data_3VUZ # _model_server_result.job_id AWaWiXUOY4yZujUTlRVuNA _model_server_result.datetime_utc '2025-03-06 21:11:23' _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 3vuz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 3VUZ # _exptl.entry_id 3VUZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 451.52 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-{[(3S)-3-amino-3-carboxypropyl](hexyl)amino}-5'-deoxyadenosine" _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 3VUZ _cell.length_a 101.807 _cell.length_b 39.223 _cell.length_c 67.045 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VUZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H33 N7 O5' _chem_comp.formula_weight 451.52 _chem_comp.id K15 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl](hexyl)amino}-5'-deoxyadenosine" _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 N6 C6 K15 sing 173 n n N1 C6 K15 doub 174 n y N1 C2 K15 sing 175 n y C6 C5 K15 sing 176 n y C2 N3 K15 doub 177 n y C5 C4 K15 doub 178 n y C5 N7 K15 sing 179 n y N3 C4 K15 sing 180 n y C4 N9 K15 sing 181 n y N7 C8 K15 doub 182 n y N CA K15 sing 183 n n O C K15 doub 184 n n N9 C8 K15 sing 185 n y N9 C1' K15 sing 186 n n C1' O4' K15 sing 187 n n C1' C2' K15 sing 188 n n CA C K15 sing 189 n n CA CB K15 sing 190 n n C OXT K15 sing 191 n n O4' C4' K15 sing 192 n n CB CG K15 sing 193 n n CG ND K15 sing 194 n n C2' O2' K15 sing 195 n n C2' C3' K15 sing 196 n n C4' C5' K15 sing 197 n n C4' C3' K15 sing 198 n n C5' ND K15 sing 199 n n ND CE K15 sing 200 n n C3' O3' K15 sing 201 n n CE C11 K15 sing 202 n n C11 C12 K15 sing 203 n n C12 C13 K15 sing 204 n n C14 C13 K15 sing 205 n n C14 C15 K15 sing 206 n n CA H1 K15 sing 207 n n N H2 K15 sing 208 n n N H3 K15 sing 209 n n CB H5 K15 sing 210 n n CB H6 K15 sing 211 n n CG H7 K15 sing 212 n n CG H8 K15 sing 213 n n CE H10 K15 sing 214 n n CE H11 K15 sing 215 n n C11 H12 K15 sing 216 n n C11 H13 K15 sing 217 n n C12 H14 K15 sing 218 n n C12 H15 K15 sing 219 n n C13 H16 K15 sing 220 n n C13 H17 K15 sing 221 n n C14 H18 K15 sing 222 n n C14 H19 K15 sing 223 n n C15 H20 K15 sing 224 n n C15 H21 K15 sing 225 n n C15 H22 K15 sing 226 n n C5' H23 K15 sing 227 n n C5' H24 K15 sing 228 n n C4' H25 K15 sing 229 n n C1' H26 K15 sing 230 n n C2' H27 K15 sing 231 n n O2' H28 K15 sing 232 n n C3' H29 K15 sing 233 n n O3' H30 K15 sing 234 n n C8 H31 K15 sing 235 n n N6 H32 K15 sing 236 n n N6 H33 K15 sing 237 n n C2 H34 K15 sing 238 n n OXT H35 K15 sing 239 n n # _atom_sites.entry_id 3VUZ _atom_sites.fract_transf_matrix[1][1] 0.009823 _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] 0.025495 _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] 0.014915 _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 B 2 K15 A 1 401 401 K15 K15 . C 3 HOH A 1 501 8 HOH HOH . C 3 HOH A 2 502 9 HOH HOH . C 3 HOH A 3 503 10 HOH HOH . C 3 HOH A 4 504 11 HOH HOH . C 3 HOH A 5 505 12 HOH HOH . C 3 HOH A 6 506 13 HOH HOH . C 3 HOH A 7 507 14 HOH HOH . C 3 HOH A 8 508 15 HOH HOH . C 3 HOH A 9 509 16 HOH HOH . C 3 HOH A 10 510 17 HOH HOH . C 3 HOH A 11 511 18 HOH HOH . C 3 HOH A 12 512 19 HOH HOH . C 3 HOH A 13 513 20 HOH HOH . C 3 HOH A 14 514 21 HOH HOH . C 3 HOH A 15 515 22 HOH HOH . C 3 HOH A 16 516 23 HOH HOH . C 3 HOH A 17 517 24 HOH HOH . C 3 HOH A 18 518 25 HOH HOH . C 3 HOH A 19 519 26 HOH HOH . C 3 HOH A 20 520 27 HOH HOH . C 3 HOH A 21 521 28 HOH HOH . C 3 HOH A 22 522 29 HOH HOH . C 3 HOH A 23 523 30 HOH HOH . C 3 HOH A 24 524 31 HOH HOH . C 3 HOH A 25 525 32 HOH HOH . C 3 HOH A 26 526 33 HOH HOH . C 3 HOH A 27 527 34 HOH HOH . C 3 HOH A 28 528 35 HOH HOH . C 3 HOH A 29 529 36 HOH HOH . C 3 HOH A 30 530 37 HOH HOH . C 3 HOH A 31 531 38 HOH HOH . C 3 HOH A 32 532 39 HOH HOH . C 3 HOH A 33 533 40 HOH HOH . C 3 HOH A 34 534 41 HOH HOH . C 3 HOH A 35 535 42 HOH HOH . C 3 HOH A 36 536 43 HOH HOH . C 3 HOH A 37 537 44 HOH HOH . C 3 HOH A 38 538 45 HOH HOH . C 3 HOH A 39 539 46 HOH HOH . C 3 HOH A 40 540 47 HOH HOH . C 3 HOH A 41 541 48 HOH HOH . C 3 HOH A 42 542 49 HOH HOH . C 3 HOH A 43 543 50 HOH HOH . C 3 HOH A 44 544 51 HOH HOH . C 3 HOH A 45 545 52 HOH HOH . C 3 HOH A 46 546 53 HOH HOH . C 3 HOH A 47 547 54 HOH HOH . C 3 HOH A 48 548 55 HOH HOH . C 3 HOH A 49 549 56 HOH HOH . C 3 HOH A 50 550 57 HOH HOH . C 3 HOH A 51 551 58 HOH HOH . C 3 HOH A 52 552 59 HOH HOH . C 3 HOH A 53 553 60 HOH HOH . C 3 HOH A 54 554 61 HOH HOH . C 3 HOH A 55 555 62 HOH HOH . C 3 HOH A 56 556 63 HOH HOH . C 3 HOH A 57 557 64 HOH HOH . C 3 HOH A 58 558 65 HOH HOH . C 3 HOH A 59 559 66 HOH HOH . C 3 HOH A 60 560 67 HOH HOH . C 3 HOH A 61 561 68 HOH HOH . C 3 HOH A 62 562 69 HOH HOH . C 3 HOH A 63 563 70 HOH HOH . C 3 HOH A 64 564 71 HOH HOH . C 3 HOH A 65 565 72 HOH HOH . C 3 HOH A 66 566 73 HOH HOH . C 3 HOH A 67 567 74 HOH HOH . C 3 HOH A 68 568 75 HOH HOH . C 3 HOH A 69 569 76 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 O O K15 . . . B 2 -38.41 6.424 -22.259 1 49.58 ? O K15 401 A 1 HETATM 2 C C K15 . . . B 2 -38.163 5.752 -21.239 1 60.86 ? C K15 401 A 1 HETATM 3 C CA K15 . . . B 2 -38.037 4.251 -21.371 1 66.33 ? CA K15 401 A 1 HETATM 4 N N K15 . . . B 2 -38.26 3.851 -22.758 1 62.51 ? N K15 401 A 1 HETATM 5 C CB K15 . . . B 2 -36.658 3.771 -20.907 1 57.41 ? CB K15 401 A 1 HETATM 6 C CG K15 . . . B 2 -36.623 2.276 -20.593 1 52.46 ? CG K15 401 A 1 HETATM 7 N ND K15 . . . B 2 -37.193 2.021 -19.255 1 57.52 ? ND K15 401 A 1 HETATM 8 C CE K15 . . . B 2 -36.095 1.906 -18.273 1 54.53 ? CE K15 401 A 1 HETATM 9 C C11 K15 . . . B 2 -35.692 0.467 -17.97 1 54.73 ? C11 K15 401 A 1 HETATM 10 C C12 K15 . . . B 2 -34.301 0.423 -17.352 1 52.44 ? C12 K15 401 A 1 HETATM 11 C C13 K15 . . . B 2 -34.219 -0.579 -16.205 1 54.09 ? C13 K15 401 A 1 HETATM 12 C C14 K15 . . . B 2 -34.255 -2.032 -16.671 1 46.45 ? C14 K15 401 A 1 HETATM 13 C C15 K15 . . . B 2 -34.651 -2.934 -15.525 1 45.38 ? C15 K15 401 A 1 HETATM 14 C C5' K15 . . . B 2 -38.048 0.819 -19.266 1 62.28 ? C5' K15 401 A 1 HETATM 15 C C4' K15 . . . B 2 -39.457 1.313 -19.569 1 65.45 ? C4' K15 401 A 1 HETATM 16 O O4' K15 . . . B 2 -39.59 1.515 -20.981 1 64.85 ? O4' K15 401 A 1 HETATM 17 C C1' K15 . . . B 2 -40.727 0.829 -21.488 1 65.29 ? C1' K15 401 A 1 HETATM 18 C C2' K15 . . . B 2 -41.573 0.475 -20.283 1 58.77 ? C2' K15 401 A 1 HETATM 19 O O2' K15 . . . B 2 -42.52 1.545 -20.096 1 46.75 ? O2' K15 401 A 1 HETATM 20 C C3' K15 . . . B 2 -40.567 0.364 -19.153 1 61.23 ? C3' K15 401 A 1 HETATM 21 O O3' K15 . . . B 2 -41.127 0.781 -17.901 1 62.83 ? O3' K15 401 A 1 HETATM 22 N N9 K15 . . . B 2 -40.214 -0.352 -22.219 1 75.3 ? N9 K15 401 A 1 HETATM 23 C C8 K15 . . . B 2 -38.96 -0.838 -22.169 1 74.83 ? C8 K15 401 A 1 HETATM 24 N N7 K15 . . . B 2 -38.808 -1.906 -22.994 1 70.83 ? N7 K15 401 A 1 HETATM 25 C C5 K15 . . . B 2 -39.99 -2.109 -23.603 1 77.73 ? C5 K15 401 A 1 HETATM 26 C C6 K15 . . . B 2 -40.533 -3.07 -24.591 1 76.46 ? C6 K15 401 A 1 HETATM 27 N N6 K15 . . . B 2 -39.773 -4.057 -25.116 1 76.11 ? N6 K15 401 A 1 HETATM 28 C C4 K15 . . . B 2 -40.905 -1.076 -23.099 1 81.78 ? C4 K15 401 A 1 HETATM 29 N N3 K15 . . . B 2 -42.179 -1.055 -23.548 1 84.57 ? N3 K15 401 A 1 HETATM 30 C C2 K15 . . . B 2 -42.595 -1.963 -24.443 1 82.17 ? C2 K15 401 A 1 HETATM 31 N N1 K15 . . . B 2 -41.819 -2.933 -24.952 1 75.82 ? N1 K15 401 A 1 HETATM 32 O OXT K15 . . . B 2 -38.023 6.285 -20.117 1 65.57 ? OXT K15 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #