data_5EY8
#
_model_server_result.job_id            oBDtZx3lJfRkVQIZ5G6k3A 
_model_server_result.datetime_utc      '2024-11-05 00:24:28' 
_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          5ey8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":701}' 
#
_entry.id    5EY8 
#
_exptl.entry_id    5EY8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              627.753 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate' 
_entity.pdbx_number_of_molecules    8 
_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            5EY8 
_cell.length_a            164.04 
_cell.length_b            164.04 
_cell.length_c            231.53 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EY8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        75 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 4' 
#
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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
? monomeric 1 author_defined_assembly 6 
? monomeric 1 author_defined_assembly 7 
? monomeric 1 author_defined_assembly 8 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,I 1 1 
B,J 2 1 
C,K 3 1 
D,L 4 1 
E,M,N 5 1 
F,O,P 6 1 
G,Q 7 1 
H,R 8 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 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 O N N 
? 2 Q N N 
? 2 R N N 
#
_chem_comp.formula           'C30 H54 N5 O7 P' 
_chem_comp.formula_weight    627.753 
_chem_comp.id                5SV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl 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
C24 C23 5SV sing 1 n n 
C23 C22 5SV sing 2 n n 
C22 C21 5SV sing 3 n n 
C21 C20 5SV sing 4 n n 
C20 C19 5SV sing 5 n n 
C19 C18 5SV sing 6 n n 
C18 C17 5SV sing 7 n n 
C17 C16 5SV sing 8 n n 
C16 C15 5SV sing 9 n n 
C15 C14 5SV sing 10 n n 
C14 C13 5SV sing 11 n n 
C13 C12 5SV sing 12 n n 
C12 C11 5SV sing 13 n n 
C11 C10 5SV sing 14 n n 
N6 C6 5SV sing 15 n n 
C10 C9 5SV sing 16 n n 
C9 O3P 5SV sing 17 n n 
C6 C5 5SV doub 18 n y 
C6 N1 5SV sing 19 n y 
N7 C5 5SV sing 20 n y 
N7 C8 5SV doub 21 n y 
C5 C4 5SV sing 22 n y 
N1 C2 5SV doub 23 n y 
C8 N9 5SV sing 24 n y 
O3P P 5SV sing 25 n n 
C4 N9 5SV sing 26 n y 
C4 N3 5SV doub 27 n y 
C2 N3 5SV sing 28 n y 
O1P P 5SV doub 29 n n 
N9 C1' 5SV sing 30 n n 
P O5' 5SV sing 31 n n 
P O2P 5SV sing 32 n n 
C5' O5' 5SV sing 33 n n 
C5' C4' 5SV sing 34 n n 
C1' C2' 5SV sing 35 n n 
C1' O4' 5SV sing 36 n n 
C3' C2' 5SV sing 37 n n 
C3' C4' 5SV sing 38 n n 
C3' O3' 5SV sing 39 n n 
C2' O2' 5SV sing 40 n n 
O4' C4' 5SV sing 41 n n 
C2 H1 5SV sing 42 n n 
C8 H2 5SV sing 43 n n 
C9 H3 5SV sing 44 n n 
C9 H4 5SV sing 45 n n 
C10 H5 5SV sing 46 n n 
C10 H6 5SV sing 47 n n 
C11 H7 5SV sing 48 n n 
C11 H8 5SV sing 49 n n 
C12 H9 5SV sing 50 n n 
C12 H10 5SV sing 51 n n 
C13 H11 5SV sing 52 n n 
C13 H12 5SV sing 53 n n 
C14 H13 5SV sing 54 n n 
C14 H14 5SV sing 55 n n 
C15 H15 5SV sing 56 n n 
C15 H16 5SV sing 57 n n 
O2P H17 5SV sing 58 n n 
C5' H18 5SV sing 59 n n 
C5' H19 5SV sing 60 n n 
C4' H20 5SV sing 61 n n 
C3' H21 5SV sing 62 n n 
O3' H22 5SV sing 63 n n 
C2' H23 5SV sing 64 n n 
O2' H24 5SV sing 65 n n 
C1' H25 5SV sing 66 n n 
N6 H26 5SV sing 67 n n 
N6 H27 5SV sing 68 n n 
C16 H28 5SV sing 69 n n 
C16 H29 5SV sing 70 n n 
C17 H30 5SV sing 71 n n 
C17 H31 5SV sing 72 n n 
C18 H32 5SV sing 73 n n 
C18 H33 5SV sing 74 n n 
C19 H34 5SV sing 75 n n 
C19 H35 5SV sing 76 n n 
C20 H36 5SV sing 77 n n 
C20 H37 5SV sing 78 n n 
C21 H38 5SV sing 79 n n 
C21 H39 5SV sing 80 n n 
C22 H40 5SV sing 81 n n 
C22 H41 5SV sing 82 n n 
C23 H42 5SV sing 83 n n 
C24 H43 5SV sing 84 n n 
C24 H44 5SV sing 85 n n 
C24 C25 5SV sing 86 n n 
C25 C26 5SV sing 87 n n 
C26 C27 5SV sing 88 n n 
C27 C28 5SV sing 89 n n 
C23 H45 5SV sing 90 n n 
C25 H46 5SV sing 91 n n 
C25 H47 5SV sing 92 n n 
C26 H48 5SV sing 93 n n 
C26 H49 5SV sing 94 n n 
C27 H50 5SV sing 95 n n 
C27 H51 5SV sing 96 n n 
C28 H52 5SV sing 97 n n 
C28 H53 5SV sing 98 n n 
C28 H54 5SV sing 99 n n 
#
_atom_sites.entry_id                     5EY8 
_atom_sites.fract_transf_matrix[1][1]    0.006096 
_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]    0.006096 
_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]    0.004319 
_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
I 2 5SV A 1 701 631 5SV KK2 . 
J 2 5SV B 1 701 631 5SV KK2 . 
K 2 5SV C 1 701 631 5SV KK2 . 
L 2 5SV D 1 701 631 5SV KK2 . 
M 2 5SV E 1 701 631 5SV KK2 . 
N 3 GOL E 1 702 637 GOL GOL . 
O 2 5SV F 1 701 631 5SV KK2 . 
P 3 GOL F 1 702 637 GOL GOL . 
Q 2 5SV G 1 701 631 5SV KK2 . 
R 2 5SV H 1 701 631 5SV KK2 . 
#
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 C2 5SV . . . R 2 38.664 81.231 230.655 1 38.71 ? C2 5SV 701 H 1 
HETATM 2 C C4 5SV . . . R 2 38.982 79.02 230.448 1 38.45 ? C4 5SV 701 H 1 
HETATM 3 C C6 5SV . . . R 2 39.36 80.496 228.572 1 38.7 ? C6 5SV 701 H 1 
HETATM 4 C C5 5SV . . . R 2 39.372 79.185 229.093 1 38.52 ? C5 5SV 701 H 1 
HETATM 5 N N1 5SV . . . R 2 39.006 81.545 229.374 1 38.8 ? N1 5SV 701 H 1 
HETATM 6 N N3 5SV . . . R 2 38.607 80.03 231.283 1 38.54 ? N3 5SV 701 H 1 
HETATM 7 C C8 5SV . . . R 2 39.545 77.058 229.516 1 39.05 ? C8 5SV 701 H 1 
HETATM 8 C C9 5SV . . . R 2 40.992 73.088 227.924 1 45.62 ? C9 5SV 701 H 1 
HETATM 9 C C10 5SV . . . R 2 41.016 74.368 227.071 1 45.34 ? C10 5SV 701 H 1 
HETATM 10 C C11 5SV . . . R 2 41.31 74.048 225.608 1 42.93 ? C11 5SV 701 H 1 
HETATM 11 C C12 5SV . . . R 2 41.343 75.318 224.77 1 38.26 ? C12 5SV 701 H 1 
HETATM 12 C C13 5SV . . . R 2 40.833 75.083 223.348 1 38.29 ? C13 5SV 701 H 1 
HETATM 13 C C14 5SV . . . R 2 41.967 74.621 222.399 1 38.28 ? C14 5SV 701 H 1 
HETATM 14 C C15 5SV . . . R 2 41.977 73.099 222.18 1 38.13 ? C15 5SV 701 H 1 
HETATM 15 O O2P 5SV . . . R 2 42.376 72.45 230.926 1 43.39 ? O2P 5SV 701 H 1 
HETATM 16 P P 5SV . . . R 2 40.943 72.606 230.577 1 42.37 ? P 5SV 701 H 1 
HETATM 17 O O1P 5SV . . . R 2 40.099 71.293 230.29 1 37.63 ? O1P 5SV 701 H 1 
HETATM 18 O O5' 5SV . . . R 2 40.037 73.28 231.69 1 41.82 ? O5' 5SV 701 H 1 
HETATM 19 C C5' 5SV . . . R 2 38.673 73.484 231.652 1 46.38 ? C5' 5SV 701 H 1 
HETATM 20 C C4' 5SV . . . R 2 38.368 74.792 232.384 1 51.53 ? C4' 5SV 701 H 1 
HETATM 21 O O4' 5SV . . . R 2 39.327 75.759 231.998 1 51.79 ? O4' 5SV 701 H 1 
HETATM 22 C C3' 5SV . . . R 2 36.972 75.353 232.046 1 53.38 ? C3' 5SV 701 H 1 
HETATM 23 O O3' 5SV . . . R 2 36.125 74.803 232.994 1 50.06 ? O3' 5SV 701 H 1 
HETATM 24 C C2' 5SV . . . R 2 37.193 76.89 232.164 1 60.32 ? C2' 5SV 701 H 1 
HETATM 25 O O2' 5SV . . . R 2 36.806 77.284 233.434 1 59.57 ? O2' 5SV 701 H 1 
HETATM 26 C C1' 5SV . . . R 2 38.749 77.046 232.007 1 48.32 ? C1' 5SV 701 H 1 
HETATM 27 N N9 5SV . . . R 2 39.088 77.663 230.716 1 42.15 ? N9 5SV 701 H 1 
HETATM 28 N N7 5SV . . . R 2 39.722 77.952 228.525 1 38.4 ? N7 5SV 701 H 1 
HETATM 29 N N6 5SV . . . R 2 39.659 80.758 227.283 1 38.78 ? N6 5SV 701 H 1 
HETATM 30 O O3P 5SV . . . R 2 40.635 73.425 229.235 1 37.88 ? O3P 5SV 701 H 1 
HETATM 31 C C16 5SV . . . R 2 42.491 72.719 220.79 1 38.14 ? C16 5SV 701 H 1 
HETATM 32 C C17 5SV . . . R 2 43.991 72.918 220.577 1 38.19 ? C17 5SV 701 H 1 
HETATM 33 C C18 5SV . . . R 2 44.472 72.397 219.211 1 38.19 ? C18 5SV 701 H 1 
HETATM 34 C C19 5SV . . . R 2 45.985 72.61 219.073 1 57.28 ? C19 5SV 701 H 1 
HETATM 35 C C20 5SV . . . R 2 46.542 71.984 217.79 1 38.24 ? C20 5SV 701 H 1 
#
_model_server_stats.io_time_ms              64 
_model_server_stats.parse_time_ms           34 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           35 
#