data_9JJF # _model_server_result.job_id Zo6Y5BqGzPH3g1nn-n9xHg _model_server_result.datetime_utc '2024-11-07 04:40:36' _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 9jjf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":4001}' # _entry.id 9JJF # _exptl.entry_id 9JJF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 639.296 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE' _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 9JJF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JJF _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 ? _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 B NAG 1 B 1 NAG B 1 NAG 2 n B NAG 2 B 2 NAG B 2 NAG # 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 A ND2 ASN 1017 A ASN 1017 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? metalc ? metalc1 A OE1 GLU 893 A GLU 893 1_555 C CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? metalc ? metalc2 A OE2 GLU 893 A GLU 893 1_555 C CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc3 A OE1 GLN 896 A GLN 896 1_555 C CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc4 A OD1 ASN 918 A ASN 918 1_555 C CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc5 A OD2 ASP 921 A ASP 921 1_555 C CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? # _chem_comp.formula 'C15 H24 N5 O17 P3' _chem_comp.formula_weight 639.296 _chem_comp.id A2R _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN 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 OP3 P2' A2R sing 1 n n OP3 HOP3 A2R sing 2 n n P2' OP2 A2R doub 3 n n P2' OP1 A2R sing 4 n n P2' O2' A2R sing 5 n n OP1 HOP1 A2R sing 6 n n O2' C2' A2R sing 7 n n C2' C1' A2R sing 8 n n C2' C3' A2R sing 9 n n C2' H2' A2R sing 10 n n C1' N9 A2R sing 11 n n C1' O4' A2R sing 12 n n C1' H1' A2R sing 13 n n N9 C4 A2R sing 14 n y N9 C8 A2R sing 15 n y C4 C5 A2R doub 16 n y C4 N3 A2R sing 17 n y N3 C2 A2R doub 18 n y C2 N1 A2R sing 19 n y C2 H2 A2R sing 20 n n N1 C6 A2R doub 21 n y C6 N6 A2R sing 22 n n C6 C5 A2R sing 23 n y N6 HN61 A2R sing 24 n n N6 HN62 A2R sing 25 n n C5 N7 A2R sing 26 n y N7 C8 A2R doub 27 n y C8 H8 A2R sing 28 n n O4' C4' A2R sing 29 n n C3' C4' A2R sing 30 n n C3' O3' A2R sing 31 n n C3' H3' A2R sing 32 n n O3' HO3' A2R sing 33 n n C4' C5' A2R sing 34 n n C4' H4' A2R sing 35 n n C5' O5' A2R sing 36 n n C5' "H5'1" A2R sing 37 n n C5' "H5'2" A2R sing 38 n n O5' P A2R sing 39 n n P O1 A2R doub 40 n n P O3 A2R sing 41 n n P O2 A2R sing 42 n n O2 HO2 A2R sing 43 n n O3 P1 A2R sing 44 n n P1 O15' A2R sing 45 n n P1 O12 A2R doub 46 n n P1 O11 A2R sing 47 n n O11 HO11 A2R sing 48 n n O15' C15' A2R sing 49 n n C15' C14' A2R sing 50 n n C15' "H5'3" A2R sing 51 n n C15' "H5'4" A2R sing 52 n n C14' C13' A2R sing 53 n n C14' O14' A2R sing 54 n n C14' H14' A2R sing 55 n n C13' O13' A2R sing 56 n n C13' C12' A2R sing 57 n n C13' H13' A2R sing 58 n n O13' H16' A2R sing 59 n n C12' O12' A2R sing 60 n n C12' C11' A2R sing 61 n n C12' H12' A2R sing 62 n n O12' H15' A2R sing 63 n n C11' O14' A2R sing 64 n n C11' O11' A2R sing 65 n n C11' H11' A2R sing 66 n n O11' H17' A2R sing 67 n n # _atom_sites.entry_id 9JJF _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 3 CA A 1 4000 4000 CA CA . D 4 A2R A 1 4001 4001 A2R A2R . # 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 OP3 A2R . . . D 4 131.632 145.779 224.752 1 57.72 ? OP3 A2R 4001 A 1 HETATM 2 P P2' A2R . . . D 4 131.765 145.038 226.068 1 57.72 ? P2' A2R 4001 A 1 HETATM 3 O OP1 A2R . . . D 4 132.23 143.625 225.805 1 57.72 ? OP1 A2R 4001 A 1 HETATM 4 O OP2 A2R . . . D 4 130.399 144.984 226.742 1 57.72 ? OP2 A2R 4001 A 1 HETATM 5 O O2' A2R . . . D 4 132.813 145.839 227.069 1 57.72 ? O2' A2R 4001 A 1 HETATM 6 C C2' A2R . . . D 4 134.293 145.638 227.044 1 57.72 ? C2' A2R 4001 A 1 HETATM 7 C C1' A2R . . . D 4 134.894 145.626 225.528 1 57.72 ? C1' A2R 4001 A 1 HETATM 8 N N9 A2R . . . D 4 136.044 144.76 225.351 1 57.72 ? N9 A2R 4001 A 1 HETATM 9 C C4 A2R . . . D 4 136.275 144.028 224.268 1 57.72 ? C4 A2R 4001 A 1 HETATM 10 N N3 A2R . . . D 4 135.551 143.883 223.137 1 57.72 ? N3 A2R 4001 A 1 HETATM 11 C C2 A2R . . . D 4 135.986 143.001 222.041 1 57.72 ? C2 A2R 4001 A 1 HETATM 12 N N1 A2R . . . D 4 137.221 142.257 222.162 1 57.72 ? N1 A2R 4001 A 1 HETATM 13 C C6 A2R . . . D 4 137.985 142.407 223.359 1 57.72 ? C6 A2R 4001 A 1 HETATM 14 N N6 A2R . . . D 4 139.192 141.71 223.529 1 57.72 ? N6 A2R 4001 A 1 HETATM 15 C C5 A2R . . . D 4 137.459 143.344 224.451 1 57.72 ? C5 A2R 4001 A 1 HETATM 16 N N7 A2R . . . D 4 137.942 143.675 225.631 1 57.72 ? N7 A2R 4001 A 1 HETATM 17 C C8 A2R . . . D 4 137.078 144.558 226.198 1 57.72 ? C8 A2R 4001 A 1 HETATM 18 O O4' A2R . . . D 4 135.219 146.848 225.187 1 57.72 ? O4' A2R 4001 A 1 HETATM 19 C C3' A2R . . . D 4 134.911 146.889 227.642 1 57.72 ? C3' A2R 4001 A 1 HETATM 20 O O3' A2R . . . D 4 133.973 147.517 228.608 1 57.72 ? O3' A2R 4001 A 1 HETATM 21 C C4' A2R . . . D 4 135.058 147.783 226.351 1 57.72 ? C4' A2R 4001 A 1 HETATM 22 C C5' A2R . . . D 4 136.204 148.604 226.446 1 57.72 ? C5' A2R 4001 A 1 HETATM 23 O O5' A2R . . . D 4 137.076 148.301 225.342 1 57.72 ? O5' A2R 4001 A 1 HETATM 24 P P A2R . . . D 4 138.745 148.573 225.556 1 57.72 ? P A2R 4001 A 1 HETATM 25 O O1 A2R . . . D 4 138.986 149.076 226.954 1 57.72 ? O1 A2R 4001 A 1 HETATM 26 O O2 A2R . . . D 4 139.219 149.613 224.58 1 57.72 ? O2 A2R 4001 A 1 HETATM 27 O O3 A2R . . . D 4 139.587 147.15 225.296 1 57.72 ? O3 A2R 4001 A 1 HETATM 28 P P1 A2R . . . D 4 141.003 146.723 226.138 1 57.72 ? P1 A2R 4001 A 1 HETATM 29 O O11 A2R . . . D 4 142.086 147.725 225.805 1 57.72 ? O11 A2R 4001 A 1 HETATM 30 O O12 A2R . . . D 4 140.696 146.76 227.612 1 57.72 ? O12 A2R 4001 A 1 HETATM 31 O O15' A2R . . . D 4 141.486 145.182 225.69 1 57.72 ? O15' A2R 4001 A 1 HETATM 32 C C15' A2R . . . D 4 141.493 144.852 224.288 1 57.72 ? C15' A2R 4001 A 1 HETATM 33 C C14' A2R . . . D 4 142.135 143.62 224.057 1 57.72 ? C14' A2R 4001 A 1 HETATM 34 C C13' A2R . . . D 4 143.412 143.49 224.921 1 57.72 ? C13' A2R 4001 A 1 HETATM 35 O O13' A2R . . . D 4 143.259 142.352 225.865 1 57.72 ? O13' A2R 4001 A 1 HETATM 36 C C12' A2R . . . D 4 144.387 143.223 224.089 1 57.72 ? C12' A2R 4001 A 1 HETATM 37 O O12' A2R . . . D 4 144.646 141.782 224.066 1 57.72 ? O12' A2R 4001 A 1 HETATM 38 C C11' A2R . . . D 4 143.91 143.715 222.628 1 57.72 ? C11' A2R 4001 A 1 HETATM 39 O O14' A2R . . . D 4 142.608 143.544 222.592 1 57.72 ? O14' A2R 4001 A 1 HETATM 40 O O11' A2R . . . D 4 144.228 145.05 222.452 1 57.72 ? O11' A2R 4001 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #