data_3VV0 # _model_server_result.job_id 5HQ8nPJiS5vmtIwN08DpXQ _model_server_result.datetime_utc '2024-11-05 01:23:43' _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 3vv0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 3VV0 # _exptl.entry_id 3VV0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 494.588 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-{[(3S)-3-amino-3-carboxypropyl][2-(hexylamino)ethyl]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 3VV0 _cell.length_a 101.836 _cell.length_b 39.126 _cell.length_c 67.322 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VV0 _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_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 'C22 H38 N8 O5' _chem_comp.formula_weight 494.588 _chem_comp.id KH3 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl][2-(hexylamino)ethyl]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 N1 C2 KH3 doub 173 n y N1 C6 KH3 sing 174 n y N6 C6 KH3 sing 175 n n C2 N3 KH3 sing 176 n y C6 C5 KH3 doub 177 n y N3 C4 KH3 doub 178 n y C5 C4 KH3 sing 179 n y C5 N7 KH3 sing 180 n y C4 N9 KH3 sing 181 n y N7 C8 KH3 doub 182 n y N CA KH3 sing 183 n n N9 C8 KH3 sing 184 n y N9 C1' KH3 sing 185 n n O C KH3 doub 186 n n C1' O4' KH3 sing 187 n n C1' C2' KH3 sing 188 n n CA C KH3 sing 189 n n CA CB KH3 sing 190 n n C OXT KH3 sing 191 n n O4' C4' KH3 sing 192 n n CB CG KH3 sing 193 n n CG ND KH3 sing 194 n n C2' O2' KH3 sing 195 n n C2' C3' KH3 sing 196 n n C4' C5' KH3 sing 197 n n C4' C3' KH3 sing 198 n n ND C5' KH3 sing 199 n n ND CE KH3 sing 200 n n C3' O3' KH3 sing 201 n n CE C11 KH3 sing 202 n n C11 N12 KH3 sing 203 n n N12 C13 KH3 sing 204 n n C13 C14 KH3 sing 205 n n C16 C17 KH3 sing 206 n n C16 C15 KH3 sing 207 n n C14 C15 KH3 sing 208 n n C17 C18 KH3 sing 209 n n CA H1 KH3 sing 210 n n N H2 KH3 sing 211 n n N H3 KH3 sing 212 n n CB H5 KH3 sing 213 n n CB H6 KH3 sing 214 n n CG H7 KH3 sing 215 n n CG H8 KH3 sing 216 n n CE H10 KH3 sing 217 n n CE H11 KH3 sing 218 n n C11 H12 KH3 sing 219 n n C11 H13 KH3 sing 220 n n N12 H14 KH3 sing 221 n n C13 H16 KH3 sing 222 n n C13 H17 KH3 sing 223 n n C14 H18 KH3 sing 224 n n C14 H19 KH3 sing 225 n n C15 H20 KH3 sing 226 n n C15 H21 KH3 sing 227 n n C16 H22 KH3 sing 228 n n C16 H23 KH3 sing 229 n n C17 H24 KH3 sing 230 n n C17 H25 KH3 sing 231 n n C18 H26 KH3 sing 232 n n C18 H27 KH3 sing 233 n n C18 H28 KH3 sing 234 n n C5' H29 KH3 sing 235 n n C5' H30 KH3 sing 236 n n C4' H31 KH3 sing 237 n n C1' H32 KH3 sing 238 n n C2' H33 KH3 sing 239 n n O2' H34 KH3 sing 240 n n C3' H35 KH3 sing 241 n n O3' H36 KH3 sing 242 n n C8 H37 KH3 sing 243 n n N6 H38 KH3 sing 244 n n N6 H39 KH3 sing 245 n n C2 H40 KH3 sing 246 n n OXT H41 KH3 sing 247 n n # _atom_sites.entry_id 3VV0 _atom_sites.fract_transf_matrix[1][1] 0.00982 _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] 0.025558 _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] 0.014854 _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 KH3 A 1 401 401 KH3 KH3 . C 3 HOH A 1 501 1 HOH HOH . C 3 HOH A 2 502 2 HOH HOH . C 3 HOH A 3 503 3 HOH HOH . C 3 HOH A 4 504 4 HOH HOH . C 3 HOH A 5 505 5 HOH HOH . C 3 HOH A 6 506 6 HOH HOH . C 3 HOH A 7 507 7 HOH HOH . C 3 HOH A 8 508 8 HOH HOH . C 3 HOH A 9 509 9 HOH HOH . C 3 HOH A 10 510 10 HOH HOH . C 3 HOH A 11 511 11 HOH HOH . C 3 HOH A 12 512 12 HOH HOH . C 3 HOH A 13 513 13 HOH HOH . C 3 HOH A 14 514 14 HOH HOH . C 3 HOH A 15 515 15 HOH HOH . C 3 HOH A 16 516 16 HOH HOH . C 3 HOH A 17 517 17 HOH HOH . C 3 HOH A 18 518 18 HOH HOH . C 3 HOH A 19 519 19 HOH HOH . C 3 HOH A 20 520 20 HOH HOH . C 3 HOH A 21 521 21 HOH HOH . C 3 HOH A 22 522 22 HOH HOH . C 3 HOH A 23 523 23 HOH HOH . C 3 HOH A 24 524 24 HOH HOH . C 3 HOH A 25 525 25 HOH HOH . C 3 HOH A 26 526 26 HOH HOH . C 3 HOH A 27 527 27 HOH HOH . C 3 HOH A 28 528 28 HOH HOH . C 3 HOH A 29 529 29 HOH HOH . C 3 HOH A 30 530 30 HOH HOH . C 3 HOH A 31 531 31 HOH HOH . C 3 HOH A 32 532 32 HOH HOH . C 3 HOH A 33 533 33 HOH HOH . C 3 HOH A 34 534 34 HOH HOH . C 3 HOH A 35 535 35 HOH HOH . C 3 HOH A 36 536 36 HOH HOH . C 3 HOH A 37 537 37 HOH HOH . C 3 HOH A 38 538 38 HOH HOH . C 3 HOH A 39 539 39 HOH HOH . C 3 HOH A 40 540 40 HOH HOH . C 3 HOH A 41 541 41 HOH HOH . C 3 HOH A 42 542 42 HOH HOH . C 3 HOH A 43 543 43 HOH HOH . C 3 HOH A 44 544 44 HOH HOH . C 3 HOH A 45 545 45 HOH HOH . C 3 HOH A 46 546 46 HOH HOH . C 3 HOH A 47 547 47 HOH HOH . C 3 HOH A 48 548 48 HOH HOH . C 3 HOH A 49 549 49 HOH HOH . C 3 HOH A 50 550 50 HOH HOH . C 3 HOH A 51 551 51 HOH HOH . C 3 HOH A 52 552 52 HOH HOH . C 3 HOH A 53 553 53 HOH HOH . C 3 HOH A 54 554 54 HOH HOH . C 3 HOH A 55 555 55 HOH HOH . C 3 HOH A 56 556 56 HOH HOH . C 3 HOH A 57 557 57 HOH HOH . C 3 HOH A 58 558 58 HOH HOH . C 3 HOH A 59 559 59 HOH HOH . C 3 HOH A 60 560 60 HOH HOH . C 3 HOH A 61 561 61 HOH HOH . C 3 HOH A 62 562 62 HOH HOH . C 3 HOH A 63 563 63 HOH HOH . C 3 HOH A 64 564 64 HOH HOH . C 3 HOH A 65 565 65 HOH HOH . C 3 HOH A 66 566 66 HOH HOH . C 3 HOH A 67 567 67 HOH HOH . C 3 HOH A 68 568 68 HOH HOH . C 3 HOH A 69 569 69 HOH HOH . C 3 HOH A 70 570 70 HOH HOH . C 3 HOH A 71 571 71 HOH HOH . C 3 HOH A 72 572 72 HOH HOH . C 3 HOH A 73 573 73 HOH HOH . C 3 HOH A 74 574 74 HOH HOH . C 3 HOH A 75 575 75 HOH HOH . C 3 HOH A 76 576 76 HOH HOH . C 3 HOH A 77 577 77 HOH HOH . C 3 HOH A 78 578 78 HOH HOH . C 3 HOH A 79 579 79 HOH HOH . C 3 HOH A 80 580 80 HOH HOH . C 3 HOH A 81 581 81 HOH HOH . C 3 HOH A 82 582 82 HOH HOH . C 3 HOH A 83 583 83 HOH HOH . C 3 HOH A 84 584 84 HOH HOH . C 3 HOH A 85 585 85 HOH HOH . C 3 HOH A 86 586 86 HOH HOH . C 3 HOH A 87 587 87 HOH HOH . C 3 HOH A 88 588 88 HOH HOH . C 3 HOH A 89 589 89 HOH HOH . C 3 HOH A 90 590 90 HOH HOH . C 3 HOH A 91 591 91 HOH HOH . C 3 HOH A 92 592 92 HOH HOH . C 3 HOH A 93 593 93 HOH HOH . C 3 HOH A 94 594 94 HOH HOH . C 3 HOH A 95 595 95 HOH HOH . C 3 HOH A 96 596 96 HOH HOH . C 3 HOH A 97 597 97 HOH HOH . C 3 HOH A 98 598 98 HOH HOH . C 3 HOH A 99 599 99 HOH HOH . C 3 HOH A 100 600 100 HOH HOH . C 3 HOH A 101 601 101 HOH HOH . C 3 HOH A 102 602 102 HOH HOH . C 3 HOH A 103 603 103 HOH HOH . C 3 HOH A 104 604 104 HOH HOH . C 3 HOH A 105 605 105 HOH HOH . C 3 HOH A 106 606 106 HOH HOH . C 3 HOH A 107 607 107 HOH HOH . C 3 HOH A 108 608 108 HOH HOH . C 3 HOH A 109 609 109 HOH HOH . C 3 HOH A 110 610 110 HOH HOH . C 3 HOH A 111 611 111 HOH HOH . C 3 HOH A 112 612 112 HOH HOH . C 3 HOH A 113 613 113 HOH HOH . C 3 HOH A 114 614 114 HOH HOH . C 3 HOH A 115 615 115 HOH HOH . C 3 HOH A 116 616 116 HOH HOH . C 3 HOH A 117 617 117 HOH HOH . C 3 HOH A 118 618 118 HOH HOH . C 3 HOH A 119 619 119 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 KH3 . . . B 2 -38.722 6.128 -22.689 1 42.9 ? O KH3 401 A 1 HETATM 2 C C KH3 . . . B 2 -38.245 5.48 -21.726 1 42.8 ? C KH3 401 A 1 HETATM 3 C CA KH3 . . . B 2 -38.149 3.98 -21.834 1 47.74 ? CA KH3 401 A 1 HETATM 4 N N KH3 . . . B 2 -38.466 3.559 -23.19 1 42.34 ? N KH3 401 A 1 HETATM 5 C CB KH3 . . . B 2 -36.734 3.532 -21.479 1 39.43 ? CB KH3 401 A 1 HETATM 6 C CG KH3 . . . B 2 -36.69 2.063 -21.086 1 39.03 ? CG KH3 401 A 1 HETATM 7 N ND KH3 . . . B 2 -37.45 1.933 -19.84 1 46.11 ? ND KH3 401 A 1 HETATM 8 C CE KH3 . . . B 2 -36.481 1.969 -18.748 1 29.41 ? CE KH3 401 A 1 HETATM 9 C C11 KH3 . . . B 2 -36.15 0.556 -18.3 1 44.54 ? C11 KH3 401 A 1 HETATM 10 N N12 KH3 . . . B 2 -34.973 0.449 -17.428 1 48.9 ? N12 KH3 401 A 1 HETATM 11 C C13 KH3 . . . B 2 -35.003 -0.957 -16.965 1 59.78 ? C13 KH3 401 A 1 HETATM 12 C C14 KH3 . . . B 2 -33.726 -1.393 -16.263 1 61.8 ? C14 KH3 401 A 1 HETATM 13 C C15 KH3 . . . B 2 -33.944 -2.678 -15.47 1 59.99 ? C15 KH3 401 A 1 HETATM 14 C C16 KH3 . . . B 2 -34.176 -3.876 -16.379 1 67.19 ? C16 KH3 401 A 1 HETATM 15 C C17 KH3 . . . B 2 -34.209 -5.17 -15.571 1 65.61 ? C17 KH3 401 A 1 HETATM 16 C C18 KH3 . . . B 2 -32.819 -5.635 -15.198 1 65.99 ? C18 KH3 401 A 1 HETATM 17 C C5' KH3 . . . B 2 -38.23 0.679 -19.798 1 54.26 ? C5' KH3 401 A 1 HETATM 18 C C4' KH3 . . . B 2 -39.673 1.051 -20.081 1 51.4 ? C4' KH3 401 A 1 HETATM 19 O O4' KH3 . . . B 2 -39.782 1.275 -21.489 1 61.8 ? O4' KH3 401 A 1 HETATM 20 C C1' KH3 . . . B 2 -40.844 0.493 -22.037 1 68.56 ? C1' KH3 401 A 1 HETATM 21 C C2' KH3 . . . B 2 -41.694 0.093 -20.854 1 66.09 ? C2' KH3 401 A 1 HETATM 22 O O2' KH3 . . . B 2 -42.6 1.166 -20.584 1 67.22 ? O2' KH3 401 A 1 HETATM 23 C C3' KH3 . . . B 2 -40.686 -0.03 -19.739 1 61.94 ? C3' KH3 401 A 1 HETATM 24 O O3' KH3 . . . B 2 -41.311 0.207 -18.474 1 65.63 ? O3' KH3 401 A 1 HETATM 25 N N9 KH3 . . . B 2 -40.279 -0.709 -22.691 1 76.5 ? N9 KH3 401 A 1 HETATM 26 C C8 KH3 . . . B 2 -39.043 -1.217 -22.525 1 75.41 ? C8 KH3 401 A 1 HETATM 27 N N7 KH3 . . . B 2 -38.86 -2.311 -23.302 1 73.6 ? N7 KH3 401 A 1 HETATM 28 C C5 KH3 . . . B 2 -39.997 -2.515 -23.987 1 76.31 ? C5 KH3 401 A 1 HETATM 29 C C6 KH3 . . . B 2 -40.481 -3.5 -24.979 1 75.88 ? C6 KH3 401 A 1 HETATM 30 N N6 KH3 . . . B 2 -39.686 -4.514 -25.404 1 69.75 ? N6 KH3 401 A 1 HETATM 31 C C4 KH3 . . . B 2 -40.926 -1.449 -23.588 1 78.95 ? C4 KH3 401 A 1 HETATM 32 N N3 KH3 . . . B 2 -42.167 -1.416 -24.126 1 80.91 ? N3 KH3 401 A 1 HETATM 33 C C2 KH3 . . . B 2 -42.542 -2.34 -25.024 1 80.47 ? C2 KH3 401 A 1 HETATM 34 N N1 KH3 . . . B 2 -41.742 -3.34 -25.44 1 77.63 ? N1 KH3 401 A 1 HETATM 35 O OXT KH3 . . . B 2 -37.853 6.022 -20.666 1 45.45 ? OXT KH3 401 A 1 # _model_server_stats.io_time_ms 120 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 35 #