data_3V3L # _model_server_result.job_id MVc2J7cVv9wvU1vebxeSqA _model_server_result.datetime_utc '2024-11-13 12:45:14' _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 3v3l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 3V3L # _exptl.entry_id 3V3L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)" _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 3V3L _cell.length_a 55.343 _cell.length_b 55.343 _cell.length_c 146.471 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V3L _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 2' # 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,E 1 1 B,D,F 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 ? 2 C N N ? 2 D 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 covale ? covale1 A C GLU 38 A GLU 136 1_555 A N MSE 39 A MSE 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C MSE 39 A MSE 137 1_555 A N LEU 40 A LEU 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 A C ASN 52 A ASN 150 1_555 A N MSE 53 A MSE 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 53 A MSE 151 1_555 A N VAL 54 A VAL 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 B C GLU 38 B GLU 136 1_555 B N MSE 39 B MSE 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale6 B C MSE 39 B MSE 137 1_555 B N LEU 40 B LEU 138 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.331 ? covale ? covale7 B C MSE 39 B MSE 137 1_555 B N LEU 40 B LEU 138 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.331 ? covale ? covale8 B C ASN 52 B ASN 150 1_555 B N MSE 53 B MSE 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale9 B C MSE 53 B MSE 151 1_555 B N VAL 54 B VAL 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id V3L _chem_comp.mon_nstd_flag n _chem_comp.name "2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)" _chem_comp.type 'rna linking' _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 N1 C6 V3L doub 345 n y N1 C2 V3L sing 346 n y C2 N3 V3L doub 347 n y C2 H2 V3L sing 348 n n C4 N3 V3L sing 349 n y C5 C4 V3L doub 350 n y C4 N9 V3L sing 351 n y C6 C5 V3L sing 352 n y C5 N7 V3L sing 353 n y N6 C6 V3L sing 354 n n N6 HN6 V3L sing 355 n n N6 HN6A V3L sing 356 n n N7 C8 V3L doub 357 n y C8 N9 V3L sing 358 n y C8 H8 V3L sing 359 n n N9 C1' V3L sing 360 n n OP1 P V3L doub 361 n n P O5' V3L sing 362 n n P OP3 V3L sing 363 n n P OP2 V3L sing 364 n n O15 PB V3L sing 365 n n O2B PB V3L doub 366 n n PB O3B V3L sing 367 n n PB O1B V3L sing 368 n n O2' C10 V3L sing 369 n n C10 C12 V3L sing 370 n n C10 O14 V3L sing 371 n n C10 "H1''" V3L sing 