data_9JJE # _model_server_result.job_id TU05P88ge7mCCpm-NqwbDA _model_server_result.datetime_utc '2024-12-04 05:26:20' _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 9jje # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":4001}' # _entry.id 9JJE # _exptl.entry_id 9JJE _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 4 _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 9JJE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JJE _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 J N N ? 4 L N N ? 4 N N N ? 4 P N 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 E NAG 1 E 1 NAG E 1 NAG 2 n E NAG 2 E 2 NAG E 2 NAG 2 n F NAG 1 F 1 NAG F 1 NAG 2 n F NAG 2 F 2 NAG F 2 NAG 2 n G NAG 1 G 1 NAG G 1 NAG 2 n G NAG 2 G 2 NAG G 2 NAG 2 n H NAG 1 H 1 NAG H 1 NAG 2 n H NAG 2 H 2 NAG H 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 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 1017 B ASN 1017 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 C ND2 ASN 1017 C ASN 1017 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 D ND2 ASN 1017 D ASN 1017 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A OE1 GLU 893 A GLU 893 1_555 I CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc2 A OE2 GLU 893 A GLU 893 1_555 I CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc3 A OE1 GLN 896 A GLN 896 1_555 I CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc4 A OD1 ASN 918 A ASN 918 1_555 I CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc5 A OD2 ASP 921 A ASP 921 1_555 I CA CA . A CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc6 B OE1 GLU 893 B GLU 893 1_555 K CA CA . B CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc7 B OE2 GLU 893 B GLU 893 1_555 K CA CA . B CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc8 B OE1 GLN 896 B GLN 896 1_555 K CA CA . B CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc9 B OD1 ASN 918 B ASN 918 1_555 K CA CA . B CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc10 B OD2 ASP 921 B ASP 921 1_555 K CA CA . B CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc11 C OE1 GLU 893 C GLU 893 1_555 M CA CA . C CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc12 C OE2 GLU 893 C GLU 893 1_555 M CA CA . C CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc13 C OE1 GLN 896 C GLN 896 1_555 M CA CA . C CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc14 C OD1 ASN 918 C ASN 918 1_555 M CA CA . C CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc15 C OD2 ASP 921 C ASP 921 1_555 M CA CA . C CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc16 D OE1 GLU 893 D GLU 893 1_555 O CA CA . D CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc17 D OE2 GLU 893 D GLU 893 1_555 O CA CA . D CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc18 D OE1 GLN 896 D GLN 896 1_555 O CA CA . D CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc19 D OD1 ASN 918 D ASN 918 1_555 O CA CA . D CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc20 D OD2 ASP 921 D ASP 921 1_555 O CA CA . D CA 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? # _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 9JJE _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 I 3 CA A 1 4000 4000 CA CA . J 4 A2R A 1 4001 4001 A2R A2R . K 3 CA B 1 4000 4000 CA CA . L 4 A2R B 1 4001 4001 A2R A2R . M 3 CA C 1 4000 4000 CA CA . N 4 A2R C 1 4001 4001 A2R A2R . O 3 CA D 1 4000 4000 CA CA . P 4 A2R D 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 . . . L 4 204.762 131.47 224.744 1 85.53 ? OP3 A2R 4001 B 1 HETATM 2 P P2' A2R . . . L 4 205.312 131.662 226.145 1 85.53 ? P2' A2R 4001 B 1 HETATM 3 O OP1 A2R . . . L 4 206.7 132.264 226.082 1 85.53 ? OP1 A2R 4001 B 1 HETATM 4 O OP2 A2R . . . L 4 205.382 130.302 226.831 1 85.53 ? OP2 A2R 4001 B 1 HETATM 5 O O2' A2R . . . L 4 204.307 132.645 227.024 1 85.53 ? O2' A2R 4001 B 1 HETATM 6 C C2' A2R . . . L 4 204.51 134.118 227.055 1 85.53 ? C2' A2R 4001 B 1 HETATM 7 C C1' A2R . . . L 4 204.516 134.732 225.543 1 85.53 ? C1' A2R 4001 B 1 HETATM 8 N N9 A2R . . . L 4 205.4 135.868 225.371 1 85.53 ? N9 A2R 4001 B 1 HETATM 9 C C4 A2R . . . L 4 206.162 136.07 224.299 1 85.53 ? C4 A2R 4001 B 1 HETATM 10 N N3 A2R . . . L 4 206.316 135.331 223.178 1 85.53 ? N3 A2R 4001 B 1 HETATM 11 C C2 A2R . . . L 4 207.234 135.742 222.099 1 85.53 ? C2 A2R 4001 B 1 HETATM 12 N N1 A2R . . . L 4 207.996 136.966 222.237 1 85.53 ? N1 A2R 4001 B 1 HETATM 13 C C6 A2R . . . L 4 207.836 137.751 223.422 1 85.53 ? C6 A2R 4001 B 1 HETATM 14 N N6 A2R . . . L 4 208.558 138.942 223.592 1 85.53 ? N6 A2R 4001 B 1 HETATM 15 C C5 A2R . . . L 4 206.861 137.251 224.492 1 85.53 ? C5 A2R 4001 B 1 HETATM 16 N N7 A2R . . . L 4 206.512 137.746 225.665 1 85.53 ? N7 A2R 4001 B 1 HETATM 17 C C8 A2R . . . L 4 205.6 136.9 226.222 1 85.53 ? C8 A2R 4001 B 1 HETATM 18 O O4' A2R . . . L 4 203.28 135.035 225.208 1 85.53 ? O4' A2R 4001 B 1 HETATM 19 C C3' A2R . . . L 4 203.287 134.741 227.674 1 85.53 ? C3' A2R 4001 B 1 HETATM 20 O O3' A2R . . . L 4 202.649 133.814 228.659 1 85.53 ? O3' A2R 4001 B 1 HETATM 21 C C4' A2R . . . L 4 202.37 134.915 226.403 1 85.53 ? C4' A2R 4001 B 1 HETATM 22 C C5' A2R . . . L 4 201.6 136.088 226.515 1 85.53 ? C5' A2R 4001 B 1 HETATM 23 O O5' A2R . . . L 4 201.835 136.857 225.323 1 85.53 ? O5' A2R 4001 B 1 HETATM 24 P P A2R . . . L 4 201.597 138.543 225.403 1 85.53 ? P A2R 4001 B 1 HETATM 25 O O1 A2R . . . L 4 200.983 138.891 226.735 1 85.53 ? O1 A2R 4001 B 1 HETATM 26 O O2 A2R . . . L 4 200.674 138.95 224.291 1 85.53 ? O2 A2R 4001 B 1 HETATM 27 O O3 A2R . . . L 4 203.073 139.32 225.238 1 85.53 ? O3 A2R 4001 B 1 HETATM 28 P P1 A2R . . . L 4 203.395 140.835 225.955 1 85.53 ? P1 A2R 4001 B 1 HETATM 29 O O11 A2R . . . L 4 202.415 141.865 225.424 1 85.53 ? O11 A2R 4001 B 1 HETATM 30 O O12 A2R . . . L 4 203.247 140.725 227.454 1 85.53 ? O12 A2R 4001 B 1 HETATM 31 O O15' A2R . . . L 4 204.957 141.301 225.578 1 85.53 ? O15' A2R 4001 B 1 HETATM 32 C C15' A2R . . . L 4 205.447 141.12 224.234 1 85.53 ? C15' A2R 4001 B 1 HETATM 33 C C14' A2R . . . L 4 206.679 141.792 224.063 1 85.53 ? C14' A2R 4001 B 1 HETATM 34 C C13' A2R . . . L 4 206.771 143.076 224.933 1 85.53 ? C13' A2R 4001 B 1 HETATM 35 O O13' A2R . . . L 4 207.844 142.919 225.95 1 85.53 ? O13' A2R 4001 B 1 HETATM 36 C C12' A2R . . . L 4 207.117 144.041 224.12 1 85.53 ? C12' A2R 4001 B 1 HETATM 37 O O12' A2R . . . L 4 208.571 144.229 224.174 1 85.53 ? O12' A2R 4001 B 1 HETATM 38 C C11' A2R . . . L 4 206.671 143.574 222.639 1 85.53 ? C11' A2R 4001 B 1 HETATM 39 O O14' A2R . . . L 4 206.824 142.269 222.604 1 85.53 ? O14' A2R 4001 B 1 HETATM 40 O O11' A2R . . . L 4 205.346 143.902 222.417 1 85.53 ? O11' A2R 4001 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 107 _model_server_stats.query_time_ms 519 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #