data_6M7V # _model_server_result.job_id KhS3Ui7V-xovG-xOXCyS1Q _model_server_result.datetime_utc '2024-11-17 16:33:32' _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 6m7v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 6M7V # _exptl.entry_id 6M7V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 490.197 _entity.id 5 _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 90 _cell.entry_id 6M7V _cell.length_a 63.075 _cell.length_b 81.387 _cell.length_c 145.006 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M7V _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,J _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 5 _struct_asym.id E _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 C O3' 02I 1 T 02I 4 1_555 C P DC 2 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 G MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc4 A OD1 ASP 118 A ASP 115 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 G MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc6 A OE2 GLU 119 A GLU 116 1_555 G MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc7 A OD2 ASP 184 A ASP 181 1_555 D NI NI . A NI 501 2_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc8 A NE2 HIS 292 A HIS 289 1_555 D NI NI . A NI 501 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.777 ? metalc ? metalc9 A NE2 HIS 396 A HIS 393 1_555 D NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc10 A NE2 HIS 400 A HIS 397 1_555 D NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc11 E O1A DZ4 . A DZ4 502 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc12 E O1B DZ4 . A DZ4 502 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc13 E O1G DZ4 . A DZ4 502 1_555 F MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc14 E O1A DZ4 . A DZ4 502 1_555 G MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc15 G MN MN . A MN 504 1_555 H O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc16 G MN MN . A MN 504 1_555 B OP1 DT 8 P DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 P DG 2 1_555 C N3 DC 8 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 P DG 2 1_555 C O2 DC 8 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 P DG 2 1_555 C N4 DC 8 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 2 P DT 3 1_555 C N1 DA 7 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 2 P DT 3 1_555 C N6 DA 7 T DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DG 3 P DG 4 1_555 C N3 DC 6 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 DG 3 P DG 4 1_555 C O2 DC 6 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 DG 3 P DG 4 1_555 C N4 DC 6 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DT 4 P DT 5 1_555 C N1 DA 5 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O4 DT 4 P DT 5 1_555 C N6 DA 5 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DG 5 P DG 6 1_555 C N3 DC 4 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 DG 5 P DG 6 1_555 C O2 DC 4 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 5 P DG 6 1_555 C N4 DC 4 T DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 6 P DA 7 1_555 C N3 DT 3 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 6 P DA 7 1_555 C O4 DT 3 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 7 P DG 8 1_555 C N3 DC 2 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 7 P DG 8 1_555 C O2 DC 2 T DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 7 P DG 8 1_555 C N4 DC 2 T DC 5 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 6M7V _atom_sites.fract_transf_matrix[1][1] 0.015854 _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] 0.012287 _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] 0.006896 _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 NI A 1 501 452 NI NI . E 5 DZ4 A 1 502 433 DZ4 DZ4 . F 6 MN A 1 503 1 MN MN . G 6 MN A 1 504 2 MN MN . H 7 HOH A 1 601 15 HOH HOH . H 7 HOH A 2 602 13 HOH HOH . H 7 HOH A 3 603 10 HOH HOH . H 7 HOH A 4 604 42 HOH HOH . H 7 HOH A 5 605 27 HOH HOH . H 7 HOH A 6 606 1 HOH HOH . H 7 HOH A 7 607 14 HOH HOH . H 7 HOH A 8 608 2 HOH HOH . H 7 HOH A 9 609 41 HOH HOH . H 7 HOH A 10 610 17 HOH HOH . H 7 HOH A 11 611 5 HOH HOH . H 7 HOH A 12 612 37 HOH HOH . I 7 HOH P 1 101 21 HOH HOH . I 7 HOH P 2 102 3 HOH HOH . I 7 HOH P 3 103 40 HOH HOH . J 7 HOH T 1 101 18 HOH HOH . J 7 HOH T 2 102 9 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 . . . E 5 -3.085 -3.323 26.301 1 52.45 ? N1 DZ4 502 A 1 HETATM 2 C C2 DZ4 . . . E 5 -2.329 -4.406 26.318 1 42.48 ? C2 DZ4 502 A 1 HETATM 3 N N3 DZ4 . . . E 5 -1.678 -4.971 25.326 1 35.15 ? N3 DZ4 502 A 1 HETATM 4 C C4 DZ4 . . . E 5 -1.792 -4.36 24.133 1 35.48 ? C4 DZ4 502 A 1 HETATM 5 C C5 DZ4 . . . E 5 -2.569 -3.204 24.018 1 34.82 ? C5 DZ4 502 A 1 HETATM 6 C C6 DZ4 . . . E 5 -3.212 -2.7 25.129 1 43.73 ? C6 DZ4 502 A 1 HETATM 7 N N6 DZ4 . . . E 5 -3.965 -1.594 25.053 1 41.1 ? N6 DZ4 502 A 1 HETATM 8 N N7 DZ4 . . . E 5 -2.515 -2.798 22.729 1 30.82 ? N7 DZ4 502 A 1 HETATM 9 C C8 DZ4 . . . E 5 -1.734 -3.662 22.055 1 33.48 ? C8 DZ4 502 A 1 HETATM 10 N N9 DZ4 . . . E 5 -1.295 -4.613 22.911 1 37.24 ? N9 DZ4 502 A 1 HETATM 11 P PA DZ4 . . . E 5 0.767 -3.362 17.777 1 20.08 ? PA DZ4 502 A 1 HETATM 12 P PB DZ4 . . . E 5 -0.015 -5.735 16.461 1 34.79 ? PB DZ4 502 A 1 HETATM 13 P PG DZ4 . . . E 5 0.224 -4.758 13.721 1 17.37 ? PG DZ4 502 A 1 HETATM 14 C C1' DZ4 . . . E 5 -0.464 -5.584 22.325 1 34.16 ? C1' DZ4 502 A 1 HETATM 15 O O1A DZ4 . . . E 5 2.016 -3.451 17.026 1 26.81 ? O1A DZ4 502 A 1 HETATM 16 O O1B DZ4 . . . E 5 1.379 -6.048 16.762 1 27.06 ? O1B DZ4 502 A 1 HETATM 17 O O1G DZ4 . . . E 5 1.647 -4.938 13.458 1 24.28 ? O1G DZ4 502 A 1 HETATM 18 C C2' DZ4 . . . E 5 -1.245 -6.377 21.289 1 36.76 ? C2' DZ4 502 A 1 HETATM 19 O O2A DZ4 . . . E 5 0.307 -1.873 17.843 1 25.41 ? O2A DZ4 502 A 1 HETATM 20 O O2B DZ4 . . . E 5 -0.919 -6.774 17.113 1 28.87 ? O2B DZ4 502 A 1 HETATM 21 O O2G DZ4 . . . E 5 -0.553 -5.052 12.483 1 27.28 ? O2G DZ4 502 A 1 HETATM 22 C C3' DZ4 . . . E 5 -0.268 -6.585 20.136 1 30.59 ? C3' DZ4 502 A 1 HETATM 23 O O3' DZ4 . . . E 5 -0.03 -7.98 19.935 1 40.87 ? O3' DZ4 502 A 1 HETATM 24 N N3A DZ4 . . . E 5 -0.379 -4.255 17.038 1 32.65 ? N3A DZ4 502 A 1 HETATM 25 O O3B DZ4 . . . E 5 -0.235 -5.753 14.886 1 20.49 ? O3B DZ4 502 A 1 HETATM 26 O O3G DZ4 . . . E 5 -0.032 -3.32 14.149 1 21.4 ? O3G DZ4 502 A 1 HETATM 27 C C4' DZ4 . . . E 5 1.014 -5.883 20.584 1 30.01 ? C4' DZ4 502 A 1 HETATM 28 O O4' DZ4 . . . E 5 0.603 -4.957 21.623 1 28.76 ? O4' DZ4 502 A 1 HETATM 29 C C5' DZ4 . . . E 5 1.642 -5.119 19.404 1 31.89 ? C5' DZ4 502 A 1 HETATM 30 O O5' DZ4 . . . E 5 0.988 -3.902 19.234 1 20.57 ? O5' DZ4 502 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #