CYS 898 1_555 P ZN ZN . D ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
metalc ? metalc14 J SG CYS 70 J CYS 70 1_555 S ZN ZN . J ZN 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc15 J SG CYS 72 J CYS 72 1_555 S ZN ZN . J ZN 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc16 J SG CYS 85 J CYS 85 1_555 S ZN ZN . J ZN 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc17 J SG CYS 88 J CYS 88 1_555 S ZN ZN . J ZN 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc18 J OD1 ASP 460 J ASP 460 1_555 R MG MG . J MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? 
metalc ? metalc19 J OD1 ASP 462 J ASP 462 1_555 R MG MG . J MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc20 J OD2 ASP 462 J ASP 462 1_555 R MG MG . J MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc21 J OD1 ASP 464 J ASP 464 1_555 R MG MG . J MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc22 J OD2 ASP 464 J ASP 464 1_555 R MG MG . J MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc23 J SG CYS 814 J CYS 814 1_555 T ZN ZN . J ZN 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
metalc ? metalc24 J SG CYS 888 J CYS 888 1_555 T ZN ZN . J ZN 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc25 J SG CYS 895 J CYS 895 1_555 T ZN ZN . J ZN 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? 
metalc ? metalc26 J SG CYS 898 J CYS 898 1_555 T ZN ZN . J ZN 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
#
_chem_comp.formula           'C10 H13 N5 O16 P4' 
_chem_comp.formula_weight    583.129 
_chem_comp.id                ECJ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate' 
_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
O07 P06 ECJ doub 83 n n 
O03 P01 ECJ doub 84 n n 
O05 P06 ECJ sing 85 n n 
O05 P01 ECJ sing 86 n n 
O08 P06 ECJ sing 87 n n 
P06 O09 ECJ sing 88 n n 
P01 O04 ECJ sing 89 n n 
P01 O02 ECJ sing 90 n n 
N23 C22 ECJ sing 91 n n 
N20 C19 ECJ doub 92 n y 
N20 C21 ECJ sing 93 n y 
O09 C10 ECJ sing 94 n n 
C10 C11 ECJ sing 95 n n 
C22 C21 ECJ doub 96 n y 
C22 N24 ECJ sing 97 n y 
C19 N18 ECJ sing 98 n y 
C21 C28 ECJ sing 99 n y 
N24 C25 ECJ doub 100 n y 
N18 C28 ECJ sing 101 n y 
N18 C17 ECJ sing 102 n n 
O36 P33 ECJ doub 103 n n 
C28 N27 ECJ doub 104 n y 
C15 C13 ECJ sing 105 n n 
C15 C17 ECJ sing 106 n n 
C15 O16 ECJ doub 107 n n 
C11 C13 ECJ doub 108 n n 
C11 O12 ECJ sing 109 n n 
C13 O14 ECJ sing 110 n n 
C25 N27 ECJ sing 111 n y 
C17 O12 ECJ sing 112 n n 
P33 O35 ECJ sing 113 n n 
P33 O32 ECJ sing 114 n n 
P33 O34 ECJ sing 115 n n 
O14 P29 ECJ sing 116 n n 
O31 P29 ECJ doub 117 n n 
O32 P29 ECJ sing 118 n n 
P29 O30 ECJ sing 119 n n 
C10 H1 ECJ sing 120 n n 
C10 H2 ECJ sing 121 n n 
C17 H6 ECJ sing 122 n n 
C19 H7 ECJ sing 123 n n 
C25 H8 ECJ sing 124 n n 
N23 H9 ECJ sing 125 n n 
N23 H10 ECJ sing 126 n n 
O02 H11 ECJ sing 127 n n 
O04 H12 ECJ sing 128 n n 
O08 H13 ECJ sing 129 n n 
O30 H15 ECJ sing 130 n n 
O34 H16 ECJ sing 131 n n 
O35 H17 ECJ sing 132 n n 
#
_atom_sites.entry_id                     6BYU 
_atom_sites.fract_transf_matrix[1][1]    0.005369 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00491 
_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]    0.003243 
_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
M 6 ECJ C 1 1401 1 ECJ A4P . 
N 7 MG D 1 2001 2001 MG MG . 
O 8 ZN D 1 2002 3001 ZN ZN . 
P 8 ZN D 1 2003 3002 ZN ZN . 
Q 6 ECJ J 1 1501 2 ECJ A4P . 
R 7 MG J 1 1502 2001 MG MG . 
S 8 ZN J 1 1503 3001 ZN ZN . 
T 8 ZN J 1 1504 3002 ZN ZN . 
#
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 ECJ . . . Q 6 -65.937 -139.411 -47.795 0.81 78.45 ? C10 ECJ 1501 J 1 
HETATM 2 C C11 ECJ . . . Q 6 -67.343 -139.138 -47.339 0.81 75.22 ? C11 ECJ 1501 J 1 
HETATM 3 C C13 ECJ . . . Q 6 -67.851 -137.977 -48.124 0.81 86.93 ? C13 ECJ 1501 J 1 
HETATM 4 C C15 ECJ . . . Q 6 -67.077 -136.893 -47.54 0.81 87.63 ? C15 ECJ 1501 J 1 
HETATM 5 C C17 ECJ . . . Q 6 -67.145 -137.234 -46.068 0.81 90.39 ? C17 ECJ 1501 J 1 
HETATM 6 C C19 ECJ . . . Q 6 -64.838 -137.439 -45.36 0.81 90.71 ? C19 ECJ 1501 J 1 
HETATM 7 C C21 ECJ . . . Q 6 -64.651 -135.846 -43.848 0.81 74.89 ? C21 ECJ 1501 J 1 
HETATM 8 C C22 ECJ . . . Q 6 -64.313 -134.899 -42.86 0.81 71.87 ? C22 ECJ 1501 J 1 
HETATM 9 C C25 ECJ . . . Q 6 -66.498 -134.015 -42.915 0.81 74.41 ? C25 ECJ 1501 J 1 
HETATM 10 C C28 ECJ . . . Q 6 -65.955 -135.83 -44.346 0.81 84.14 ? C28 ECJ 1501 J 1 
HETATM 11 N N18 ECJ . . . Q 6 -66.018 -136.839 -45.294 0.81 90.68 ? N18 ECJ 1501 J 1 
HETATM 12 N N20 ECJ . . . Q 6 -63.992 -136.853 -44.498 0.81 85.57 ? N20 ECJ 1501 J 1 
HETATM 13 N N23 ECJ . . . Q 6 -62.987 -134.878 -42.321 0.81 63.22 ? N23 ECJ 1501 J 1 
HETATM 14 N N24 ECJ . . . Q 6 -65.272 -134.012 -42.437 0.81 81.26 ? N24 ECJ 1501 J 1 
HETATM 15 N N27 ECJ . . . Q 6 -66.835 -134.894 -43.851 0.81 85.1 ? N27 ECJ 1501 J 1 
HETATM 16 O O02 ECJ . . . Q 6 -64.422 -142.006 -44.358 0.81 101.4 ? O02 ECJ 1501 J 1 
HETATM 17 O O03 ECJ . . . Q 6 -62.285 -143.214 -44.671 0.81 96.85 ? O03 ECJ 1501 J 1 
HETATM 18 O O04 ECJ . . . Q 6 -64.202 -143.637 -46.138 0.81 112.3 ? O04 ECJ 1501 J 1 
HETATM 19 O O05 ECJ . . . Q 6 -63.005 -141.462 -46.362 0.81 117.28 ? O05 ECJ 1501 J 1 
HETATM 20 O O07 ECJ . . . Q 6 -63.173 -139.686 -48.092 0.81 91.11 ? O07 ECJ 1501 J 1 
HETATM 21 O O08 ECJ . . . Q 6 -63.97 -141.943 -48.618 0.81 105.33 ? O08 ECJ 1501 J 1 
HETATM 22 O O09 ECJ . . . Q 6 -65.323 -140.484 -47.064 0.81 80.72 ? O09 ECJ 1501 J 1 
HETATM 23 O O12 ECJ . . . Q 6 -67.322 -138.641 -45.982 0.81 77.15 ? O12 ECJ 1501 J 1 
HETATM 24 O O14 ECJ . . . Q 6 -69.194 -137.775 -47.787 0.81 114.07 ? O14 ECJ 1501 J 1 
HETATM 25 O O16 ECJ . . . Q 6 -67.691 -135.675 -47.807 0.81 83.35 ? O16 ECJ 1501 J 1 
HETATM 26 O O30 ECJ . . . Q 6 -71.526 -138.516 -48.207 0.81 147.54 ? O30 ECJ 1501 J 1 
HETATM 27 O O31 ECJ . . . Q 6 -69.816 -138.783 -50.042 0.81 143.46 ? O31 ECJ 1501 J 1 
HETATM 28 O O32 ECJ . . . Q 6 -70.667 -136.373 -49.37 0.81 168.29 ? O32 ECJ 1501 J 1 
HETATM 29 O O34 ECJ . . . Q 6 -68.38 -136.023 -50.507 0.81 169.36 ? O34 ECJ 1501 J 1 
HETATM 30 O O35 ECJ . . . Q 6 -69.921 -134.133 -50.28 0.81 174.28 ? O35 ECJ 1501 J 1 
HETATM 31 O O36 ECJ . . . Q 6 -70.455 -135.915 -51.891 0.81 177.84 ? O36 ECJ 1501 J 1 
HETATM 32 P P01 ECJ . . . Q 6 -63.492 -142.605 -45.371 0.81 118.66 ? P01 ECJ 1501 J 1 
HETATM 33 P P06 ECJ . . . Q 6 -63.853 -140.899 -47.547 0.81 100.5 ? P06 ECJ 1501 J 1 
HETATM 34 P P29 ECJ . . . Q 6 -70.307 -137.899 -48.844 0.81 147.02 ? P29 ECJ 1501 J 1 
HETATM 35 P P33 ECJ . . . Q 6 -69.836 -135.585 -50.526 0.81 175.86 ? P33 ECJ 1501 J 1 
#
_model_server_stats.io_time_ms              361 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           35 
#