data_9CJ9 # _model_server_result.job_id ME5_6e1SXdAWAKvQG1LXPA _model_server_result.datetime_utc '2024-11-27 14:55:38' _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 9cj9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 9CJ9 # _exptl.entry_id 9CJ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'incoming non-hydrolyzable nucleotide dAMPnPP' _entity.formula_weight 490.197 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine" _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 120 _cell.entry_id 9CJ9 _cell.length_a 98.08 _cell.length_b 98.08 _cell.length_c 78.66 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CJ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 B O3' DT 3 T DT 3 1_555 B P A1A0L 4 T A1A0L 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.632 ? covale ? covale2 B O2' A1A0L 4 T A1A0L 4 1_555 B P DA 5 T DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.629 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc2 A O MET 17 A MET 14 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc3 A OD2 ASP 118 A ASP 115 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc4 D O1B DZ4 . A DZ4 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.745 ? metalc ? metalc5 D O1A DZ4 . A DZ4 501 1_555 F MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.788 ? metalc ? metalc6 F MG MG . A MG 503 1_555 C O3' DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? hydrog WATSON-CRICK hydrog1 B N1 DA 5 T DA 5 1_555 C N3 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 5 T DA 5 1_555 C O4 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O4 DT 6 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DG 7 T DG 7 1_555 C N3 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N2 DG 7 T DG 7 1_555 C O2 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O6 DG 7 T DG 7 1_555 C N4 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 10 T DG 10 1_555 C N3 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 10 T DG 10 1_555 C O2 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 10 T DG 10 1_555 C N4 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 11 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 11 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 11 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 12 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 12 T DT 12 1_555 C N6 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H17 N6 O11 P3' _chem_comp.formula_weight 490.197 _chem_comp.id DZ4 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine" _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 C2 N1 DZ4 doub 269 n y N1 C6 DZ4 sing 270 n y N3 C2 DZ4 sing 271 n y C2 H2 DZ4 sing 272 n n N3 C4 DZ4 doub 273 n y N9 C4 DZ4 sing 274 n y C4 C5 DZ4 sing 275 n y C5 N7 DZ4 sing 276 n y C5 C6 DZ4 doub 277 n y C6 N6 DZ4 sing 278 n n N6 HN6 DZ4 sing 279 n n N6 HN6A DZ4 sing 280 n n C8 N7 DZ4 doub 281 n y N9 C8 DZ4 sing 282 n y C8 H8 DZ4 sing 283 n n C1' N9 DZ4 sing 284 n n O5' PA DZ4 sing 285 n n O1A PA DZ4 doub 286 n n PA O2A DZ4 sing 287 n n PA N3A DZ4 sing 288 n n O1B PB DZ4 doub 289 n n N3A PB DZ4 sing 290 n n PB O2B DZ4 sing 291 n n PB O3B DZ4 sing 292 n n O1G PG DZ4 doub 293 n n PG O3B DZ4 sing 294 n n PG O2G DZ4 sing 295 n n PG O3G DZ4 sing 296 n n O4' C1' DZ4 sing 297 n n C1' C2' DZ4 sing 298 n n C1' H1' DZ4 sing 299 n n C3' C2' DZ4 sing 300 n n C2' H2' DZ4 sing 301 n n C2' "H2'A" DZ4 sing 302 n n O2A HO2A DZ4 sing 303 n n O2B HO2B DZ4 sing 304 n n O2G HO2G DZ4 sing 305 n n C4' C3' DZ4 sing 306 n n C3' O3' DZ4 sing 307 n n C3' H3' DZ4 sing 308 n n O3' HO3' DZ4 sing 309 n n N3A HN3A DZ4 sing 310 n n O3G HO3G DZ4 sing 311 n n O4' C4' DZ4 sing 312 n n C4' C5' DZ4 sing 313 n n C4' H4' DZ4 sing 314 n n C5' O5' DZ4 sing 315 n n C5' H5' DZ4 sing 316 n n C5' "H5'A" DZ4 sing 317 n n # _atom_sites.entry_id 9CJ9 _atom_sites.fract_transf_matrix[1][1] 0.010196 _atom_sites.fract_transf_matrix[1][2] 0.005887 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011773 _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] 0.012713 _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 D 4 DZ4 A 1 501 501 DZ4 DZ4 . E 5 MG A 1 502 502 MG MG . F 5 MG A 1 503 503 MG MG . G 6 HOH A 1 601 4 HOH HOH . G 6 HOH A 2 602 10 HOH HOH . G 6 HOH A 3 603 14 HOH HOH . G 6 HOH A 4 604 20 HOH HOH . G 6 HOH A 5 605 31 HOH HOH . G 6 HOH A 6 606 27 HOH HOH . G 6 HOH A 7 607 32 HOH HOH . G 6 HOH A 8 608 7 HOH HOH . G 6 HOH A 9 609 34 HOH HOH . G 6 HOH A 10 610 25 HOH HOH . G 6 HOH A 11 611 30 HOH HOH . G 6 HOH A 12 612 5 HOH HOH . G 6 HOH A 13 613 22 HOH HOH . G 6 HOH A 14 614 29 HOH HOH . G 6 HOH A 15 615 9 HOH HOH . G 6 HOH A 16 616 33 HOH HOH . G 6 HOH A 17 617 26 HOH HOH . G 6 HOH A 18 618 18 HOH HOH . G 6 HOH A 19 619 23 HOH HOH . G 6 HOH A 20 620 12 HOH HOH . G 6 HOH A 21 621 8 HOH HOH . G 6 HOH A 22 622 21 HOH HOH . G 6 HOH A 23 623 11 HOH HOH . G 6 HOH A 24 624 15 HOH HOH . G 6 HOH A 25 625 17 HOH HOH . G 6 HOH A 26 626 3 HOH HOH . G 6 HOH A 27 627 13 HOH HOH . G 6 HOH A 28 628 19 HOH HOH . G 6 HOH A 29 629 1 HOH HOH . G 6 HOH A 30 630 6 HOH HOH . H 6 HOH T 1 101 24 HOH HOH . H 6 HOH T 2 102 28 HOH HOH . H 6 HOH T 3 103 2 HOH HOH . I 6 HOH P 1 101 16 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 N N1 DZ4 . . . D 4 -43.721 -3.65 9.742 1 45.48 ? N1 DZ4 501 A 1 HETATM 2 C C2 DZ4 . . . D 4 -43.93 -4.657 8.866 1 49.47 ? C2 DZ4 501 A 1 HETATM 3 N N3 DZ4 . . . D 4 -45.205 -4.935 8.457 1 48.98 ? N3 DZ4 501 A 1 HETATM 4 C C4 DZ4 . . . D 4 -46.245 -4.213 8.924 1 46.72 ? C4 DZ4 501 A 1 HETATM 5 C C5 DZ4 . . . D 4 -46.025 -3.22 9.796 1 48.92 ? C5 DZ4 501 A 1 HETATM 6 C C6 DZ4 . . . D 4 -44.746 -2.938 10.21 1 44.77 ? C6 DZ4 501 A 1 HETATM 7 N N6 DZ4 . . . D 4 -44.199 -1.948 11.134 1 48.38 ? N6 DZ4 501 A 1 HETATM 8 N N7 DZ4 . . . D 4 -47.214 -2.658 10.112 1 51.21 ? N7 DZ4 501 A 1 HETATM 9 C C8 DZ4 . . . D 4 -48.182 -3.31 9.428 1 42.35 ? C8 DZ4 501 A 1 HETATM 10 N N9 DZ4 . . . D 4 -47.595 -4.268 8.696 1 43.36 ? N9 DZ4 501 A 1 HETATM 11 P PA DZ4 . . . D 4 -51.684 -2.166 8.819 1 44.89 ? PA DZ4 501 A 1 HETATM 12 P PB DZ4 . . . D 4 -53.927 -3.931 9.614 1 41.27 ? PB DZ4 501 A 1 HETATM 13 P PG DZ4 . . . D 4 -55.832 -2.382 10.907 1 45.32 ? PG DZ4 501 A 1 HETATM 14 C C1' DZ4 . . . D 4 -48.032 -5.21 7.83 1 41.61 ? C1' DZ4 501 A 1 HETATM 15 O O1A DZ4 . . . D 4 -52.102 -1.331 7.669 1 29.71 ? O1A DZ4 501 A 1 HETATM 16 O O1B DZ4 . . . D 4 -54.485 -3.942 8.212 1 29.57 ? O1B DZ4 501 A 1 HETATM 17 O O1G DZ4 . . . D 4 -57.211 -2.672 11.463 1 42.52 ? O1G DZ4 501 A 1 HETATM 18 C C2' DZ4 . . . D 4 -48.894 -6.274 8.514 1 34.61 ? C2' DZ4 501 A 1 HETATM 19 O O2A DZ4 . . . D 4 -50.527 -1.487 9.555 1 31.14 ? O2A DZ4 501 A 1 HETATM 20 O O2B DZ4 . . . D 4 -53.107 -5.137 9.891 1 34.32 ? O2B DZ4 501 A 1 HETATM 21 O O2G DZ4 . . . D 4 -54.943 -1.615 11.797 1 36.37 ? O2G DZ4 501 A 1 HETATM 22 C C3' DZ4 . . . D 4 -50.144 -5.972 8.213 1 30.16 ? C3' DZ4 501 A 1 HETATM 23 O O3' DZ4 . . . D 4 -50.972 -7.177 8.069 1 27.04 ? O3' DZ4 501 A 1 HETATM 24 N N3A DZ4 . . . D 4 -52.99 -2.434 9.875 1 44.47 ? N3A DZ4 501 A 1 HETATM 25 O O3B DZ4 . . . D 4 -55.149 -3.883 10.67 1 36.11 ? O3B DZ4 501 A 1 HETATM 26 O O3G DZ4 . . . D 4 -55.941 -1.629 9.651 1 36.72 ? O3G DZ4 501 A 1 HETATM 27 C C4' DZ4 . . . D 4 -50.108 -5.16 6.824 1 29.96 ? C4' DZ4 501 A 1 HETATM 28 O O4' DZ4 . . . D 4 -48.946 -4.577 6.726 1 43.61 ? O4' DZ4 501 A 1 HETATM 29 C C5' DZ4 . . . D 4 -51.178 -4.088 6.929 1 31.93 ? C5' DZ4 501 A 1 HETATM 30 O O5' DZ4 . . . D 4 -51.317 -3.743 8.313 1 35.57 ? O5' DZ4 501 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 30 #