data_6DFE # _model_server_result.job_id qpXqMYAZrMn8GDSL9CcpQA _model_server_result.datetime_utc '2025-03-25 03:47:51' _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 6dfe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":405}' # _entry.id 6DFE # _exptl.entry_id 6DFE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 581.468 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R)-1-{(2S,3S,4R,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl}propan-2-yl hydrogen (R)-phosphate (non-preferred name)' _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 6DFE _cell.length_a 80.82 _cell.length_b 92.33 _cell.length_c 94.94 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DFE _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,E,G 1 1 B,D,F,H 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 ? 3 E N N ? 3 F N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 GN4 GN1 C1 O1 . O6 HO6 . sing 2 ? 2 3 2 KDO GN4 C2 O2 . O6 HO6 . sing 3 ? 2 4 3 KDO KDO C2 O2 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C GN1 1 C 1 GN1 C 4 GN1 2 n C GN4 2 C 2 GN4 C 3 GN4 2 n C KDO 3 C 3 KDO C 2 KDO 2 n C KDO 4 C 4 KDO C 1 KDO 2 n D GN1 1 D 1 GN1 D 4 GN1 2 n D GN4 2 D 2 GN4 D 3 GN4 2 n D KDO 3 D 3 KDO D 2 KDO 2 n D KDO 4 D 4 KDO D 1 KDO # 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 covale ? covale1 C O6 GN1 . C GN1 1 1_555 C C1 GN4 . C GN4 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale2 C O6 GN4 . C GN4 2 1_555 C C2 KDO . C KDO 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale3 C O4 KDO . C KDO 3 1_555 C C2 KDO . C KDO 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale4 D O6 GN1 . D GN1 1 1_555 D C1 GN4 . D GN4 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale5 D O6 GN4 . D GN4 2 1_555 D C2 KDO . D KDO 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale6 D O4 KDO . D KDO 3 1_555 D C2 KDO . D KDO 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? # _chem_comp.formula 'C20 H32 N5 O13 P' _chem_comp.formula_weight 581.468 _chem_comp.id GA7 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R)-1-{(2S,3S,4R,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl}propan-2-yl hydrogen (R)-phosphate (non-preferred name)' _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 N C9 GA7 doub 83 n y N C12 GA7 sing 84 n y C9 N1 GA7 sing 85 n y N4 C12 GA7 sing 86 n n C12 C11 GA7 doub 87 n y N1 C10 GA7 doub 88 n y C11 C10 GA7 sing 89 n y C11 N3 GA7 sing 90 n y C10 N2 GA7 sing 91 n y N3 C13 GA7 doub 92 n y N2 C13 GA7 sing 93 n y N2 C16 GA7 sing 94 n n C16 O8 GA7 sing 95 n n C16 C15 GA7 sing 96 n n O8 C17 GA7 sing 97 n n O9 C15 GA7 sing 98 n n C15 C14 GA7 sing 99 n n O10 C14 GA7 sing 100 n n C17 C14 GA7 sing 101 n n C17 C18 GA7 sing 102 n n C8 C7 GA7 sing 103 n n C18 O5 GA7 sing 104 n n O5 P GA7 sing 105 n n C7 C4 GA7 sing 106 n n C7 O4 GA7 sing 107 n n C4 C GA7 sing 108 n n O4 P GA7 sing 109 n n P O7 GA7 doub 110 n n P O6 GA7 sing 111 n n O3 C5 GA7 sing 112 n