372 n n O4' C1' V3L sing 373 n n C1' C2' V3L sing 374 n n C1' H1' V3L sing 375 n n OP3 HOP3 V3L sing 376 n n O1B HO1B V3L sing 377 n n O12 C12 V3L sing 378 n n C12 C13 V3L sing 379 n n C12 "H2''" V3L sing 380 n n O12 HO2' V3L sing 381 n n C3' C2' V3L sing 382 n n C2' O2' V3L sing 383 n n C2' H2' V3L sing 384 n n O13 C13 V3L sing 385 n n C13 C14 V3L sing 386 n n C13 "H3''" V3L sing 387 n n O13 HO13 V3L sing 388 n n C4' C3' V3L sing 389 n n C3' O3' V3L sing 390 n n C3' H3' V3L sing 391 n n O3' HO3' V3L sing 392 n n OP2 HOP2 V3L sing 393 n n O3B HO3B V3L sing 394 n n O14 C14 V3L sing 395 n n C14 C15 V3L sing 396 n n C14 "H4''" V3L sing 397 n n O4' C4' V3L sing 398 n n C5' C4' V3L sing 399 n n C4' H4' V3L sing 400 n n C15 O15 V3L sing 401 n n C15 "H5''" V3L sing 402 n n C15 H5AA V3L sing 403 n n C5' O5' V3L sing 404 n n C5' H5' V3L sing 405 n n C5' "H5'A" V3L sing 406 n n # _atom_sites.entry_id 3V3L _atom_sites.fract_transf_matrix[1][1] 0.018069 _atom_sites.fract_transf_matrix[1][2] 0.010432 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020864 _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] 0.006827 _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 V3L A 1 1 1 V3L IAR . D 2 V3L B 1 1 1 V3L IAR . E 3 HOH A 1 3 3 HOH HOH . E 3 HOH A 2 7 7 HOH HOH . E 3 HOH A 3 9 9 HOH HOH . E 3 HOH A 4 10 10 HOH HOH . E 3 HOH A 5 14 14 HOH HOH . E 3 HOH A 6 15 15 HOH HOH . E 3 HOH A 7 16 16 HOH HOH . E 3 HOH A 8 19 19 HOH HOH . E 3 HOH A 9 20 20 HOH HOH . E 3 HOH A 10 21 21 HOH HOH . E 3 HOH A 11 22 22 HOH HOH . E 3 HOH A 12 23 23 HOH HOH . E 3 HOH A 13 28 28 HOH HOH . E 3 HOH A 14 32 32 HOH HOH . E 3 HOH A 15 37 37 HOH HOH . E 3 HOH A 16 55 55 HOH HOH . E 3 HOH A 17 83 83 HOH HOH . E 3 HOH A 18 84 84 HOH HOH . E 3 HOH A 19 85 85 HOH HOH . E 3 HOH A 20 86 86 HOH HOH . E 3 HOH A 21 87 87 HOH HOH . E 3 HOH A 22 88 88 HOH HOH . E 3 HOH A 23 89 89 HOH HOH . E 3 HOH A 24 90 90 HOH HOH . E 3 HOH A 25 91 91 HOH HOH . E 3 HOH A 26 95 95 HOH HOH . E 3 HOH A 27 98 98 HOH HOH . E 3 HOH A 28 184 1 HOH HOH . E 3 HOH A 29 185 99 HOH HOH . E 3 HOH A 30 186 100 HOH HOH . E 3 HOH A 31 187 101 HOH HOH . E 3 HOH A 32 188 102 HOH HOH . E 3 HOH A 33 189 103 HOH HOH . E 3 HOH A 34 190 104 HOH HOH . E 3 HOH A 35 191 106 HOH HOH . E 3 HOH A 36 192 107 HOH HOH . E 3 HOH A 37 193 108 HOH HOH . E 3 HOH A 38 194 109 HOH HOH . E 3 HOH A 39 195 110 HOH HOH . E 3 HOH A 40 196 111 HOH HOH . E 3 HOH A 41 197 112 HOH HOH . E 3 HOH A 42 198 114 HOH HOH . E 3 HOH A 43 199 115 HOH HOH . E 3 HOH A 44 200 116 HOH HOH . E 3 HOH A 45 201 117 HOH HOH . E 3 HOH A 46 202 118 HOH HOH . E 3 HOH A 47 203 119 HOH HOH . E 3 HOH A 48 204 120 HOH HOH . E 3 HOH A 49 205 121 HOH HOH . E 3 HOH A 50 206 122 HOH HOH . E 3 HOH A 51 207 124 HOH HOH . E 3 HOH A 52 208 125 HOH HOH . E 3 HOH A 53 209 126 HOH HOH . E 3 HOH A 54 210 127 HOH HOH . E 3 HOH A 55 211 128 HOH HOH . E 3 HOH A 56 212 129 HOH HOH . E 3 HOH A 57 213 132 HOH HOH . E 3 HOH A 58 214 135 HOH HOH . E 3 HOH A 59 215 136 HOH HOH . E 3 HOH A 60 216 137 HOH HOH . E 3 HOH A 61 217 144 HOH HOH . E 3 HOH A 62 218 146 HOH HOH . E 3 HOH A 63 219 147 HOH HOH . F 3 HOH B 1 4 4 HOH HOH . F 3 HOH B 2 5 5 HOH HOH . F 3 HOH B 3 6 6 HOH HOH . F 3 HOH B 4 8 8 HOH HOH . F 3 HOH B 5 11 11 HOH HOH . F 3 HOH B 6 12 12 HOH HOH . F 3 HOH B 7 13 13 HOH HOH . F 3 HOH B 8 24 24 HOH HOH . F 3 HOH B 9 25 25 HOH HOH . F 3 HOH B 10 27 27 HOH HOH . F 3 HOH B 11 29 29 HOH HOH . F 3 HOH B 12 30 30 HOH HOH . F 3 HOH B 13 31 31 HOH HOH . F 3 HOH B 14 33 33 HOH HOH . F 3 HOH B 15 34 34 HOH HOH . F 3 HOH B 16 35 35 HOH HOH . F 3 HOH B 17 36 36 HOH HOH . F 3 HOH B 18 38 38 HOH HOH . F 3 HOH B 19 39 39 HOH HOH . F 3 HOH B 20 40 40 HOH HOH . F 3 HOH B 21 41 41 HOH HOH . F 3 HOH B 22 42 42 HOH HOH . F 3 HOH B 23 43 43 HOH HOH . F 3 HOH B 24 44 44 HOH HOH . F 3 HOH B 25 45 45 HOH HOH . F 3 HOH B 26 47 47 HOH HOH . F 3 HOH B 27 49 49 HOH HOH . F 3 HOH B 28 50 50 HOH HOH . F 3 HOH B 29 51 51 HOH HOH . F 3 HOH B 30 54 54 HOH HOH . F 3 HOH B 31 58 58 HOH HOH . F 3 HOH B 32 62 62 HOH HOH . F 3 HOH B 33 63 63 HOH HOH . F 3 HOH B 34 64 64 HOH HOH . F 3 HOH B 35 65 65 HOH HOH . F 3 HOH B 36 67 67 HOH HOH . F 3 HOH B 37 74 74 HOH HOH . F 3 HOH B 38 76 76 HOH HOH . F 3 HOH B 39 77 77 HOH HOH . F 3 HOH B 40 78 78 HOH HOH . F 3 HOH B 41 79 79 HOH HOH . F 3 HOH B 42 80 80 HOH HOH . F 3 HOH B 43 81 81 HOH HOH . F 3 HOH B 44 82 82 HOH HOH . F 3 HOH B 45 93 93 HOH HOH . F 3 HOH B 46 96 96 HOH HOH . F 3 HOH B 47 97 97 HOH HOH . F 3 HOH B 48 184 105 HOH HOH . F 3 HOH B 49 185 113 HOH HOH . F 3 HOH B 50 186 123 HOH HOH . F 3 HOH B 51 187 130 HOH HOH . F 3 HOH B 52 188 131 HOH HOH . F 3 HOH B 53 189 133 HOH HOH . F 3 HOH B 54 190 134 HOH HOH . F 3 HOH B 55 191 138 HOH HOH . F 3 HOH B 56 192 139 HOH HOH . F 3 HOH B 57 193 140 HOH HOH . F 3 HOH B 58 194 141 HOH HOH . F 3 HOH B 59 195 142 HOH HOH . F 3 HOH B 60 196 143 HOH HOH . F 3 HOH B 61 197 145 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 V3L . . . D 2 19.45 44.291 88.54 1 27.99 ? N1 V3L 1 B 1 HETATM 2 C C2 V3L . . . D 2 20.669 44.862 88.548 1 29.14 ? C2 V3L 1 B 1 HETATM 3 N N3 V3L . . . D 2 20.863 46.203 88.466 1 26.93 ? N3 V3L 1 B 1 HETATM 4 C C4 V3L . . . D 2 19.806 47.036 88.339 1 27.77 ? C4 V3L 1 B 1 HETATM 5 C C5 V3L . . . D 2 18.451 46.496 88.318 1 27.44 ? C5 V3L 1 B 1 HETATM 6 C C6 V3L . . . D 2 18.324 45.04 88.429 1 26.58 ? C6 V3L 1 B 1 HETATM 7 N N6 V3L . . . D 2 17.096 44.506 88.417 1 28.89 ? N6 V3L 1 B 1 HETATM 8 N N7 V3L . . . D 2 17.587 47.527 88.219 1 28.54 ? N7 V3L 1 B 1 HETATM 9 C C8 V3L . . . D 2 18.318 48.652 88.166 1 27.31 ? C8 V3L 1 B 1 HETATM 10 N N9 V3L . . . D 2 19.64 48.347 88.247 1 26.44 ? N9 V3L 1 B 1 HETATM 11 P P V3L . . . D 2 17.053 52.691 87.662 0.77 29.45 ? P V3L 1 B 1 HETATM 12 P PB V3L . . . D 2 22.645 49.513 79.58 0.93 26.23 ? PB V3L 1 B 1 HETATM 13 C C10 V3L . . . D 2 21.421 48.632 84.548 1 26.67 ? C10 V3L 1 B 1 HETATM 14 C C1' V3L . . . D 2 20.756 49.309 88.139 1 28.15 ? C1' V3L 1 B 1 HETATM 15 O OP3 V3L . . . D 2 16.754 52.709 89.157 1 32.88 ? OP3 V3L 1 B 1 HETATM 16 O O1B V3L . . . D 2 22.185 48.221 78.976 1 26.46 ? O1B V3L 1 B 1 HETATM 17 C C12 V3L . . . D 2 22.23 47.453 84.045 1 26.19 ? C12 V3L 1 B 1 HETATM 18 O O12 V3L . . . D 2 22.315 46.383 84.979 1 27.43 ? O12 V3L 1 B 1 HETATM 19 C C2' V3L . . . D 2 20.86 49.722 86.662 1 27.98 ? C2' V3L 1 B 1 HETATM 20 O O2' V3L . . . D 2 21.731 48.826 85.919 1 28.12 ? O2' V3L 1 B 1 HETATM 21 O OP1 V3L . . . D 2 16.195 51.783 86.833 1 31.99 ? OP1 V3L 1 B 1 HETATM 22 O O2B V3L . . . D 2 21.563 50.579 79.56 1 30.3 ? O2B V3L 1 B 1 HETATM 23 C C13 V3L . . . D 2 23.588 48.072 83.745 1 28.94 ? C13 V3L 1 B 1 HETATM 24 O O13 V3L . . . D 2 24.514 47.945 84.826 1 29.04 ? O13 V3L 1 B 1 HETATM 25 C C3' V3L . . . D 2 21.29 51.198 86.73 1 28.26 ? C3' V3L 1 B 1 HETATM 26 O O3' V3L . . . D 2 22.685 51.364 86.555 1 29.26 ? O3' V3L 1 B 1 HETATM 27 O OP2 V3L . . . D 2 17.204 54.111 87.162 1 33.64 ? OP2 V3L 1 B 1 HETATM 28 O O3B V3L . . . D 2 23.998 50.018 79.121 1 29.64 ? O3B V3L 1 B 1 HETATM 29 C C14 V3L . . . D 2 23.277 49.538 83.468 1 29.04 ? C14 V3L 1 B 1 HETATM 30 O O14 V3L . . . D 2 21.891 49.741 83.764 1 26.94 ? O14 V3L 1 B 1 HETATM 31 C C4' V3L . . . D 2 20.864 51.654 88.142 1 29.65 ? C4' V3L 1 B 1 HETATM 32 O O4' V3L . . . D 2 20.473 50.48 88.848 1 28.93 ? O4' V3L 1 B 1 HETATM 33 C C15 V3L . . . D 2 23.569 49.942 82.029 1 29.01 ? C15 V3L 1 B 1 HETATM 34 O O15 V3L . . . D 2 22.882 49.081 81.111 1 27.06 ? O15 V3L 1 B 1 HETATM 35 C C5' V3L . . . D 2 19.654 52.588 88.205 1 30.99 ? C5' V3L 1 B 1 HETATM 36 O O5' V3L . . . D 2 18.512 52.03 87.535 1 28.87 ? O5' V3L 1 B 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #