0.015421 0.000000 0.000000 0.000000 0.015421 0.000000 0.000000 0.000000 0.009427 0.00000 0.00000 0.00000 0000-0003-1791-8937 Park, J. 0000-0002-3400-7353 Hyun, S. 0000-0002-5524-9802 Lee, S.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 96 90.00 90.00 90.00 64.846 64.846 106.077 C3 H7 N O2 89.093 D-ALANINE D-peptide linking C3 H7 N O2 S 121.158 D-CYSTEINE D-peptide linking C6 H13 N O2 131.173 D-LEUCINE D-peptide linking C6 H14 N2 O2 146.188 D-LYSINE D-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer N 1 N N N 2 R C N 3 N C N 4 N C N 5 N O N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N S N 20 N O N 21 N H N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N N N 29 R C N 30 N C N 31 N C N 32 N C N 33 N C N 34 N C N 35 N O N 36 N O N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N N N 51 R C N 52 N C N 53 N O N 54 N C N 55 N C N 56 N C N 57 N C N 58 N N N 59 N O N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 N C N 76 N C N 77 N O N 78 N O N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N O N 85 N H N 86 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N doub N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N doub N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N doub N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing US Acs Omega 2470-1343 9 32991 32999 39100342 De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure 2024 0000-0003-1791-8937 0000-0002-3400-7353 0000-0002-5524-9802 10.2210/pdb9j3s/pdb pdb_00009j3s 100 1 N PIXEL 2021-12-08 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 1.26 1.0 BL44XU SPring-8 1.26 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1800.414 DLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY 6 syn polymer 18.015 water 17 nat water no yes (DLE)(DLY)(DLY)(DLE)(DCY)(DLY)(DLE)(DLE)(DLY)(DLY)(DLE)(DCY)(DLY)(DLE)(DAL)G LKKLCKLLKKLCKLAG A,C,B,D,E,F polypeptide(D) n n n n n n n n n n n n n n n n 1 3.16 61.10 VAPOR DIFFUSION, SITTING DROP 60% PEG 400 293 repository Initial release 1 0 2025-06-25 Korea, Republic Of National Research Foundation (NRF, Korea) sjlee@chungbuk.ac.kr 0000-0002-5524-9802 Soo Jae Lee principal investigator/group leader N PDBJ Y PDBJ 2024-08-08 REL REL HOH water 32630 synthetic construct sample 1 16 N Y A DCY 5 Disulfide bridge SG A DCY 5 B DCY 12 SG C DCY 12 1_555 1_555 None A DCY 12 Disulfide bridge SG A DCY 12 B DCY 5 SG C DCY 5 1_555 1_555 None C DCY 5 Disulfide bridge SG B DCY 5 D DCY 12 SG D DCY 12 1_555 1_555 None C DCY 12 Disulfide bridge SG B DCY 12 D DCY 5 SG D DCY 5 1_555 1_555 None E DCY 5 Disulfide bridge SG E DCY 5 F DCY 12 SG F DCY 12 1_555 1_555 None E DCY 12 Disulfide bridge SG E DCY 12 F DCY 5 SG F DCY 5 1_555 1_555 None HOH 4 2 HOH HOH 101 C HOH 15 2 HOH HOH 102 C HOH 3 2 HOH HOH 103 C HOH 5 2 HOH HOH 104 C HOH 17 2 HOH HOH 101 B HOH 2 2 HOH HOH 102 B HOH 13 2 HOH HOH 103 B HOH 11 2 HOH HOH 101 D HOH 8 2 HOH HOH 102 D HOH 9 2 HOH HOH 103 D HOH 1 2 HOH HOH 104 D HOH 16 2 HOH HOH 105 D HOH 6 2 HOH HOH 106 D HOH 10 2 HOH HOH 101 E HOH 14 2 HOH HOH 102 E HOH 7 2 HOH HOH 103 E HOH 12 2 HOH HOH 104 E DLE 1 n 1 DLE 1 A DLY 2 n 2 DLY 2 A DLY 3 n 3 DLY 3 A DLE 4 n 4 DLE 4 A DCY 5 n 5 DCY 5 A DLY 6 n 6 DLY 6 A DLE 7 n 7 DLE 7 A DLE 8 n 8 DLE 8 A DLY 9 n 9 DLY 9 A DLY 10 n 10 DLY 10 A DLE 11 n 11 DLE 11 A DCY 12 n 12 DCY 12 A DLY 13 n 13 DLY 13 A DLE 14 n 14 DLE 14 A DAL 15 n 15 DAL 15 A GLY 16 n 16 GLY 16 A DLE 1 n 1 DLE 1 C DLY 2 n 2 DLY 2 C DLY 3 n 3 DLY 3 C DLE 4 n 4 DLE 4 C DCY 5 n 5 DCY 5 C DLY 6 n 6 DLY 6 C DLE 7 n 7 DLE 7 C DLE 8 n 8 DLE 8 C DLY 9 n 9 DLY 9 C DLY 10 n 10 DLY 10 C DLE 11 n 11 DLE 11 C DCY 12 n 12 DCY 12 C DLY 13 n 13 DLY 13 C DLE 14 n 14 DLE 14 C DAL 15 n 15 DAL 15 C GLY 16 n 16 GLY 16 C DLE 1 n 1 DLE 1 B DLY 2 n 2 DLY 2 B DLY 3 n 3 DLY 3 B DLE 4 n 4 DLE 4 B DCY 5 n 5 DCY 5 B DLY 6 n 6 DLY 6 B DLE 7 n 7 DLE 7 B DLE 8 n 8 DLE 8 B DLY 9 n 9 DLY 9 B DLY 10 n 10 DLY 10 B DLE 11 n 11 DLE 11 B DCY 12 n 12 DCY 12 B DLY 13 n 13 DLY 13 B DLE 14 n 14 DLE 14 B DAL 15 n 15 DAL 15 B n 16 16 B DLE 1 n 1 DLE 1 D DLY 2 n 2 DLY 2 D DLY 3 n 3 DLY 3 D DLE 4 n 4 DLE 4 D DCY 5 n 5 DCY 5 D DLY 6 n 6 DLY 6 D DLE 7 n 7 DLE 7 D DLE 8 n 8 DLE 8 D DLY 9 n 9 DLY 9 D DLY 10 n 10 DLY 10 D DLE 11 n 11 DLE 11 D DCY 12 n 12 DCY 12 D DLY 13 n 13 DLY 13 D DLE 14 n 14 DLE 14 D DAL 15 n 15 DAL 15 D GLY 16 n 16 GLY 16 D DLE 1 n 1 DLE 1 E DLY 2 n 2 DLY 2 E DLY 3 n 3 DLY 3 E DLE 4 n 4 DLE 4 E DCY 5 n 5 DCY 5 E DLY 6 n 6 DLY 6 E DLE 7 n 7 DLE 7 E DLE 8 n 8 DLE 8 E DLY 9 n 9 DLY 9 E DLY 10 n 10 DLY 10 E DLE 11 n 11 DLE 11 E DCY 12 n 12 DCY 12 E DLY 13 n 13 DLY 13 E DLE 14 n 14 DLE 14 E DAL 15 n 15 DAL 15 E n 16 16 E DLE 1 n 1 DLE 1 F DLY 2 n 2 DLY 2 F DLY 3 n 3 DLY 3 F DLE 4 n 4 DLE 4 F DCY 5 n 5 DCY 5 F DLY 6 n 6 DLY 6 F DLE 7 n 7 DLE 7 F DLE 8 n 8 DLE 8 F DLY 9 n 9 DLY 9 F DLY 10 n 10 DLY 10 F DLE 11 n 11 DLE 11 F DCY 12 n 12 DCY 12 F DLY 13 n 13 DLY 13 F DLE 14 n 14 DLE 14 F DAL 15 n 15 DAL 15 F n 16 16 F author_and_software_defined_assembly PISA 6 hexameric gel filtration 4460 -81 6610 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 F CG DLE 1 F CG DLE 1 1 Y 1 F CD1 DLE 1 F CD1 DLE 1 1 Y 1 F CD2 DLE 1 F CD2 DLE 1 1 Y 1 B GLY 16 C GLY 16 1 Y 1 E GLY 16 E GLY 16 1 Y 1 F GLY 16 F GLY 16 1 Y 1 E E O O DLE HOH 1 101 2.13 1 D D O O HOH HOH 103 104 2.19 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.3352 0.3209 0.3216 1.68 45.85 651 13375 4.87 99.98 0.22 RANDOM 1 THROUGHOUT 1.35 SAD 39.74 0.90 1.11 MAXIMUM LIKELIHOOD MASK 1.68 45.85 17 742 0 0 725 0.009 719 1.629 927 22.901 315 0.139 125 0.004 89 0.3978 0.3452 1.81 119 2502 100.00 0.3562 0.3436 1.99 140 2472 100.00 0.3615 0.3002 2.27 140 2512 100.00 0.3377 0.3224 2.87 116 2555 100.00 0.3240 0.3211 45.85 136 2683 100.00 1.6 45.90 9J3S 13375 1 1 24.67 13.6 99.94 1.92 4.39 1304 0.47 1 refinement PHENIX (1.19.2_4158: ???) data reduction XDS data scaling Aimless phasing PHENIX N De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure 1 N N 1 N N 1 N N 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N A DLE 1 A DLE 1 HELX_P A GLY 16 A GLY 16 1 AA1 16 C DLY 2 B DLY 2 HELX_P C GLY 16 B GLY 16 1 AA2 15 B DLY 2 C DLY 2 HELX_P B DAL 15 C DAL 15 1 AA3 14 D DLY 2 D DLY 2 HELX_P D GLY 16 D GLY 16 1 AA4 15 E DLY 2 E DLY 2 HELX_P E DAL 15 E DAL 15 1 AA5 14 F DLY 2 F DLY 2 HELX_P F DAL 15 F DAL 15 1 AA6 14 disulf 2.030 A DCY 5 A SG DCY 5 1_555 B DCY 12 C SG DCY 12 1_555 disulf 2.015 A DCY 12 A SG DCY 12 1_555 B DCY 5 C SG DCY 5 1_555 disulf 2.023 C DCY 5 B SG DCY 5 1_555 D DCY 12 D SG DCY 12 1_555 disulf 2.019 C DCY 12 B SG DCY 12 1_555 D DCY 5 D SG DCY 5 1_555 disulf 2.030 E DCY 5 E SG DCY 5 1_555 F DCY 12 F SG DCY 12 1_555 disulf 2.029 E DCY 12 E SG DCY 12 1_555 F DCY 5 F SG DCY 5 1_555 covale 1.328 both A DLE 1 A C DLE 1 1_555 A DLY 2 A N DLY 2 1_555 covale 1.331 both A DLY 2 A C DLY 2 1_555 A DLY 3 A N DLY 3 1_555 covale 1.332 both A DLY 3 A C DLY 3 1_555 A DLE 4 A N DLE 4 1_555 covale 1.327 both A DLE 4 A C DLE 4 1_555 A DCY 5 A N DCY 5 1_555 covale 1.324 both A DCY 5 A C DCY 5 1_555 A DLY 6 A N DLY 6 1_555 covale 1.330 both A DLY 6 A C DLY 6 1_555 A DLE 7 A N DLE 7 1_555 covale 1.332 both A DLE 7 A C DLE 7 1_555 A DLE 8 A N DLE 8 1_555 covale 1.321 both A DLE 8 A C DLE 8 1_555 A DLY 9 A N DLY 9 1_555 covale 1.324 both A DLY 9 A C DLY 9 1_555 A DLY 10 A N DLY 10 1_555 covale 1.337 both A DLY 10 A C DLY 10 1_555 A DLE 11 A N DLE 11 1_555 covale 1.320 both A DLE 11 A C DLE 11 1_555 A DCY 12 A N DCY 12 1_555 covale 1.327 both A DCY 12 A C DCY 12 1_555 A DLY 13 A N DLY 13 1_555 covale 1.341 both A DLY 13 A C DLY 13 1_555 A DLE 14 A N DLE 14 1_555 covale 1.330 both A DLE 14 A C DLE 14 1_555 A DAL 15 A N DAL 15 1_555 covale 1.332 both A DAL 15 A C DAL 15 1_555 A GLY 16 A N GLY 16 1_555 covale 1.328 both C DLE 1 B C DLE 1 1_555 C DLY 2 B N DLY 2 1_555 covale 1.331 both C DLY 2 B C DLY 2 1_555 C DLY 3 B N DLY 3 1_555 covale 1.332 both C DLY 3 B C DLY 3 1_555 C DLE 4 B N DLE 4 1_555 covale 1.326 both C DLE 4 B C DLE 4 1_555 C DCY 5 B N DCY 5 1_555 covale 1.334 both C DCY 5 B C DCY 5 1_555 C DLY 6 B N DLY 6 1_555 covale 1.334 both C DLY 6 B C DLY 6 1_555 C DLE 7 B N DLE 7 1_555 covale 1.330 both C DLE 7 B C DLE 7 1_555 C DLE 8 B N DLE 8 1_555 covale 1.331 both C DLE 8 B C DLE 8 1_555 C DLY 9 B N DLY 9 1_555 covale 1.320 both C DLY 9 B C DLY 9 1_555 C DLY 10 B N DLY 10 1_555 covale 1.339 both C DLY 10 B C DLY 10 1_555 C DLE 11 B N DLE 11 1_555 covale 1.324 both C DLE 11 B C DLE 11 1_555 C DCY 12 B N DCY 12 1_555 covale 1.336 both C DCY 12 B C DCY 12 1_555 C DLY 13 B N DLY 13 1_555 covale 1.330 both C DLY 13 B C DLY 13 1_555 C DLE 14 B N DLE 14 1_555 covale 1.321 both C DLE 14 B C DLE 14 1_555 C DAL 15 B N DAL 15 1_555 covale 1.322 both C DAL 15 B C DAL 15 1_555 C GLY 16 B N GLY 16 1_555 covale 1.333 both B DLE 1 C C DLE 1 1_555 B DLY 2 C N DLY 2 1_555 covale 1.330 both B DLY 2 C C DLY 2 1_555 B DLY 3 C N DLY 3 1_555 covale 1.329 both B DLY 3 C C DLY 3 1_555 B DLE 4 C N DLE 4 1_555 covale 1.326 both B DLE 4 C C DLE 4 1_555 B DCY 5 C N DCY 5 1_555 covale 1.330 both B DCY 5 C C DCY 5 1_555 B DLY 6 C N DLY 6 1_555 covale 1.330 both B DLY 6 C C DLY 6 1_555 B DLE 7 C N DLE 7 1_555 covale 1.330 both B DLE 7 C C DLE 7 1_555 B DLE 8 C N DLE 8 1_555 covale 1.326 both B DLE 8 C C DLE 8 1_555 B DLY 9 C N DLY 9 1_555 covale 1.330 both B DLY 9 C C DLY 9 1_555 B DLY 10 C N DLY 10 1_555 covale 1.328 both B DLY 10 C C DLY 10 1_555 B DLE 11 C N DLE 11 1_555 covale 1.330 both B DLE 11 C C DLE 11 1_555 B DCY 12 C N DCY 12 1_555 covale 1.327 both B DCY 12 C C DCY 12 1_555 B DLY 13 C N DLY 13 1_555 covale 1.331 both B DLY 13 C C DLY 13 1_555 B DLE 14 C N DLE 14 1_555 covale 1.326 both B DLE 14 C C DLE 14 1_555 B DAL 15 C N DAL 15 1_555 covale 1.320 both D DLE 1 D C DLE 1 1_555 D DLY 2 D N DLY 2 1_555 covale 1.333 both D DLY 2 D C DLY 2 1_555 D DLY 3 D N DLY 3 1_555 covale 1.327 both D DLY 3 D C DLY 3 1_555 D DLE 4 D N DLE 4 1_555 covale 1.326 both D DLE 4 D C DLE 4 1_555 D DCY 5 D N DCY 5 1_555 covale 1.326 both D DCY 5 D C DCY 5 1_555 D DLY 6 D N DLY 6 1_555 covale 1.335 both D DLY 6 D C DLY 6 1_555 D DLE 7 D N DLE 7 1_555 covale 1.331 both D DLE 7 D C DLE 7 1_555 D DLE 8 D N DLE 8 1_555 covale 1.326 both D DLE 8 D C DLE 8 1_555 D DLY 9 D N DLY 9 1_555 covale 1.328 both D DLY 9 D C DLY 9 1_555 D DLY 10 D N DLY 10 1_555 covale 1.330 both D DLY 10 D C DLY 10 1_555 D DLE 11 D N DLE 11 1_555 covale 1.324 both D DLE 11 D C DLE 11 1_555 D DCY 12 D N DCY 12 1_555 covale 1.323 both D DCY 12 D C DCY 12 1_555 D DLY 13 D N DLY 13 1_555 covale 1.335 both D DLY 13 D C DLY 13 1_555 D DLE 14 D N DLE 14 1_555 covale 1.327 both D DLE 14 D C DLE 14 1_555 D DAL 15 D N DAL 15 1_555 covale 1.328 both D DAL 15 D C DAL 15 1_555 D GLY 16 D N GLY 16 1_555 covale 1.327 both E DLE 1 E C DLE 1 1_555 E DLY 2 E N DLY 2 1_555 covale 1.333 both E DLY 2 E C DLY 2 1_555 E DLY 3 E N DLY 3 1_555 covale 1.332 both E DLY 3 E C DLY 3 1_555 E DLE 4 E N DLE 4 1_555 covale 1.330 both E DLE 4 E C DLE 4 1_555 E DCY 5 E N DCY 5 1_555 covale 1.329 both E DCY 5 E C DCY 5 1_555 E DLY 6 E N DLY 6 1_555 covale 1.331 both E DLY 6 E C DLY 6 1_555 E DLE 7 E N DLE 7 1_555 covale 1.329 both E DLE 7 E C DLE 7 1_555 E DLE 8 E N DLE 8 1_555 covale 1.326 both E DLE 8 E C DLE 8 1_555 E DLY 9 E N DLY 9 1_555 covale 1.328 both E DLY 9 E C DLY 9 1_555 E DLY 10 E N DLY 10 1_555 covale 1.331 both E DLY 10 E C DLY 10 1_555 E DLE 11 E N DLE 11 1_555 covale 1.329 both E DLE 11 E C DLE 11 1_555 E DCY 12 E N DCY 12 1_555 covale 1.324 both E DCY 12 E C DCY 12 1_555 E DLY 13 E N DLY 13 1_555 covale 1.330 both E DLY 13 E C DLY 13 1_555 E DLE 14 E N DLE 14 1_555 covale 1.331 both E DLE 14 E C DLE 14 1_555 E DAL 15 E N DAL 15 1_555 covale 1.332 both F DLE 1 F C DLE 1 1_555 F DLY 2 F N DLY 2 1_555 covale 1.329 both F DLY 2 F C DLY 2 1_555 F DLY 3 F N DLY 3 1_555 covale 1.332 both F DLY 3 F C DLY 3 1_555 F DLE 4 F N DLE 4 1_555 covale 1.325 both F DLE 4 F C DLE 4 1_555 F DCY 5 F N DCY 5 1_555 covale 1.328 both F DCY 5 F C DCY 5 1_555 F DLY 6 F N DLY 6 1_555 covale 1.334 both F DLY 6 F C DLY 6 1_555 F DLE 7 F N DLE 7 1_555 covale 1.327 both F DLE 7 F C DLE 7 1_555 F DLE 8 F N DLE 8 1_555 covale 1.327 both F DLE 8 F C DLE 8 1_555 F DLY 9 F N DLY 9 1_555 covale 1.332 both F DLY 9 F C DLY 9 1_555 F DLY 10 F N DLY 10 1_555 covale 1.332 both F DLY 10 F C DLY 10 1_555 F DLE 11 F N DLE 11 1_555 covale 1.327 both F DLE 11 F C DLE 11 1_555 F DCY 12 F N DCY 12 1_555 covale 1.331 both F DCY 12 F C DCY 12 1_555 F DLY 13 F N DLY 13 1_555 covale 1.330 both F DLY 13 F C DLY 13 1_555 F DLE 14 F N DLE 14 1_555 covale 1.330 both F DLE 14 F C DLE 14 1_555 F DAL 15 F N DAL 15 1_555 DE NOVO PROTEIN CPP, Protein design, Peptide self-assembly, Amphipathic peptides, Cell-penetration, DE NOVO PROTEIN 9J3S PDB 1 1 9J3S 1 16 9J3S 1 16 9J3S A 1 1 16 1 16 9J3S 1 16 9J3S C 1 1 16 1 16 9J3S 1 16 9J3S B 1 1 16 1 16 9J3S 1 16 9J3S D 1 1 16 1 16 9J3S 1 16 9J3S E 1 1 16 1 16 9J3S 1 16 9J3S F 1 1 16 98 I 41 2 2