data_3VFQ
#
_model_server_result.job_id            h8zR1tNAuqHuwnNLbfYeIw 
_model_server_result.datetime_utc      '2025-01-03 04:18:55' 
_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          3vfq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1201}' 
#
_entry.id    3VFQ 
#
_exptl.entry_id    3VFQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_entity.pdbx_number_of_molecules    1 
_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            3VFQ 
_cell.length_a            46.62 
_cell.length_b            59.94 
_cell.length_c            144.34 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VFQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        17 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                AR6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Adenosine-5-Diphosphoribose 
#
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
N1 C2 AR6 doub 13 n y 
N1 C6 AR6 sing 14 n y 
C2 N3 AR6 sing 15 n y 
N3 C4 AR6 doub 16 n y 
C4 C5 AR6 sing 17 n y 
C4 N9 AR6 sing 18 n y 
C5 C6 AR6 doub 19 n y 
C5 N7 AR6 sing 20 n y 
C6 N6 AR6 sing 21 n n 
N7 C8 AR6 doub 22 n y 
C8 N9 AR6 sing 23 n y 
N9 C1' AR6 sing 24 n n 
PA O1A AR6 sing 25 n n 
PA O2A AR6 doub 26 n n 
PA O3A AR6 sing 27 n n 
PA O5' AR6 sing 28 n n 
PB O1B AR6 sing 29 n n 
PB O2B AR6 doub 30 n n 
PB O3A AR6 sing 31 n n 
PB O5D AR6 sing 32 n n 
C1' C2' AR6 sing 33 n n 
C1' O4' AR6 sing 34 n n 
C1D O1D AR6 sing 35 n n 
C1D C2D AR6 sing 36 n n 
C1D O4D AR6 sing 37 n n 
C2' O2' AR6 sing 38 n n 
C2' C3' AR6 sing 39 n n 
C2D O2D AR6 sing 40 n n 
C2D C3D AR6 sing 41 n n 
C3' O3' AR6 sing 42 n n 
C3' C4' AR6 sing 43 n n 
C3D O3D AR6 sing 44 n n 
C3D C4D AR6 sing 45 n n 
C4' O4' AR6 sing 46 n n 
C4' C5' AR6 sing 47 n n 
C4D O4D AR6 sing 48 n n 
C4D C5D AR6 sing 49 n n 
C5' O5' AR6 sing 50 n n 
C5D O5D AR6 sing 51 n n 
C2 H2 AR6 sing 52 n n 
N6 HN6 AR6 sing 53 n n 
N6 HN6A AR6 sing 54 n n 
C8 H8 AR6 sing 55 n n 
C1' H1' AR6 sing 56 n n 
C1D H1D AR6 sing 57 n n 
C2' H2' AR6 sing 58 n n 
O2' HO2' AR6 sing 59 n n 
C2D H2D AR6 sing 60 n n 
O2D HO2D AR6 sing 61 n n 
C3' H3' AR6 sing 62 n n 
O3' HO3' AR6 sing 63 n n 
C3D H3D AR6 sing 64 n n 
O3D HO3D AR6 sing 65 n n 
C4' H4' AR6 sing 66 n n 
C4D H4D AR6 sing 67 n n 
C5' H5' AR6 sing 68 n n 
C5' "H5'A" AR6 sing 69 n n 
C5D H5D AR6 sing 70 n n 
C5D H5DA AR6 sing 71 n n 
O1A H1A AR6 sing 72 n n 
O1B H1B AR6 sing 73 n n 
O1D HD1 AR6 sing 74 n n 
#
_atom_sites.entry_id                     3VFQ 
_atom_sites.fract_transf_matrix[1][1]    0.02145 
_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]    0.016683 
_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]    0.006928 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          B 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           AR6 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      1201 
_pdbx_nonpoly_scheme.auth_seq_num     800 
_pdbx_nonpoly_scheme.pdb_mon_id       AR6 
_pdbx_nonpoly_scheme.auth_mon_id      APR 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 N N1 AR6 . . . B 2 25.104 -1.913 16.672 1 32.94 ? N1 AR6 1201 A 1 
HETATM 2 C C2 AR6 . . . B 2 24.193 -1.049 17.12 1 33.31 ? C2 AR6 1201 A 1 
HETATM 3 N N3 AR6 . . . B 2 23.485 -0.29 16.28 1 34.26 ? N3 AR6 1201 A 1 
HETATM 4 C C4 AR6 . . . B 2 23.693 -0.396 14.938 1 34.97 ? C4 AR6 1201 A 1 
HETATM 5 C C5 AR6 . . . B 2 24.647 -1.283 14.452 1 33.86 ? C5 AR6 1201 A 1 
HETATM 6 C C6 AR6 . . . B 2 25.351 -2.035 15.35 1 33.49 ? C6 AR6 1201 A 1 
HETATM 7 N N6 AR6 . . . B 2 26.248 -2.878 14.857 1 35.63 ? N6 AR6 1201 A 1 
HETATM 8 N N7 AR6 . . . B 2 24.684 -1.218 13.126 1 35.35 ? N7 AR6 1201 A 1 
HETATM 9 C C8 AR6 . . . B 2 23.779 -0.292 12.772 1 36.25 ? C8 AR6 1201 A 1 
HETATM 10 N N9 AR6 . . . B 2 23.182 0.21 13.866 1 34.58 ? N9 AR6 1201 A 1 
HETATM 11 P PA AR6 . . . B 2 19.094 -0.954 9.709 1 39.85 ? PA AR6 1201 A 1 
HETATM 12 P PB AR6 . . . B 2 16.359 -0.749 10.086 1 40.7 ? PB AR6 1201 A 1 
HETATM 13 C C1' AR6 . . . B 2 22.156 1.21 13.878 1 34.77 ? C1' AR6 1201 A 1 
HETATM 14 O O1A AR6 . . . B 2 20.105 -2.055 9.775 1 39.24 ? O1A AR6 1201 A 1 
HETATM 15 O O1B AR6 . . . B 2 15.605 -1.126 11.293 1 41.39 ? O1B AR6 1201 A 1 
HETATM 16 C C1D AR6 . . . B 2 14.569 -3.593 6.45 1 46.73 ? C1D AR6 1201 A 1 
HETATM 17 O O1D AR6 . . . B 2 13.814 -4.759 6.229 1 46.01 ? O1D AR6 1201 A 1 
HETATM 18 C C2' AR6 . . . B 2 22.131 2.101 12.643 1 35.63 ? C2' AR6 1201 A 1 
HETATM 19 O O2' AR6 . . . B 2 22.79 3.344 12.924 1 37.24 ? O2' AR6 1201 A 1 
HETATM 20 O O2A AR6 . . . B 2 18.875 -0.206 8.436 1 37.71 ? O2A AR6 1201 A 1 
HETATM 21 O O2B AR6 . . . B 2 16.505 0.677 9.695 1 39.58 ? O2B AR6 1201 A 1 
HETATM 22 C C2D AR6 . . . B 2 15.743 -3.536 5.459 1 46.59 ? C2D AR6 1201 A 1 
HETATM 23 O O2D AR6 . . . B 2 15.647 -4.572 4.48 1 45.72 ? O2D AR6 1201 A 1 
HETATM 24 C C3' AR6 . . . B 2 20.633 2.363 12.455 1 35.56 ? C3' AR6 1201 A 1 
HETATM 25 O O3' AR6 . . . B 2 20.26 3.466 13.283 1 32.44 ? O3' AR6 1201 A 1 
HETATM 26 O O3A AR6 . . . B 2 17.717 -1.532 10.203 1 37.73 ? O3A AR6 1201 A 1 
HETATM 27 C C3D AR6 . . . B 2 16.969 -3.772 6.329 1 48.21 ? C3D AR6 1201 A 1 
HETATM 28 O O3D AR6 . . . B 2 17.259 -5.17 6.454 1 49.73 ? O3D AR6 1201 A 1 
HETATM 29 C C4' AR6 . . . B 2 19.977 1.101 13.056 1 37.69 ? C4' AR6 1201 A 1 
HETATM 30 O O4' AR6 . . . B 2 21.124 0.307 13.61 1 36.44 ? O4' AR6 1201 A 1 
HETATM 31 C C4D AR6 . . . B 2 16.502 -3.283 7.707 1 48.16 ? C4D AR6 1201 A 1 
HETATM 32 O O4D AR6 . . . B 2 15.137 -3.767 7.784 1 48.68 ? O4D AR6 1201 A 1 
HETATM 33 C C5' AR6 . . . B 2 19.012 0.23 12.108 1 38.43 ? C5' AR6 1201 A 1 
HETATM 34 O O5' AR6 . . . B 2 19.623 0.059 10.835 1 38.5 ? O5' AR6 1201 A 1 
HETATM 35 C C5D AR6 . . . B 2 16.424 -1.766 7.826 1 46.42 ? C5D AR6 1201 A 1 
HETATM 36 O O5D AR6 . . . B 2 15.626 -1.457 8.93 1 42.58 ? O5D AR6 1201 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           36 
#