data_9JJE # _model_server_result.job_id 4GtY5h_m9_lCjMLBcUcjNw _model_server_result.datetime_utc '2024-12-04 05:11:14' _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":"P","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 . . . P 4 146.201 219.495 224.74 1 85.76 ? OP3 A2R 4001 D 1 HETATM 2 P P2' A2R . . . P 4 145.651 219.303 226.141 1 85.76 ? P2' A2R 4001 D 1 HETATM 3 O OP1 A2R . . . P 4 144.263 218.702 226.078 1 85.76 ? OP1 A2R 4001 D 1 HETATM 4 O OP2 A2R . . . P 4 145.581 220.663 226.827 1 85.76 ? OP2 A2R 4001 D 1 HETATM 5 O O2' A2R . . . P 4 146.656 218.32 227.02 1 85.76 ? O2' A2R 4001 D 1 HETATM 6 C C2' A2R . . . P 4 146.453 216.848 227.051 1 85.76 ? C2' A2R 4001 D 1 HETATM 7 C C1' A2R . . . P 4 146.447 216.234 225.538 1 85.76 ? C1' A2R 4001 D 1 HETATM 8 N N9 A2R . . . P 4 145.563 215.097 225.367 1 85.76 ? N9 A2R 4001 D 1 HETATM 9 C C4 A2R . . . P 4 144.801 214.895 224.295 1 85.76 ? C4 A2R 4001 D 1 HETATM 10 N N3 A2R . . . P 4 144.647 215.633 223.174 1 85.76 ? N3 A2R 4001 D 1 HETATM 11 C C2 A2R . . . P 4 143.729 215.222 222.095 1 85.76 ? C2 A2R 4001 D 1 HETATM 12 N N1 A2R . . . P 4 142.967 213.999 222.233 1 85.76 ? N1 A2R 4001 D 1 HETATM 13 C C6 A2R . . . P 4 143.127 213.214 223.419 1 85.76 ? C6 A2R 4001 D 1 HETATM 14 N N6 A2R . . . P 4 142.405 212.023 223.588 1 85.76 ? N6 A2R 4001 D 1 HETATM 15 C C5 A2R . . . P 4 144.102 213.714 224.488 1 85.76 ? C5 A2R 4001 D 1 HETATM 16 N N7 A2R . . . P 4 144.451 213.22 225.661 1 85.76 ? N7 A2R 4001 D 1 HETATM 17 C C8 A2R . . . P 4 145.364 214.066 226.218 1 85.76 ? C8 A2R 4001 D 1 HETATM 18 O O4' A2R . . . P 4 147.683 215.931 225.204 1 85.76 ? O4' A2R 4001 D 1 HETATM 19 C C3' A2R . . . P 4 147.676 216.224 227.67 1 85.76 ? C3' A2R 4001 D 1 HETATM 20 O O3' A2R . . . P 4 148.314 217.151 228.655 1 85.76 ? O3' A2R 4001 D 1 HETATM 21 C C4' A2R . . . P 4 148.593 216.05 226.399 1 85.76 ? C4' A2R 4001 D 1 HETATM 22 C C5' A2R . . . P 4 149.363 214.876 226.511 1 85.76 ? C5' A2R 4001 D 1 HETATM 23 O O5' A2R . . . P 4 149.128 214.108 225.319 1 85.76 ? O5' A2R 4001 D 1 HETATM 24 P P A2R . . . P 4 149.366 212.422 225.399 1 85.76 ? P A2R 4001 D 1 HETATM 25 O O1 A2R . . . P 4 149.981 212.074 226.73 1 85.76 ? O1 A2R 4001 D 1 HETATM 26 O O2 A2R . . . P 4 150.289 212.014 224.286 1 85.76 ? O2 A2R 4001 D 1 HETATM 27 O O3 A2R . . . P 4 147.89 211.645 225.234 1 85.76 ? O3 A2R 4001 D 1 HETATM 28 P P1 A2R . . . P 4 147.569 210.13 225.951 1 85.76 ? P1 A2R 4001 D 1 HETATM 29 O O11 A2R . . . P 4 148.548 209.1 225.42 1 85.76 ? O11 A2R 4001 D 1 HETATM 30 O O12 A2R . . . P 4 147.717 210.24 227.45 1 85.76 ? O12 A2R 4001 D 1 HETATM 31 O O15' A2R . . . P 4 146.007 209.664 225.573 1 85.76 ? O15' A2R 4001 D 1 HETATM 32 C C15' A2R . . . P 4 145.516 209.845 224.23 1 85.76 ? C15' A2R 4001 D 1 HETATM 33 C C14' A2R . . . P 4 144.284 209.172 224.059 1 85.76 ? C14' A2R 4001 D 1 HETATM 34 C C13' A2R . . . P 4 144.192 207.889 224.929 1 85.76 ? C13' A2R 4001 D 1 HETATM 35 O O13' A2R . . . P 4 143.119 208.046 225.946 1 85.76 ? O13' A2R 4001 D 1 HETATM 36 C C12' A2R . . . P 4 143.846 206.924 224.116 1 85.76 ? C12' A2R 4001 D 1 HETATM 37 O O12' A2R . . . P 4 142.392 206.736 224.17 1 85.76 ? O12' A2R 4001 D 1 HETATM 38 C C11' A2R . . . P 4 144.292 207.391 222.635 1 85.76 ? C11' A2R 4001 D 1 HETATM 39 O O14' A2R . . . P 4 144.139 208.696 222.6 1 85.76 ? O14' A2R 4001 D 1 HETATM 40 O O11' A2R . . . P 4 145.617 207.063 222.413 1 85.76 ? O11' A2R 4001 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 125 _model_server_stats.query_time_ms 454 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 40 #