0.031196 0.000000 0.000000 0.000000 0.018369 0.000000 0.000000 0.000000 0.046688 0.00000 0.00000 0.00000 Park, S. Kanazawa, H. Kondo, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 32.055 54.440 21.419 C4 H12 N O5 P 185.116 acyclic D-threoninol nucleic acid [(2~{S},3~{S})-2-azanyl-3-oxidanyl-butyl] dihydrogen phosphate DNA linking Ba 2 137.327 BARIUM ION non-polymer C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N C N 6 S C N 7 N N N 8 S C N 9 N O N 10 N C N 11 N H N 12 N H N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H N 22 N O N 23 N H N 24 N BA N 25 N O N 26 N P N 27 N O N 28 N O N 29 N O N 30 N C N 31 R C N 32 N O N 33 S C N 34 N O N 35 N C N 36 R C Y 37 N N Y 38 N C Y 39 N N Y 40 N C N 41 N C N 42 N O N 43 N N N 44 N C N 45 N N N 46 N N Y 47 N C N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N O N 63 N P N 64 N O N 65 N O N 66 N O N 67 N C N 68 R C N 69 N O N 70 S C N 71 N O N 72 N C N 73 R C N 74 N N N 75 N C N 76 N O N 77 N N N 78 N C N 79 N O N 80 N C N 81 N C N 82 N C N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N O N 99 N H N 100 N H N 101 N N N 102 S C N 103 N C N 104 N O N 105 N C Y 106 N C Y 107 N C Y 108 N C Y 109 N C Y 110 N C Y 111 N C N 112 N O N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 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 sing 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 sing N 20 N sing N 21 N doub N 22 N sing N 23 N sing N 24 N sing N 25 N doub 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 sing N 45 N sing Y 46 N sing Y 47 N sing Y 48 N doub N 49 N sing Y 50 N sing N 51 N sing Y 52 N doub N 53 N doub N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N doub N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub 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 sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N doub N 88 N sing N 89 N sing N 90 N sing N 91 N doub N 92 N sing N 93 N sing N 94 N doub N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing Y 112 N doub Y 113 N sing Y 114 N sing N 115 N sing Y 116 N doub N 117 N sing Y 118 N doub N 119 N sing Y 120 N sing N 121 N sing N 122 N sing N 123 N sing To Be Published 0353 Crystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer 10.2210/pdb9u3i/pdb pdb_00009u3i 100 1 N PIXEL 2023-06-11 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 0.98 1.0 BL-17A Photon Factory 0.98 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 4605.959 DNA (5'-D(*GP*G*(FNH)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3') 1 syn polymer 165.189 PHENYLALANINE 1 syn non-polymer 137.327 BARIUM ION 1 syn non-polymer 18.015 water 67 nat water no yes (DG)(DG)(A1L8S)(DT)(DG)(DG)(DT)(DG)(DT)(DG)(DG)(DT)(DT)(DG)(DG) GGXTGGTGTGGTTGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n 1 2.02 39.21 VAPOR DIFFUSION, SITTING DROP 7.0 MOPS, spermine, barium chloride, MPD 293 -2.443 3 6 B 10 B 15 -90.402 B_DG10:DG15_B 1 -16.338 1.354 0.223 3.514 8.880 3 6 B 11 B 14 91.550 B_DG11:DG14_B 2 1.978 -1.333 -0.559 -3.551 -1.917 2 12 B 4 B 13 177.655 B_DT4:DT13_B 3 -42.625 1.370 -0.004 -1.607 0.186 179.712 B B 10 11 -73.134 B B 15 14 0.108 -146.265 -0.887 -3.690 BB_DG10DG11:DG14DG15_BB 1 86.691 -43.347 176.681 -1.843 0.445 -0.426 166.709 B B 11 4 84.611 B B 14 13 1.709 159.832 -2.432 -0.337 BB_DG11DT4:DT13DG14_BB 2 45.095 -23.872 34.694 -0.625 1.353 repository Initial release 1 0 2026-03-25 Japan Japan Agency for Medical Research and Development (AMED) j.kondo@sophia.ac.jp 0000-0002-5682-3685 Jiro Kondo principal investigator/group leader N PDBJ N PDBJ 2025-03-18 REL REL A1L8S A1L8S SUBJECT OF INVESTIGATION PHE PHE SUBJECT OF INVESTIGATION PHE PHENYLALANINE BA BARIUM ION HOH water 32630 synthetic construct sample 1 15 2853804 DNA molecule sample Y N 7D31 PDB experimental model FNH 3 2 PHE PHE 101 B BA 1 3 BA BA 102 B HOH 44 4 HOH HOH 201 B HOH 23 4 HOH HOH 202 B HOH 27 4 HOH HOH 203 B HOH 40 4 HOH HOH 204 B HOH 37 4 HOH HOH 205 B HOH 5 4 HOH HOH 206 B HOH 8 4 HOH HOH 207 B HOH 39 4 HOH HOH 208 B HOH 4 4 HOH HOH 209 B HOH 50 4 HOH HOH 210 B HOH 57 4 HOH HOH 211 B HOH 59 4 HOH HOH 212 B HOH 3 4 HOH HOH 213 B HOH 38 4 HOH HOH 214 B HOH 16 4 HOH HOH 215 B HOH 1 4 HOH HOH 216 B HOH 14 4 HOH HOH 217 B HOH 61 4 HOH HOH 218 B HOH 6 4 HOH HOH 219 B HOH 34 4 HOH HOH 220 B HOH 46 4 HOH HOH 221 B HOH 10 4 HOH HOH 222 B HOH 21 4 HOH HOH 223 B HOH 33 4 HOH HOH 224 B HOH 15 4 HOH HOH 225 B HOH 2 4 HOH HOH 226 B HOH 30 4 HOH HOH 227 B HOH 43 4 HOH HOH 228 B HOH 13 4 HOH HOH 229 B HOH 52 4 HOH HOH 230 B HOH 65 4 HOH HOH 231 B HOH 36 4 HOH HOH 232 B HOH 26 4 HOH HOH 233 B HOH 58 4 HOH HOH 234 B HOH 45 4 HOH HOH 235 B HOH 17 4 HOH HOH 236 B HOH 24 4 HOH HOH 237 B HOH 19 4 HOH HOH 238 B HOH 32 4 HOH HOH 239 B HOH 22 4 HOH HOH 240 B HOH 67 4 HOH HOH 241 B HOH 11 4 HOH HOH 242 B HOH 7 4 HOH HOH 243 B HOH 41 4 HOH HOH 244 B HOH 9 4 HOH HOH 245 B HOH 55 4 HOH HOH 246 B HOH 60 4 HOH HOH 247 B HOH 48 4 HOH HOH 248 B HOH 12 4 HOH HOH 249 B HOH 64 4 HOH HOH 250 B HOH 53 4 HOH HOH 251 B HOH 28 4 HOH HOH 252 B HOH 63 4 HOH HOH 253 B HOH 20 4 HOH HOH 254 B HOH 51 4 HOH HOH 255 B HOH 18 4 HOH HOH 256 B HOH 47 4 HOH HOH 257 B HOH 62 4 HOH HOH 258 B HOH 66 4 HOH HOH 259 B HOH 35 4 HOH HOH 260 B HOH 56 4 HOH HOH 261 B HOH 49 4 HOH HOH 262 B HOH 25 4 HOH HOH 263 B HOH 31 4 HOH HOH 264 B HOH 54 4 HOH HOH 265 B HOH 29 4 HOH HOH 266 B HOH 42 4 HOH HOH 267 B DG 1 n 1 DG 1 B DG 2 n 2 DG 2 B FNH 3 n 3 A1L8S 3 B DT 4 n 4 DT 4 B DG 5 n 5 DG 5 B DG 6 n 6 DG 6 B DT 7 n 7 DT 7 B DG 8 n 8 DG 8 B DT 9 n 9 DT 9 B DG 10 n 10 DG 10 B DG 11 n 11 DG 11 B DT 12 n 12 DT 12 B DT 13 n 13 DT 13 B DG 14 n 14 DG 14 B DG 15 n 15 DG 15 B author_and_software_defined_assembly PISA 1 monomeric none 0 0 3110 B DG 1 A O6 DG 1 1_555 B BA 102 C BA BA 1_555 B DG 2 A O6 DG 2 1_555 68.8 B DG 1 A O6 DG 1 1_555 B BA 102 C BA BA 1_555 B DG 5 A O6 DG 5 1_555 116.0 B DG 2 A O6 DG 2 1_555 B BA 102 C BA BA 1_555 B DG 5 A O6 DG 5 1_555 70.8 B DG 1 A O6 DG 1 1_555 B BA 102 C BA BA 1_555 B DG 6 A O6 DG 6 1_555 71.2 B DG 2 A O6 DG 2 1_555 B BA 102 C BA BA 1_555 B DG 6 A O6 DG 6 1_555 100.5 B DG 5 A O6 DG 5 1_555 B BA 102 C BA BA 1_555 B DG 6 A O6 DG 6 1_555 70.0 B DG 1 A O6 DG 1 1_555 B BA 102 C BA BA 1_555 B DG 10 A O6 DG 10 1_555 113.4 B DG 2 A O6 DG 2 1_555 B BA 102 C BA BA 1_555 B DG 10 A O6 DG 10 1_555 171.3 B DG 5 A O6 DG 5 1_555 B BA 102 C BA BA 1_555 B DG 10 A O6 DG 10 1_555 101.2 B DG 6 A O6 DG 6 1_555 B BA 102 C BA BA 1_555 B DG 10 A O6 DG 10 1_555 73.1 B DG 1 A O6 DG 1 1_555 B BA 102 C BA BA 1_555 B DG 11 A O6 DG 11 1_555 170.8 B DG 2 A O6 DG 2 1_555 B BA 102 C BA BA 1_555 B DG 11 A O6 DG 11 1_555 111.8 B DG 5 A O6 DG 5 1_555 B BA 102 C BA BA 1_555 B DG 11 A O6 DG 11 1_555 72.0 B DG 6 A O6 DG 6 1_555 B BA 102 C BA BA 1_555 B DG 11 A O6 DG 11 1_555 117.1 B DG 10 A O6 DG 10 1_555 B BA 102 C BA BA 1_555 B DG 11 A O6 DG 11 1_555 67.5 B DG 1 A O6 DG 1 1_555 B BA 102 C BA BA 1_555 B DG 14 A O6 DG 14 1_555 98.1 B DG 2 A O6 DG 2 1_555 B BA 102 C BA BA 1_555 B DG 14 A O6 DG 14 1_555 71.3 B DG 5 A O6 DG 5 1_555 B BA 102 C BA BA 1_555 B DG 14 A O6 DG 14 1_555 113.0 B DG 6 A O6 DG 6 1_555 B BA 102 C BA BA 1_555 B DG 14 A O6 DG 14 1_555 168.6 B DG 10 A O6 DG 10 1_555 B BA 102 C BA BA 1_555 B DG 14 A O6 DG 14 1_555 115.9 B DG 11 A O6 DG 11 1_555 B BA 102 C BA BA 1_555 B DG 14 A O6 DG 14 1_555 73.9 B DG 1 A O6 DG 1 1_555 B BA 102 C BA BA 1_555 B DG 15 A O6 DG 15 1_555 72.7 B DG 2 A O6 DG 2 1_555 B BA 102 C BA BA 1_555 B DG 15 A O6 DG 15 1_555 117.7 B DG 5 A O6 DG 5 1_555 B BA 102 C BA BA 1_555 B DG 15 A O6 DG 15 1_555 170.4 B DG 6 A O6 DG 6 1_555 B BA 102 C BA BA 1_555 B DG 15 A O6 DG 15 1_555 111.0 B DG 10 A O6 DG 10 1_555 B BA 102 C BA BA 1_555 B DG 15 A O6 DG 15 1_555 70.6 B DG 11 A O6 DG 11 1_555 B BA 102 C BA BA 1_555 B DG 15 A O6 DG 15 1_555 99.7 B DG 14 A O6 DG 14 1_555 B BA 102 C BA BA 1_555 B DG 15 A O6 DG 15 1_555 68.0 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 B HOH 243 D HOH 1 B B O3' P DG A1L8S 2 3 -0.142 0.012 1.607 1.465 Y 1 B B O3' P A1L8S DT 3 4 -0.075 0.012 1.607 1.532 Y 0.2049 0.1787 0.1814 1.20 27.62 1228 12263 10.01 99.14 0.09 1 FREE R-VALUE 1.44 MOLECULAR REPLACEMENT 19.90 0.90 1.10 7D31 ML FLAT BULK SOLVENT MODEL 1.20 27.62 67 384 12 305 0 0.019 351 1.346 536 33.308 135 0.044 58 0.051 17 0.1990 0.1847 1.25 131 1180 97.00 0.1875 0.1757 1.30 132 1188 99.00 0.2298 0.1764 1.37 133 1191 99.00 0.1979 0.1801 1.46 133 1205 99.00 0.1903 0.1740 1.57 136 1211 99.00 0.1881 0.1705 1.73 136 1230 100.00 0.1949 0.1752 1.98 138 1240 100.00 0.2078 0.1901 2.49 140 1254 100.00 0.2170 0.1772 27.62 149 1336 99.00 1.2 27.62 9U3I 12268 0.9990000000000001 0.078 0.08199999999999999 1 22.73 12.3 99.3 0.32299999999999995 1.20 1.23 867 0.992 0.336 1 0.27 1.23 1.26 868 0.992 0.281 1 0.268 1.26 1.3 828 0.995 0.27899999999999997 1 0.244 1.30 1.34 824 0.995 0.255 1 0.233 1.34 1.38 787 0.993 0.243 1 0.18899999999999997 1.38 1.43 782 0.995 0.19699999999999998 1 0.163 1.43 1.49 719 0.996 0.17 1 0.141 1.49 1.55 734 0.998 0.147 1 0.10800000000000001 1.55 1.62 689 0.997 0.113 1 0.095 1.62 1.69 667 0.997 0.1 1 0.087 1.69 1.79 646 0.998 0.091 1 0.08199999999999999 1.79 1.89 596 0.996 0.086 1 0.081 1.89 2.03 574 0.996 0.085 1 0.073 2.03 2.19 531 0.998 0.076 1 0.073 2.19 2.4 504 0.997 0.076 1 0.065 2.40 2.68 455 0.998 0.068 1 0.065 2.68 3.09 397 0.998 0.068 1 0.055999999999999994 3.09 3.79 350 0.9990000000000001 0.059000000000000004 1 0.05 3.79 5.36 288 0.9990000000000001 0.052000000000000005 1 0.049 5.36 27.62 162 0.998 0.052000000000000005 1 refinement PHENIX (1.20.1_4487: ???) data scaling XSCALE data reduction XDS phasing PHASER N Crystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer 1 N N 2 N N 3 N N 4 N N covale 1.465 both B DG 2 A O3' DG 2 1_555 B A1L8S 3 A P A1L8S 3 1_555 covale 1.532 one B A1L8S 3 A O3' A1L8S 3 1_555 B DT 4 A P DT 4 1_555 covale 1.435 both B A1L8S 3 A N4' A1L8S 3 1_555 B PHE 101 B C PHE 1_555 metalc 2.593 B DG 1 A O6 DG 1 1_555 B BA 102 C BA BA 1_555 metalc 2.664 B DG 2 A O6 DG 2 1_555 B BA 102 C BA BA 1_555 metalc 2.675 B DG 5 A O6 DG 5 1_555 B BA 102 C BA BA 1_555 metalc 2.698 B DG 6 A O6 DG 6 1_555 B BA 102 C BA BA 1_555 metalc 2.631 B DG 10 A O6 DG 10 1_555 B BA 102 C BA BA 1_555 metalc 2.578 B DG 11 A O6 DG 11 1_555 B BA 102 C BA BA 1_555 metalc 2.572 B DG 14 A O6 DG 14 1_555 B BA 102 C BA BA 1_555 metalc 2.646 B DG 15 A O6 DG 15 1_555 B BA 102 C BA BA 1_555 hydrog TYPE_6_PAIR B DG 1 A N1 DG 1 1_555 B DG 6 A O6 DG 6 1_555 hydrog TYPE_6_PAIR B DG 1 A N2 DG 1 1_555 B DG 6 A N7 DG 6 1_555 hydrog TYPE_6_PAIR B DG 1 A N7 DG 1 1_555 B DG 15 A N2 DG 15 1_555 hydrog TYPE_6_PAIR B DG 1 A O6 DG 1 1_555 B DG 15 A N1 DG 15 1_555 hydrog TYPE_6_PAIR B DG 2 A N7 DG 2 1_555 B DG 5 A N2 DG 5 1_555 hydrog TYPE_6_PAIR B DG 2 A O6 DG 2 1_555 B DG 5 A N1 DG 5 1_555 hydrog TYPE_6_PAIR B DG 2 A N1 DG 2 1_555 B DG 14 A O6 DG 14 1_555 hydrog TYPE_6_PAIR B DG 2 A N2 DG 2 1_555 B DG 14 A N7 DG 14 1_555 hydrog TYPE_12_PAIR B DT 4 A N3 DT 4 1_555 B DT 13 A O4 DT 13 1_555 hydrog TYPE_12_PAIR B DT 4 A O4 DT 4 1_555 B DT 13 A N3 DT 13 1_555 hydrog TYPE_6_PAIR B DG 5 A N7 DG 5 1_555 B DG 11 A N2 DG 11 1_555 hydrog TYPE_6_PAIR B DG 5 A O6 DG 5 1_555 B DG 11 A N1 DG 11 1_555 hydrog TYPE_6_PAIR B DG 6 A N1 DG 6 1_555 B DG 10 A O6 DG 10 1_555 hydrog TYPE_6_PAIR B DG 6 A N2 DG 6 1_555 B DG 10 A N7 DG 10 1_555 hydrog TYPE_6_PAIR B DG 10 A N1 DG 10 1_555 B DG 15 A O6 DG 15 1_555 hydrog TYPE_6_PAIR B DG 10 A N2 DG 10 1_555 B DG 15 A N7 DG 15 1_555 hydrog TYPE_6_PAIR B DG 11 A N7 DG 11 1_555 B DG 14 A N2 DG 14 1_555 hydrog TYPE_6_PAIR B DG 11 A O6 DG 11 1_555 B DG 14 A N1 DG 14 1_555 DNA DNA, aptamer 9U3I PDB 1 1 9U3I 1 15 9U3I 1 15 9U3I B 1 1 15 18 P 21 21 2