data_5KNY # _model_server_result.job_id rlg9jTT6BjcnQIH3i8Xycw _model_server_result.datetime_utc '2024-11-16 08:40:39' _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 5kny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5KNY # _exptl.entry_id 5KNY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 496.306 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y l]-3-oxidanylidene-propyl]phosphonic acid' _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 105.95 _cell.angle_gamma 90 _cell.entry_id 5KNY _cell.length_a 54.523 _cell.length_b 86.075 _cell.length_c 79.824 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KNY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 1 1 A,B,E,F,G,H,M,N 2 1 C,D,I,J,K,L,O,P 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K N 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 metalc ? metalc1 A OD1 ASP 187 A ASP 182 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 E OAI YPG . A YPG 301 1_555 F MG MG . A MG 302 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc3 E OAB YPG . A YPG 301 1_555 F MG MG . A MG 302 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc4 E OAH YPG . A YPG 301 1_555 F MG MG . A MG 302 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc5 F MG MG . A MG 302 1_555 M O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc6 F MG MG . A MG 302 1_555 M O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc7 F MG MG . A MG 302 1_555 M O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc8 B OD1 ASP 187 B ASP 182 1_555 H MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc9 G OAI YPG . B YPG 301 1_555 H MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc10 H MG MG . B MG 302 1_555 N O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc11 H MG MG . B MG 302 1_555 N O HOH . B HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc12 H MG MG . B MG 302 1_555 N O HOH . B HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc13 C OD1 ASP 187 C ASP 182 1_555 J MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc14 I OAI YPG . C YPG 301 1_555 J MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc15 J MG MG . C MG 302 1_555 O O HOH . C HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc16 D OD2 ASP 187 D ASP 182 1_555 L MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc17 K OAI YPG . D YPG 301 1_555 L MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? # _chem_comp.formula 'C14 H22 N6 O10 P2' _chem_comp.formula_weight 496.306 _chem_comp.id YPG _chem_comp.mon_nstd_flag . _chem_comp.name '[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y l]-3-oxidanylidene-propyl]phosphonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine' # 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 OAJ PBF YPG doub 376 n n OAI PBF YPG sing 377 n n OAF CAZ YPG sing 378 n n PBF CAZ YPG sing 379 n n PBF OAE YPG sing 380 n n CAZ CAN YPG sing 381 n n CAN OAT YPG sing 382 n n OAT CBA YPG sing 383 n n CBA CAO YPG sing 384 n n CBA CBB YPG sing 385 n n CAO NBC YPG sing 386 n n OAH PBE YPG doub 387 n n C8 N7 YPG doub 388 n y C8 N9 YPG sing 389 n y N7 C5 YPG sing 390 n y CBB N9 YPG sing 391 n n CBB CAP YPG sing 392 n n N9 C4 YPG sing 393 n y CAL CAM YPG sing 394 n n CAL CAU YPG sing 395 n n NBC CAU YPG sing 396 n n NBC CAP YPG sing 397 n n C5 C4 YPG doub 398 n y C5 C6 YPG sing 399 n n C4 N3 YPG sing 400 n n CAM PBE YPG sing 401 n n PBE OAG YPG sing 402 n n PBE OAD YPG sing 403 n n CAU OAB YPG doub 404 n n O6 C6 YPG doub 405 n n C6 N1 YPG sing 406 n n N3 C2 YPG doub 407 n n N1 C2 YPG sing 408 n n C2 N2 YPG sing 409 n n C8 H1 YPG sing 410 n n N1 H2 YPG sing 411 n n N2 H3 YPG sing 412 n n N2 H4 YPG sing 413 n n OAI H5 YPG sing 414 n n OAE H6 YPG sing 415 n n CAZ H7 YPG sing 416 n n OAF H8 YPG sing 417 n n CAN H9 YPG sing 418 n n CAN H10 YPG sing 419 n n CBA H11 YPG sing 420 n n CAO H12 YPG sing 421 n n CAO H13 YPG sing 422 n n CAL H14 YPG sing 423 n n CAL H15 YPG sing 424 n n CAM H16 YPG sing 425 n n CAM H17 YPG sing 426 n n OAG H18 YPG sing 427 n n OAD H19 YPG sing 428 n n CAP H20 YPG sing 429 n n CAP H21 YPG sing 430 n n CBB H22 YPG sing 431 n n # _atom_sites.entry_id 5KNY _atom_sites.fract_transf_matrix[1][1] 0.018341 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005242 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011618 _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] 0.013029 _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 E 2 YPG A 1 301 1 YPG DRG . F 3 MG A 1 302 2 MG MG . G 2 YPG B 1 301 2 YPG DRG . H 3 MG B 1 302 1 MG MG . I 2 YPG C 1 301 3 YPG DRG . J 3 MG C 1 302 5 MG MG . K 2 YPG D 1 301 4 YPG DRG . L 3 MG D 1 302 3 MG MG . M 4 HOH A 1 401 26 HOH HOH . M 4 HOH A 2 402 28 HOH HOH . M 4 HOH A 3 403 4 HOH HOH . M 4 HOH A 4 404 25 HOH HOH . M 4 HOH A 5 405 33 HOH HOH . M 4 HOH A 6 406 22 HOH HOH . M 4 HOH A 7 407 5 HOH HOH . N 4 HOH B 1 401 7 HOH HOH . N 4 HOH B 2 402 11 HOH HOH . N 4 HOH B 3 403 3 HOH HOH . N 4 HOH B 4 404 19 HOH HOH . N 4 HOH B 5 405 21 HOH HOH . N 4 HOH B 6 406 12 HOH HOH . N 4 HOH B 7 407 1 HOH HOH . N 4 HOH B 8 408 20 HOH HOH . N 4 HOH B 9 409 8 HOH HOH . N 4 HOH B 10 410 23 HOH HOH . O 4 HOH C 1 401 2 HOH HOH . O 4 HOH C 2 402 29 HOH HOH . O 4 HOH C 3 403 34 HOH HOH . O 4 HOH C 4 404 35 HOH HOH . O 4 HOH C 5 405 30 HOH HOH . O 4 HOH C 6 406 27 HOH HOH . P 4 HOH D 1 401 36 HOH HOH . P 4 HOH D 2 402 9 HOH HOH . P 4 HOH D 3 403 10 HOH HOH . P 4 HOH D 4 404 14 HOH HOH . P 4 HOH D 5 405 32 HOH HOH . P 4 HOH D 6 406 24 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 C C4 YPG . A . E 2 59.49 72.36 26.545 0.65 44.28 ? C4 YPG 301 A 1 HETATM 2 C C4 YPG . B . E 2 59.803 72.089 26.522 0.35 43.18 ? C4 YPG 301 A 1 HETATM 3 C C5 YPG . A . E 2 59.437 71.389 27.511 0.65 39.74 ? C5 YPG 301 A 1 HETATM 4 C C5 YPG . B . E 2 59.485 71.061 27.366 0.35 38.61 ? C5 YPG 301 A 1 HETATM 5 C C6 YPG . A . E 2 58.763 71.631 28.687 0.65 40.36 ? C6 YPG 301 A 1 HETATM 6 C C6 YPG . B . E 2 58.703 71.31 28.474 0.35 43.85 ? C6 YPG 301 A 1 HETATM 7 C C8 YPG . A . E 2 60.595 70.652 25.779 0.65 42.28 ? C8 YPG 301 A 1 HETATM 8 C C8 YPG . B . E 2 60.746 70.304 25.704 0.35 41.33 ? C8 YPG 301 A 1 HETATM 9 N N1 YPG . A . E 2 58.146 72.849 28.883 0.65 37.57 ? N1 YPG 301 A 1 HETATM 10 N N1 YPG . B . E 2 58.246 72.59 28.726 0.35 36.58 ? N1 YPG 301 A 1 HETATM 11 N N2 YPG . A . E 2 57.576 75.106 28.061 0.65 38.76 ? N2 YPG 301 A 1 HETATM 12 N N2 YPG . B . E 2 58.126 74.979 28.078 0.35 37.37 ? N2 YPG 301 A 1 HETATM 13 N N3 YPG . A . E 2 58.9 73.541 26.719 0.65 36.86 ? N3 YPG 301 A 1 HETATM 14 N N3 YPG . B . E 2 59.369 73.33 26.759 0.35 36.9 ? N3 YPG 301 A 1 HETATM 15 O OAI YPG . A . E 2 60.62 77.632 24.314 0.65 33.66 ? OAI YPG 301 A 1 HETATM 16 O OAI YPG . B . E 2 66.117 69.712 22.305 0.35 79.37 ? OAI YPG 301 A 1 HETATM 17 P PBF YPG . A . E 2 61.768 77.645 23.325 0.65 33.36 ? PBF YPG 301 A 1 HETATM 18 P PBF YPG . B . E 2 65.123 68.628 22.67 0.35 75.08 ? PBF YPG 301 A 1 HETATM 19 O OAJ YPG . A . E 2 63.076 77.684 24.08 0.65 32.77 ? OAJ YPG 301 A 1 HETATM 20 O OAJ YPG . B . E 2 65.555 67.316 22.057 0.35 79.33 ? OAJ YPG 301 A 1 HETATM 21 O OAE YPG . A . E 2 61.66 78.876 22.453 0.65 32.96 ? OAE YPG 301 A 1 HETATM 22 O OAE YPG . B . E 2 65.062 68.485 24.174 0.35 73.04 ? OAE YPG 301 A 1 HETATM 23 C CAZ YPG . A . E 2 61.701 76.155 22.3 0.65 34.5 ? CAZ YPG 301 A 1 HETATM 24 C CAZ YPG . B . E 2 63.488 69.076 22.048 0.35 59.64 ? CAZ YPG 301 A 1 HETATM 25 O OAF YPG . A . E 2 60.928 76.401 21.153 0.65 34.24 ? OAF YPG 301 A 1 HETATM 26 O OAF YPG . B . E 2 63.593 70.113 21.107 0.35 59.94 ? OAF YPG 301 A 1 HETATM 27 C CAN YPG . A . E 2 61.075 75.007 23.085 0.65 35.95 ? CAN YPG 301 A 1 HETATM 28 C CAN YPG . B . E 2 62.613 69.512 23.218 0.35 56.05 ? CAN YPG 301 A 1 HETATM 29 O OAT YPG . A . E 2 62.042 74.422 23.951 0.65 38.9 ? OAT YPG 301 A 1 HETATM 30 O OAT YPG . B . E 2 62.81 70.88 23.57 0.35 50.34 ? OAT YPG 301 A 1 HETATM 31 C CBA YPG . A . E 2 61.865 73.038 24.342 0.65 41.63 ? CBA YPG 301 A 1 HETATM 32 C CBA YPG . B . E 2 61.655 71.699 23.302 0.35 44.54 ? CBA YPG 301 A 1 HETATM 33 C CAO YPG . A . E 2 62.708 72.121 23.454 0.65 47.43 ? CAO YPG 301 A 1 HETATM 34 C CAO YPG . B . E 2 62.007 72.866 22.378 0.35 44.85 ? CAO YPG 301 A 1 HETATM 35 N NBC YPG . A . E 2 61.698 70.999 23.157 0.65 49.59 ? NBC YPG 301 A 1 HETATM 36 N NBC YPG . B . E 2 60.883 73.865 22.744 0.35 39.83 ? NBC YPG 301 A 1 HETATM 37 C CAU YPG . A . E 2 61.967 69.58 22.992 0.65 54.81 ? CAU YPG 301 A 1 HETATM 38 C CAU YPG . B . E 2 60.646 75.209 22.242 0.35 33.73 ? CAU YPG 301 A 1 HETATM 39 O OAB YPG . A . E 2 61.049 68.806 22.781 0.65 52.13 ? OAB YPG 301 A 1 HETATM 40 O OAB YPG . B . E 2 59.695 75.838 22.67 0.35 30.69 ? OAB YPG 301 A 1 HETATM 41 C CAL YPG . A . E 2 63.415 69.049 23.09 0.65 58.72 ? CAL YPG 301 A 1 HETATM 42 C CAL YPG . B . E 2 61.568 75.864 21.19 0.35 33.78 ? CAL YPG 301 A 1 HETATM 43 C CAM YPG . A . E 2 64.11 69.007 21.724 0.65 64.02 ? CAM YPG 301 A 1 HETATM 44 C CAM YPG . B . E 2 62.783 76.476 21.92 0.35 34.58 ? CAM YPG 301 A 1 HETATM 45 P PBE YPG . A . E 2 65.868 68.494 22.041 0.65 79.15 ? PBE YPG 301 A 1 HETATM 46 P PBE YPG . B . E 2 62.317 77.853 23.092 0.35 33.41 ? PBE YPG 301 A 1 HETATM 47 O OAG YPG . A . E 2 66.262 67.449 21.023 0.65 80.74 ? OAG YPG 301 A 1 HETATM 48 O OAG YPG . B . E 2 63.563 78.353 23.788 0.35 34.3 ? OAG YPG 301 A 1 HETATM 49 O OAH YPG . A . E 2 66.784 69.7 21.922 0.65 80.31 ? OAH YPG 301 A 1 HETATM 50 O OAH YPG . B . E 2 61.35 77.368 24.16 0.35 33.72 ? OAH YPG 301 A 1 HETATM 51 O OAD YPG . A . E 2 65.98 67.918 23.439 0.65 74.99 ? OAD YPG 301 A 1 HETATM 52 O OAD YPG . B . E 2 61.684 78.998 22.326 0.35 33.4 ? OAD YPG 301 A 1 HETATM 53 C CAP YPG . A . E 2 60.368 71.647 23.132 0.65 45.71 ? CAP YPG 301 A 1 HETATM 54 C CAP YPG . B . E 2 60.049 73.2 23.774 0.35 41.92 ? CAP YPG 301 A 1 HETATM 55 C CBB YPG . A . E 2 60.487 72.583 24.296 0.65 43.32 ? CBB YPG 301 A 1 HETATM 56 C CBB YPG . B . E 2 61.098 72.382 24.45 0.35 45.69 ? CBB YPG 301 A 1 HETATM 57 N N9 YPG . A . E 2 60.184 71.847 25.564 0.65 37.14 ? N9 YPG 301 A 1 HETATM 58 N N9 YPG . B . E 2 60.537 71.559 25.572 0.35 40.19 ? N9 YPG 301 A 1 HETATM 59 C C2 YPG . A . E 2 58.213 73.829 27.879 0.65 39.57 ? C2 YPG 301 A 1 HETATM 60 C C2 YPG . B . E 2 58.584 73.632 27.848 0.35 41.53 ? C2 YPG 301 A 1 HETATM 61 O O6 YPG . A . E 2 58.704 70.643 29.679 0.65 38.3 ? O6 YPG 301 A 1 HETATM 62 O O6 YPG . B . E 2 58.369 70.265 29.345 0.35 38.31 ? O6 YPG 301 A 1 HETATM 63 N N7 YPG . A . E 2 60.147 70.296 27.013 0.65 42.31 ? N7 YPG 301 A 1 HETATM 64 N N7 YPG . B . E 2 60.092 69.919 26.836 0.35 41.36 ? N7 YPG 301 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 64 #