data_5VPY # _model_server_result.job_id 05S2lKulWXlr9XQzvS3gWA _model_server_result.datetime_utc '2024-11-01 18:24:21' _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 5vpy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":202}' # _entry.id 5VPY # _exptl.entry_id 5VPY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-amino-9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-alpha-L-xylofuranosyl}-1,9-dihydro-6H-purin-6-one _entity.pdbx_number_of_molecules 2 _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 5VPY _cell.length_a 94.609 _cell.length_b 94.609 _cell.length_c 120.808 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VPY _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,H 1 1 B,E,F,G,I 2 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 ? 3 D N N ? 3 F 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 OG SER 18 A SER 17 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc2 A OD1 ASP 58 A ASP 57 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc3 C MG MG . A MG 201 1_555 D O7 9GM . A 9GM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc4 C MG MG . A MG 201 1_555 D O10 9GM . A 9GM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc5 B OG SER 18 B SER 17 1_555 E MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc6 E MG MG . B MG 201 1_555 F O10 9GM . B 9GM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc7 E MG MG . B MG 201 1_555 F O6 9GM . B 9GM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id 9GM _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-alpha-L-xylofuranosyl}-1,9-dihydro-6H-purin-6-one _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 O13 C10 9GM doub 1 n n N6 C10 9GM sing 2 n n N6 C1 9GM sing 3 n n N1 C1 9GM sing 4 n n C10 C3 9GM sing 5 n n C1 N2 9GM doub 6 n n C3 C2 9GM doub 7 n y C3 N3 9GM sing 8 n y N2 C2 9GM sing 9 n n C2 N4 9GM sing 10 n y N3 C4 9GM doub 11 n y N4 C4 9GM sing 12 n y N4 C5 9GM sing 13 n n C5 O1 9GM sing 14 n n C5 C9 9GM sing 15 n n O1 C6 9GM sing 16 n n O12 C9 9GM sing 17 n n C9 C8 9GM sing 18 n n C6 C8 9GM sing 19 n n C6 C7 9GM sing 20 n n O2 C7 9GM sing 21 n n O2 P1 9GM sing 22 n n C8 O11 9GM sing 23 n n O4 P1 9GM doub 24 n n O7 P2 9GM doub 25 n n O5 P1 9GM sing 26 n n O5 P2 9GM sing 27 n n P1 O3 9GM sing 28 n n P2 O6 9GM sing 29 n n P2 N5 9GM sing 30 n n N5 P3 9GM sing 31 n n O9 P3 9GM doub 32 n n P3 O10 9GM sing 33 n n P3 O8 9GM sing 34 n n C4 H1 9GM sing 35 n n C5 H2 9GM sing 36 n n C6 H3 9GM sing 37 n n O6 H4 9GM sing 38 n n O8 H5 9GM sing 39 n n O10 H6 9GM sing 40 n n O11 H7 9GM sing 41 n n O12 H8 9GM sing 42 n n N1 H9 9GM sing 43 n n N1 H10 9GM sing 44 n n C7 H11 9GM sing 45 n n C7 H12 9GM sing 46 n n O3 H13 9GM sing 47 n n N5 H14 9GM sing 48 n n C8 H15 9GM sing 49 n n C9 H16 9GM sing 50 n n N6 H17 9GM sing 51 n n # _atom_sites.entry_id 5VPY _atom_sites.fract_transf_matrix[1][1] 0.01057 _atom_sites.fract_transf_matrix[1][2] 0.006102 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012205 _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] 0.008278 _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 C 2 MG A 1 201 1 MG MG . D 3 9GM A 1 202 2 9GM GNN . E 2 MG B 1 201 2 MG MG . F 3 9GM B 1 202 1 9GM GNN . G 4 PG4 B 1 203 1 PG4 4PE . H 5 HOH A 1 301 106 HOH HOH . H 5 HOH A 2 302 107 HOH HOH . H 5 HOH A 3 303 79 HOH HOH . H 5 HOH A 4 304 9 HOH HOH . H 5 HOH A 5 305 14 HOH HOH . H 5 HOH A 6 306 41 HOH HOH . H 5 HOH A 7 307 76 HOH HOH . H 5 HOH A 8 308 43 HOH HOH . H 5 HOH A 9 309 67 HOH HOH . H 5 HOH A 10 310 82 HOH HOH . H 5 HOH A 11 311 66 HOH HOH . H 5 HOH A 12 312 34 HOH HOH . H 5 HOH A 13 313 78 HOH HOH . H 5 HOH A 14 314 128 HOH HOH . H 5 HOH A 15 315 2 HOH HOH . H 5 HOH A 16 316 31 HOH HOH . H 5 HOH A 17 317 1 HOH HOH . H 5 HOH A 18 318 24 HOH HOH . H 5 HOH A 19 319 60 HOH HOH . H 5 HOH A 20 320 15 HOH HOH . H 5 HOH A 21 321 17 HOH HOH . H 5 HOH A 22 322 54 HOH HOH . H 5 HOH A 23 323 86 HOH HOH . H 5 HOH A 24 324 91 HOH HOH . H 5 HOH A 25 325 110 HOH HOH . H 5 HOH A 26 326 26 HOH HOH . H 5 HOH A 27 327 55 HOH HOH . H 5 HOH A 28 328 129 HOH HOH . H 5 HOH A 29 329 19 HOH HOH . H 5 HOH A 30 330 48 HOH HOH . H 5 HOH A 31 331 95 HOH HOH . H 5 HOH A 32 332 85 HOH HOH . H 5 HOH A 33 333 96 HOH HOH . H 5 HOH A 34 334 3 HOH HOH . H 5 HOH A 35 335 5 HOH HOH . H 5 HOH A 36 336 47 HOH HOH . H 5 HOH A 37 337 68 HOH HOH . H 5 HOH A 38 338 101 HOH HOH . H 5 HOH A 39 339 21 HOH HOH . H 5 HOH A 40 340 93 HOH HOH . H 5 HOH A 41 341 8 HOH HOH . H 5 HOH A 42 342 114 HOH HOH . H 5 HOH A 43 343 102 HOH HOH . H 5 HOH A 44 344 39 HOH HOH . H 5 HOH A 45 345 109 HOH HOH . H 5 HOH A 46 346 83 HOH HOH . H 5 HOH A 47 347 42 HOH HOH . H 5 HOH A 48 348 50 HOH HOH . H 5 HOH A 49 349 11 HOH HOH . H 5 HOH A 50 350 20 HOH HOH . H 5 HOH A 51 351 90 HOH HOH . H 5 HOH A 52 352 126 HOH HOH . H 5 HOH A 53 353 103 HOH HOH . H 5 HOH A 54 354 65 HOH HOH . H 5 HOH A 55 355 104 HOH HOH . H 5 HOH A 56 356 59 HOH HOH . H 5 HOH A 57 357 87 HOH HOH . H 5 HOH A 58 358 37 HOH HOH . H 5 HOH A 59 359 108 HOH HOH . H 5 HOH A 60 360 29 HOH HOH . H 5 HOH A 61 361 89 HOH HOH . H 5 HOH A 62 362 105 HOH HOH . H 5 HOH A 63 363 36 HOH HOH . I 5 HOH B 1 301 123 HOH HOH . I 5 HOH B 2 302 112 HOH HOH . I 5 HOH B 3 303 75 HOH HOH . I 5 HOH B 4 304 33 HOH HOH . I 5 HOH B 5 305 12 HOH HOH . I 5 HOH B 6 306 70 HOH HOH . I 5 HOH B 7 307 118 HOH HOH . I 5 HOH B 8 308 111 HOH HOH . I 5 HOH B 9 309 57 HOH HOH . I 5 HOH B 10 310 71 HOH HOH . I 5 HOH B 11 311 77 HOH HOH . I 5 HOH B 12 312 6 HOH HOH . I 5 HOH B 13 313 88 HOH HOH . I 5 HOH B 14 314 7 HOH HOH . I 5 HOH B 15 315 100 HOH HOH . I 5 HOH B 16 316 32 HOH HOH . I 5 HOH B 17 317 62 HOH HOH . I 5 HOH B 18 318 30 HOH HOH . I 5 HOH B 19 319 125 HOH HOH . I 5 HOH B 20 320 127 HOH HOH . I 5 HOH B 21 321 44 HOH HOH . I 5 HOH B 22 322 22 HOH HOH . I 5 HOH B 23 323 40 HOH HOH . I 5 HOH B 24 324 38 HOH HOH . I 5 HOH B 25 325 63 HOH HOH . I 5 HOH B 26 326 46 HOH HOH . I 5 HOH B 27 327 73 HOH HOH . I 5 HOH B 28 328 69 HOH HOH . I 5 HOH B 29 329 4 HOH HOH . I 5 HOH B 30 330 130 HOH HOH . I 5 HOH B 31 331 23 HOH HOH . I 5 HOH B 32 332 94 HOH HOH . I 5 HOH B 33 333 117 HOH HOH . I 5 HOH B 34 334 25 HOH HOH . I 5 HOH B 35 335 27 HOH HOH . I 5 HOH B 36 336 116 HOH HOH . I 5 HOH B 37 337 51 HOH HOH . I 5 HOH B 38 338 113 HOH HOH . I 5 HOH B 39 339 98 HOH HOH . I 5 HOH B 40 340 74 HOH HOH . I 5 HOH B 41 341 13 HOH HOH . I 5 HOH B 42 342 80 HOH HOH . I 5 HOH B 43 343 16 HOH HOH . I 5 HOH B 44 344 35 HOH HOH . I 5 HOH B 45 345 92 HOH HOH . I 5 HOH B 46 346 58 HOH HOH . I 5 HOH B 47 347 10 HOH HOH . I 5 HOH B 48 348 124 HOH HOH . I 5 HOH B 49 349 81 HOH HOH . I 5 HOH B 50 350 45 HOH HOH . I 5 HOH B 51 351 115 HOH HOH . I 5 HOH B 52 352 61 HOH HOH . I 5 HOH B 53 353 84 HOH HOH . I 5 HOH B 54 354 49 HOH HOH . I 5 HOH B 55 355 64 HOH HOH . I 5 HOH B 56 356 97 HOH HOH . I 5 HOH B 57 357 99 HOH HOH . I 5 HOH B 58 358 18 HOH HOH . I 5 HOH B 59 359 56 HOH HOH . I 5 HOH B 60 360 72 HOH HOH . I 5 HOH B 61 361 119 HOH HOH . I 5 HOH B 62 362 122 HOH HOH . I 5 HOH B 63 363 28 HOH HOH . I 5 HOH B 64 364 121 HOH HOH . I 5 HOH B 65 365 53 HOH HOH . I 5 HOH B 66 366 120 HOH HOH . I 5 HOH B 67 367 52 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 C1 9GM . . . F 3 16.89 -7.382 10.668 1 15.62 ? C1 9GM 202 B 1 HETATM 2 C C2 9GM . . . F 3 17.14 -6.101 12.472 1 15.21 ? C2 9GM 202 B 1 HETATM 3 C C3 9GM . . . F 3 17.747 -5.059 11.817 1 14.26 ? C3 9GM 202 B 1 HETATM 4 C C4 9GM . . . F 3 17.594 -4.467 13.871 1 15.48 ? C4 9GM 202 B 1 HETATM 5 C C5 9GM . . . F 3 16.305 -6.523 14.749 1 22.17 ? C5 9GM 202 B 1 HETATM 6 C C6 9GM . . . F 3 16.238 -5.402 16.62 1 25.87 ? C6 9GM 202 B 1 HETATM 7 N N2 9GM . . . F 3 16.671 -7.268 11.969 1 15.9 ? N2 9GM 202 B 1 HETATM 8 O O1 9GM . . . F 3 15.453 -5.638 15.443 1 20.29 ? O1 9GM 202 B 1 HETATM 9 O O4 9GM . . . F 3 18.652 -1.95 17.522 1 21.16 -1 O4 9GM 202 B 1 HETATM 10 O O5 9GM . . . F 3 16.24 -1.26 17.995 1 22.9 ? O5 9GM 202 B 1 HETATM 11 O O6 9GM . . . F 3 17.517 0.456 19.091 1 22.09 ? O6 9GM 202 B 1 HETATM 12 P P1 9GM . . . F 3 17.363 -2.412 18.119 1 24.52 ? P1 9GM 202 B 1 HETATM 13 O O7 9GM . . . F 3 15.521 1.106 17.603 1 23.52 -1 O7 9GM 202 B 1 HETATM 14 O O8 9GM . . . F 3 14.236 0.159 22.296 1 52.4 ? O8 9GM 202 B 1 HETATM 15 O O9 9GM . . . F 3 14.491 2.231 21.003 1 49.06 -1 O9 9GM 202 B 1 HETATM 16 P P2 9GM . . . F 3 16.124 0.187 18.64 1 23.15 ? P2 9GM 202 B 1 HETATM 17 O O10 9GM . . . F 3 16.506 0.953 21.737 1 44.2 -1 O10 9GM 202 B 1 HETATM 18 O O11 9GM . . . F 3 15.512 -7.631 17.541 1 29.06 ? O11 9GM 202 B 1 HETATM 19 O O12 9GM . . . F 3 18.488 -7.198 15.792 1 27 ? O12 9GM 202 B 1 HETATM 20 N N1 9GM . . . F 3 16.503 -8.492 10.021 1 17.26 ? N1 9GM 202 B 1 HETATM 21 N N3 9GM . . . F 3 18.035 -4.029 12.709 1 15.18 ? N3 9GM 202 B 1 HETATM 22 N N4 9GM . . . F 3 17.044 -5.734 13.779 1 15.94 ? N4 9GM 202 B 1 HETATM 23 C C7 9GM . . . F 3 15.655 -4.328 17.472 1 24.79 ? C7 9GM 202 B 1 HETATM 24 O O2 9GM . . . F 3 16.574 -3.304 17.114 1 20.71 ? O2 9GM 202 B 1 HETATM 25 O O3 9GM . . . F 3 17.338 -2.998 19.486 1 27.06 ? O3 9GM 202 B 1 HETATM 26 N N5 9GM . . . F 3 15.09 -0.053 19.863 1 31.89 ? N5 9GM 202 B 1 HETATM 27 P P3 9GM . . . F 3 15.075 0.844 21.234 1 49.15 ? P3 9GM 202 B 1 HETATM 28 C C8 9GM . . . F 3 16.579 -6.792 17.136 1 24.49 ? C8 9GM 202 B 1 HETATM 29 C C9 9GM . . . F 3 17.093 -7.335 15.802 1 24.98 ? C9 9GM 202 B 1 HETATM 30 C C10 9GM . . . F 3 17.974 -5.18 10.424 1 13.95 ? C10 9GM 202 B 1 HETATM 31 O O13 9GM . . . F 3 18.477 -4.361 9.648 1 13.8 ? O13 9GM 202 B 1 HETATM 32 N N6 9GM . . . F 3 17.475 -6.386 9.924 1 15 ? N6 9GM 202 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 32 #