n C C5 GA7 sing 113 n n C O GA7 sing 114 n n C5 C6 GA7 sing 115 n n O C2 GA7 sing 116 n n C6 O2 GA7 sing 117 n n C6 C1 GA7 sing 118 n n C19 C3 GA7 sing 119 n n C19 O11 GA7 sing 120 n n C2 C3 GA7 sing 121 n n C2 C1 GA7 sing 122 n n O12 C3 GA7 sing 123 n n C1 O1 GA7 sing 124 n n O6 H1 GA7 sing 125 n n C7 H2 GA7 sing 126 n n C8 H3 GA7 sing 127 n n C8 H4 GA7 sing 128 n n C8 H5 GA7 sing 129 n n C4 H6 GA7 sing 130 n n C4 H7 GA7 sing 131 n n C H8 GA7 sing 132 n n C5 H9 GA7 sing 133 n n O3 H10 GA7 sing 134 n n C6 H11 GA7 sing 135 n n O2 H12 GA7 sing 136 n n C1 H13 GA7 sing 137 n n O1 H14 GA7 sing 138 n n C2 H15 GA7 sing 139 n n C3 H16 GA7 sing 140 n n O12 H17 GA7 sing 141 n n C19 H18 GA7 sing 142 n n C19 H19 GA7 sing 143 n n O11 H20 GA7 sing 144 n n C18 H21 GA7 sing 145 n n C18 H22 GA7 sing 146 n n C17 H23 GA7 sing 147 n n C14 H24 GA7 sing 148 n n O10 H25 GA7 sing 149 n n C15 H26 GA7 sing 150 n n O9 H27 GA7 sing 151 n n C16 H28 GA7 sing 152 n n C9 H29 GA7 sing 153 n n N4 H30 GA7 sing 154 n n N4 H31 GA7 sing 155 n n C13 H32 GA7 sing 156 n n # _atom_sites.entry_id 6DFE _atom_sites.fract_transf_matrix[1][1] 0.012373 _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] 0.010831 _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] 0.010533 _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 E 3 GA7 A 1 405 1 GA7 don . F 3 GA7 B 1 405 2 GA7 don . G 4 HOH A 1 501 36 HOH HOH . G 4 HOH A 2 502 62 HOH HOH . G 4 HOH A 3 503 45 HOH HOH . G 4 HOH A 4 504 13 HOH HOH . G 4 HOH A 5 505 44 HOH HOH . G 4 HOH A 6 506 43 HOH HOH . G 4 HOH A 7 507 39 HOH HOH . G 4 HOH A 8 508 35 HOH HOH . G 4 HOH A 9 509 57 HOH HOH . G 4 HOH A 10 510 21 HOH HOH . G 4 HOH A 11 511 56 HOH HOH . G 4 HOH A 12 512 42 HOH HOH . G 4 HOH A 13 513 32 HOH HOH . G 4 HOH A 14 514 15 HOH HOH . G 4 HOH A 15 515 51 HOH HOH . G 4 HOH A 16 516 60 HOH HOH . G 4 HOH A 17 517 48 HOH HOH . G 4 HOH A 18 518 46 HOH HOH . G 4 HOH A 19 519 23 HOH HOH . G 4 HOH A 20 520 31 HOH HOH . G 4 HOH A 21 521 5 HOH HOH . G 4 HOH A 22 522 50 HOH HOH . G 4 HOH A 23 523 55 HOH HOH . G 4 HOH A 24 524 61 HOH HOH . H 4 HOH B 1 501 49 HOH HOH . H 4 HOH B 2 502 37 HOH HOH . H 4 HOH B 3 503 58 HOH HOH . H 4 HOH B 4 504 17 HOH HOH . H 4 HOH B 5 505 4 HOH HOH . H 4 HOH B 6 506 6 HOH HOH . H 4 HOH B 7 507 9 HOH HOH . H 4 HOH B 8 508 33 HOH HOH . H 4 HOH B 9 509 28 HOH HOH . H 4 HOH B 10 510 18 HOH HOH . H 4 HOH B 11 511 25 HOH HOH . H 4 HOH B 12 512 38 HOH HOH . H 4 HOH B 13 513 19 HOH HOH . H 4 HOH B 14 514 14 HOH HOH . H 4 HOH B 15 515 12 HOH HOH . H 4 HOH B 16 516 52 HOH HOH . H 4 HOH B 17 517 29 HOH HOH . H 4 HOH B 18 518 11 HOH HOH . H 4 HOH B 19 519 47 HOH HOH . H 4 HOH B 20 520 30 HOH HOH . H 4 HOH B 21 521 8 HOH HOH . H 4 HOH B 22 522 26 HOH HOH . H 4 HOH B 23 523 59 HOH HOH . H 4 HOH B 24 524 54 HOH HOH . H 4 HOH B 25 525 2 HOH HOH . H 4 HOH B 26 526 24 HOH HOH . H 4 HOH B 27 527 53 HOH HOH . H 4 HOH B 28 528 7 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 O O7 GA7 . . . E 3 88.963 34.359 44.89 1 84.2 ? O7 GA7 405 A 1 HETATM 2 P P GA7 . . . E 3 89.025 32.951 44.353 1 79.16 ? P GA7 405 A 1 HETATM 3 O O6 GA7 . . . E 3 88.393 31.991 45.327 1 80.03 ? O6 GA7 405 A 1 HETATM 4 O O4 GA7 . . . E 3 90.525 32.316 44.189 1 73.65 ? O4 GA7 405 A 1 HETATM 5 C C7 GA7 . . . E 3 91.781 32.962 43.918 1 72.98 ? C7 GA7 405 A 1 HETATM 6 C C8 GA7 . . . E 3 91.838 33.49 42.487 1 70.14 ? C8 GA7 405 A 1 HETATM 7 C C4 GA7 . . . E 3 92.949 31.981 44.165 1 76.64 ? C4 GA7 405 A 1 HETATM 8 C C GA7 . . . E 3 93.328 31.799 45.649 1 79.34 ? C GA7 405 A 1 HETATM 9 C C5 GA7 . . . E 3 94.622 31.023 45.922 1 80.52 ? C5 GA7 405 A 1 HETATM 10 O O3 GA7 . . . E 3 95.646 31.619 45.12 1 82.87 ? O3 GA7 405 A 1 HETATM 11 C C6 GA7 . . . E 3 95.059 31.032 47.416 1 84.99 ? C6 GA7 405 A 1 HETATM 12 O O2 GA7 . . . E 3 96.463 30.656 47.581 1 70.32 ? O2 GA7 405 A 1 HETATM 13 C C1 GA7 . . . E 3 94.843 32.4 48.113 1 84.42 ? C1 GA7 405 A 1 HETATM 14 O O1 GA7 . . . E 3 94.77 32.268 49.547 1 87.67 ? O1 GA7 405 A 1 HETATM 15 C C2 GA7 . . . E 3 93.592 33.155 47.636 1 78.72 ? C2 GA7 405 A 1 HETATM 16 C C3 GA7 . . . E 3 93.565 34.64 48.087 1 66.42 ? C3 GA7 405 A 1 HETATM 17 O O12 GA7 . . . E 3 94.682 35.44 47.647 1 54.75 ? O12 GA7 405 A 1 HETATM 18 C C19 GA7 . . . E 3 92.317 35.327 47.579 1 54.58 ? C19 GA7 405 A 1 HETATM 19 O O11 GA7 . . . E 3 91.294 34.929 48.452 1 47.86 ? O11 GA7 405 A 1 HETATM 20 O O GA7 . . . E 3 93.519 33.095 46.203 1 85.95 ? O GA7 405 A 1 HETATM 21 O O5 GA7 . . . E 3 88.155 32.98 42.985 1 75.01 ? O5 GA7 405 A 1 HETATM 22 C C18 GA7 . . . E 3 86.763 33.336 42.94 1 82.37 ? C18 GA7 405 A 1 HETATM 23 C C17 GA7 . . . E 3 85.943 32.553 41.881 1 82.53 ? C17 GA7 405 A 1 HETATM 24 C C14 GA7 . . . E 3 85.886 31.033 42.057 1 80.09 ? C14 GA7 405 A 1 HETATM 25 O O10 GA7 . . . E 3 84.625 30.524 41.583 1 75.38 ? O10 GA7 405 A 1 HETATM 26 C C15 GA7 . . . E 3 87.009 30.534 41.178 1 74.58 ? C15 GA7 405 A 1 HETATM 27 O O9 GA7 . . . E 3 86.855 29.189 40.726 1 69.29 ? O9 GA7 405 A 1 HETATM 28 C C16 GA7 . . . E 3 86.977 31.52 40.014 1 71.37 ? C16 GA7 405 A 1 HETATM 29 O O8 GA7 . . . E 3 86.475 32.748 40.556 1 80.19 ? O8 GA7 405 A 1 HETATM 30 N N2 GA7 . . . E 3 88.349 31.614 39.443 1 66.11 ? N2 GA7 405 A 1 HETATM 31 C C10 GA7 . . . E 3 88.726 31.01 38.297 1 65.83 ? C10 GA7 405 A 1 HETATM 32 N N1 GA7 . . . E 3 88.105 30.241 37.343 1 56.67 ? N1 GA7 405 A 1 HETATM 33 C C9 GA7 . . . E 3 88.809 29.778 36.274 1 61.65 ? C9 GA7 405 A 1 HETATM 34 N N GA7 . . . E 3 90.123 30.023 36.074 1 61.69 ? N GA7 405 A 1 HETATM 35 C C12 GA7 . . . E 3 90.86 30.781 36.961 1 59.93 ? C12 GA7 405 A 1 HETATM 36 N N4 GA7 . . . E 3 92.187 31.053 36.774 1 51.67 ? N4 GA7 405 A 1 HETATM 37 C C11 GA7 . . . E 3 90.169 31.327 38.155 1 60.03 ? C11 GA7 405 A 1 HETATM 38 N N3 GA7 . . . E 3 90.518 32.092 39.218 1 58.28 ? N3 GA7 405 A 1 HETATM 39 C C13 GA7 . . . E 3 89.42 32.24 39.992 1 56.35 ? C13 GA7 405 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #