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PDBsum entry 3jb9
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Top Page protein dna_rna ligands metals Protein-protein interface(s) pores links
Pore analysis for: 3jb9 calculated with MOLE 2.0 PDB id
3jb9
Pores calculated on whole structure Pores calculated excluding ligands
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72 pores, coloured by radius 71 pores, coloured by radius 71 pores, coloured as in
list below
Pores are connected internal spaces going through the structure. Only pores longer than 25 Å are shown.
Pores
Free R
Length
HPathy
HPhob
Polar
Rel Mut
Residue..type
Ligands
Radius
1 1.68 1.83 64.8 -0.96 -0.47 16.1 89 0 0 0 0 0 0 0  C 80 C U 81 C G 8 N G 9 N A 10 N U 11 N C 12 N A
13 N C 14 N
2 2.30 3.10 73.5 -1.19 -0.52 15.3 77 0 0 0 0 0 0 0  C 80 C U 81 C G 1 N A 2 N U 3 N U 11 N C 12 N
3 1.84 2.38 77.7 -2.17 -0.67 24.5 86 8 5 6 3 1 0 0  A 105 C U 106 C C 107 C
4 1.97 2.29 99.9 -1.11 -0.65 11.8 91 5 4 8 3 1 0 0  G 8 C U 9 C C 10 C A 11 C A 12 C U 81 C U 92 C A
93 C U 94 C G 96 C U 97 C U 98 C U 99 C U 100 C U
101 C G 102 C U 103 C A 104 C
5 1.30 1.30 148.2 -1.51 -0.55 20.6 76 7 4 1 2 0 0 0  U 82 N G 83 N A 84 N G 85 N A 86 N A 1 P U 2 P U
3 P C 4 P UNK 354 r UNK 355 r UNK 391 r UNK 394 r
UNK 395 r UNK 397 r UNK 400 r UNK 401 r UNK 404 r
UNK 433 r UNK 434 r UNK 436 r UNK 441 r UNK 445 r
UNK 446 r UNK 448 r UNK 449 r UNK 470 r UNK 471 r
UNK 473 r UNK 474 r UNK 475 r UNK 478 r UNK 486 r
UNK 490 r UNK 345 x UNK 346 x UNK 349 x UNK 353 x
UNK 357 x UNK 391 x UNK 395 x UNK 398 x
6 1.71 2.56 177.3 -1.23 -0.60 15.7 84 10 9 7 6 2 0 0  G 8 C U 9 C C 10 C A 11 C A 12 C U 81 C U 92 C A
93 C U 94 C G 96 C U 97 C U 98 C U 99 C U 100 C U
101 C G 102 C U 103 C A 104 C A 105 C U 106 C C
107 C
7 1.84 1.97 212.1 -2.03 -0.39 27.2 83 0 0 0 0 0 0 0  G 8 N G 9 N A 10 N U 11 N C 12 N A 13 N C 14 N
UNK 168 a UNK 298 a UNK 301 a UNK 330 a UNK 331 a
8 1.73 2.03 215.8 -1.56 -0.48 23.0 82 17 15 7 11 4 1 0  A 12 C G 14 C G 21 C C 22 C A 72 C G 74 C C 80 C
U 81 C UNK 130 K UNK 137 K UNK 140 K UNK 141 K
9 1.89 2.05 219.3 -1.12 -0.38 15.7 84 18 3 11 15 4 1 0  A 12 C G 14 C G 21 C C 22 C A 72 C G 74 C C 80 C
U 81 C G 52 N G 53 N A 78 N C 79 N A 80 N U 81 N
U 82 N G 83 N A 84 N G 85 N A 86 N A 1 P U 2 P U
3 P C 4 P G 12 P U 15 P U 16 P UNK 338 x UNK 342
x UNK 345 x UNK 349 x UNK 382 x UNK 385 x UNK 388
x UNK 391 x UNK 395 x
10 1.91 1.91 231.0 -1.74 -0.59 19.4 80 15 10 10 7 3 2 1  C 55 N C 71 N A 72 N C 73 N G 75 N G 77 N C 79 N
A 80 N U 81 N U 82 N A 84 N G 85 N A 86 N U 105 O
A 106 O U 107 O A 1 P U 2 P U 3 P C 4 P U 5 P UNK
246 W UNK 250 W UNK 254 W UNK 168 a UNK 294 a UNK
295 a UNK 298 a UNK 301 a UNK 330 a UNK 331 a UNK
335 a UNK 298 x UNK 299 x UNK 300 x UNK 302 x UNK
392 x UNK 393 x UNK 396 x
11 1.82 1.87 227.5 -1.11 -0.35 18.8 80 11 13 10 16 3 4 1  UNK 130 K UNK 137 K UNK 140 K UNK 141 K UNK 239 W
UNK 242 W UNK 246 W UNK 250 W UNK 254 W UNK 168 a
UNK 294 a UNK 295 a UNK 298 a UNK 301 a UNK 330 a
UNK 331 a UNK 335 a
12 1.79 1.85 243.0 -1.54 -0.44 20.4 82 19 12 12 14 6 3 1  G 14 C G 21 C C 22 C A 72 C G 74 C C 80 C U 81 C
UNK 239 W UNK 242 W UNK 246 W UNK 250 W UNK 254 W
UNK 168 a UNK 294 a UNK 295 a UNK 298 a UNK 301 a
UNK 330 a UNK 331 a UNK 335 a
13 1.75 1.77 247.9 -1.56 -0.45 21.1 83 0 0 0 0 0 0 0  U 20 C G 21 C C 22 C UNK 130 K UNK 137 K UNK 140
K UNK 141 K G 8 N G 9 N A 10 N U 11 N C 12 N A 13
N C 14 N U 15 N
14 1.78 1.75 251.4 -1.13 -0.37 14.4 84 0 0 0 0 0 0 0  U 20 C G 21 C C 22 C G 8 N G 9 N A 10 N U 11 N C
12 N A 13 N C 14 N U 15 N G 52 N G 53 N A 78 N C
79 N A 80 N U 81 N U 82 N G 83 N A 84 N G 85 N A
86 N A 1 P U 2 P U 3 P C 4 P G 12 P U 15 P U 16 P
UNK 338 x UNK 342 x UNK 345 x UNK 349 x UNK 382 x
UNK 385 x UNK 388 x UNK 391 x UNK 395 x
15 1.23 1.40 276.9 -1.61 -0.44 18.0 85 0 0 0 0 0 0 0  U 20 C G 21 C C 22 C A 23 C A 24 C A 25 C A 26 C
G 27 C U 29 C A 30 C C 43 C U 44 C A 58 C A 59 C
A 60 C C 61 C G 63 C G 8 N G 9 N A 10 N U 11 N C
12 N A 13 N C 14 N U 15 N
16 1.34 1.60 281.3 -2.01 -0.47 21.7 79 0 0 0 0 0 0 0  G 14 C C 15 C A 16 C C 17 C U 18 C U 29 C A 30 C
A 31 C C 43 C U 44 C A 58 C A 59 C A 60 C U 68 C
U 69 C G 70 C U 71 C A 72 C A 73 C G 74 C U 78 C
G 79 C C 80 C U 86 C G 1 N A 2 N U 3 N
17 2.49 3.34 343.2 -1.69 -0.49 19.7 83 29 15 21 15 5 6 0  A 12 C G 14 C C 15 C A 16 C C 17 C U 18 C U 29 C
A 30 C A 31 C C 43 C U 44 C U 50 C U 51 C A 58 C
A 59 C A 60 C U 68 C U 69 C G 70 C U 71 C A 72 C
A 73 C G 74 C C 80 C U 81 C U 86 C A 47 N G 48 N
U 27 P C 28 P
18 1.59 1.88 348.5 -1.96 -0.47 21.7 81 30 12 18 8 5 6 0  A 12 C G 14 C C 15 C A 16 C C 17 C U 18 C U 29 C
A 30 C A 31 C C 43 C U 44 C A 58 C A 59 C A 60 C
U 68 C U 69 C G 70 C U 71 C A 72 C A 73 C G 74 C
C 80 C U 81 C U 86 C
19 1.21 1.19 367.0 -1.77 -0.49 18.2 80 24 16 18 11 7 8 0  A 30 N C 31 N G 32 N A 33 N U 34 N C 55 N C 71 N
A 72 N C 73 N G 75 N G 77 N C 79 N A 80 N U 81 N
U 82 N A 84 N G 85 N A 86 N U 101 O A 102 O G 104
O U 105 O A 106 O U 107 O A 1 P U 2 P U 3 P C 4 P
U 5 P UNK 298 x UNK 299 x UNK 300 x UNK 302 x UNK
392 x UNK 393 x UNK 396 x
20 1.74 1.86 380.9 -1.16 -0.35 18.0 83 31 16 17 22 6 7 0  A 12 C G 14 C G 21 C C 22 C A 72 C G 74 C C 80 C
U 81 C UNK 529 W UNK 555 W UNK 558 W UNK 601 W
UNK 604 W UNK 627 W UNK 628 W UNK 629 W UNK 631 W
UNK 632 W UNK 25 x UNK 27 x UNK 28 x UNK 49 x UNK
50 x UNK 51 x UNK 52 x
21 2.18 2.18 355.3 -1.86 -0.50 20.8 82 25 15 16 14 4 6 1  C 55 N C 71 N A 72 N C 73 N U 74 N G 75 N U 105 O
A 106 O U 107 O UNK 15 R UNK 18 R UNK 22 R UNK
246 W UNK 250 W UNK 254 W UNK 168 a UNK 294 a UNK
295 a UNK 298 a UNK 301 a UNK 330 a UNK 331 a UNK
335 a UNK 379 x UNK 380 x
22 1.20 1.38 375.5 -1.55 -0.42 17.6 83 24 15 30 21 4 14 0  G 46 C C 47 C C 48 C U 50 C U 52 C A 53 C C 54 C
C 55 C U 27 P C 28 P
23 1.30 3.56 388.3 -1.59 -0.40 19.5 82 32 17 18 20 7 5 1  C 22 C A 23 C A 24 C A 25 C A 26 C G 27 C U 29 C
A 30 C C 43 C U 44 C A 58 C A 59 C A 60 C C 61 C
G 63 C UNK 239 W UNK 242 W UNK 246 W UNK 250 W
UNK 254 W UNK 168 a UNK 294 a UNK 295 a UNK 298 a
UNK 301 a UNK 330 a UNK 331 a UNK 335 a
24 1.43 1.58 393.7 -1.64 -0.43 18.8 83 0 0 0 0 0 0 0  U 20 C G 21 C C 22 C A 23 C A 24 C A 25 C A 26 C
G 27 C U 29 C A 30 C C 43 C U 44 C A 58 C A 59 C
A 60 C C 61 C G 63 C G 8 N G 9 N A 10 N U 11 N C
12 N A 13 N C 14 N U 15 N
25 1.79 1.76 397.7 -1.80 -0.51 22.5 82 0 0 0 0 0 0 0  G 8 N G 9 N A 10 N U 11 N C 12 N A 13 N C 14 N A
23 N A 24 N A 33 N U 34 N A 35 N C 36 N A 37 N G
38 N A 39 N G 43 N A 44 N G 100 O U 101 O A 29 P
A 30 P U 32 P U 496 Q A 497 Q C 498 Q U 499 Q A
500 Q A 501 Q
26 1.57 1.59 427.2 -1.09 -0.35 17.3 83 29 17 22 29 4 10 1  UNK 239 W UNK 242 W UNK 246 W UNK 250 W UNK 254 W
UNK 529 W UNK 555 W UNK 558 W UNK 601 W UNK 604 W
UNK 627 W UNK 628 W UNK 629 W UNK 631 W UNK 632 W
UNK 168 a UNK 294 a UNK 295 a UNK 298 a UNK 301 a
UNK 330 a UNK 331 a UNK 335 a UNK 25 x UNK 27 x
UNK 28 x UNK 50 x UNK 51 x UNK 52 x
27 1.47 1.73 407.5 -1.05 -0.29 15.7 79 31 14 27 25 15 5 0  A 12 C G 14 C C 15 C A 16 C C 17 C U 18 C U 29 C
A 30 C A 31 C C 43 C U 44 C U 50 C U 51 C A 58 C
A 59 C A 60 C U 68 C U 69 C G 70 C U 71 C A 72 C
A 73 C G 74 C C 80 C U 81 C U 86 C A 47 N G 48 N
A 30 P C 504 Q
28 1.50 2.62 420.8 -1.09 -0.34 15.0 79 19 18 28 25 10 7 1  A 30 N C 31 N G 32 N A 33 N U 34 N G 100 O U 101
O A 102 O G 104 O U 105 O A 106 O U 107 O UNK 246
W UNK 250 W UNK 254 W UNK 168 a UNK 294 a UNK 295
a UNK 298 a UNK 301 a UNK 330 a UNK 331 a UNK 335
a
29 1.21 1.39 458.7 -1.31 -0.24 16.4 79 23 24 34 30 14 13 0  
30 1.46 1.85 437.9 -1.40 -0.32 20.1 79 0 0 0 0 0 0 0  G 8 N G 9 N A 10 N U 11 N C 12 N A 13 N C 14 N A
23 N A 24 N
31 1.18 2.26 42.8 0.48 0.62 3.0 73 2 1 4 6 7 3 0  
32 2.33 4.12 44.2 -1.28 -0.44 17.1 85 1 5 4 5 1 1 0  
33 1.29 1.45 45.7 0.49 0.28 6.2 70 2 1 4 8 4 2 0  
34 1.70 1.70 46.4 -0.95 -0.77 8.7 78 1 0 1 0 0 0 0  UNK 155 r UNK 178 r UNK 181 r UNK 182 r UNK 184 r
UNK 185 r UNK 186 r UNK 187 r UNK 189 r UNK 191 r
UNK 192 r UNK 195 r UNK 209 r UNK 210 r UNK 211 r
UNK 213 r UNK 214 r UNK 216 r UNK 239 r UNK 242 r
UNK 246 r
35 1.40 1.40 55.0 -0.95 -0.77 8.7 78 1 0 1 0 0 0 0  UNK 150 r UNK 153 r UNK 158 r UNK 159 r UNK 176 r
UNK 178 r UNK 180 r UNK 181 r UNK 182 r UNK 183 r
UNK 184 r UNK 191 r UNK 192 r UNK 195 r UNK 209 r
UNK 210 r UNK 211 r UNK 213 r UNK 214 r UNK 216 r
UNK 239 r UNK 242 r UNK 246 r
36 1.37 1.58 66.3 0.50 0.13 8.5 76 0 4 1 18 11 1 1  
37 1.48 1.48 66.2 -2.80 -0.77 19.5 86 3 2 4 0 0 0 0  UNK 216 r UNK 224 r UNK 227 r UNK 228 r UNK 243 r
UNK 244 r UNK 245 r UNK 246 r UNK 247 r UNK 248 r
UNK 249 r UNK 258 r UNK 261 r UNK 262 r UNK 276 r
UNK 278 r UNK 280 r UNK 281 r UNK 284 r UNK 310 r
UNK 313 r UNK 316 r
38 1.51 1.51 72.3 -2.10 -0.79 14.5 88 2 2 3 0 0 0 0  UNK 216 r UNK 224 r UNK 227 r UNK 228 r UNK 243 r
UNK 244 r UNK 245 r UNK 246 r UNK 247 r UNK 248 r
UNK 249 r UNK 258 r UNK 261 r UNK 262 r UNK 276 r
UNK 278 r UNK 280 r UNK 281 r UNK 283 r UNK 284 r
UNK 287 r UNK 288 r UNK 290 r UNK 292 r UNK 310 r
UNK 313 r UNK 314 r UNK 317 r UNK 318 r UNK 322 r
39 1.38 1.55 80.2 -1.70 -0.47 16.2 83 8 7 10 4 5 4 0  
40 1.88 2.76 86.5 -1.52 -0.14 28.4 79 9 8 4 8 2 0 0  UNK 276 r UNK 280 r UNK 310 r UNK 313 r UNK 316 r
41 1.46 1.46 89.2 -2.34 -0.77 15.9 86 3 2 4 0 0 0 0  UNK 197 r UNK 200 r UNK 201 r UNK 212 r UNK 226 r
UNK 227 r UNK 228 r UNK 229 r UNK 230 r UNK 231 r
UNK 240 r UNK 241 r UNK 243 r UNK 244 r UNK 245 r
UNK 261 r UNK 262 r UNK 265 r UNK 274 r UNK 276 r
UNK 277 r UNK 278 r UNK 280 r UNK 281 r UNK 284 r
UNK 310 r UNK 313 r UNK 316 r
42 1.53 1.88 96.4 -1.88 -0.32 26.1 76 7 6 6 7 3 0 0  UNK 276 r UNK 280 r UNK 310 r UNK 313 r UNK 316 r
43 1.40 1.40 106.7 -1.03 -0.25 20.6 81 6 8 4 8 1 0 0  UNK 216 r UNK 224 r UNK 227 r UNK 228 r UNK 243 r
UNK 244 r UNK 245 r UNK 246 r UNK 247 r UNK 248 r
UNK 249 r UNK 258 r UNK 261 r UNK 262 r UNK 278 r
UNK 280 r UNK 281 r UNK 284 r
44 1.39 1.40 109.6 0.69 0.22 5.4 74 6 2 6 22 13 0 2  
45 1.84 2.70 111.3 -2.01 -0.31 28.4 80 9 9 7 9 3 1 0  UNK 276 r UNK 280 r UNK 310 r UNK 313 r UNK 316 r
46 1.17 1.33 115.9 -0.59 -0.15 15.4 82 11 5 10 16 5 4 0  
47 1.37 1.37 115.4 -1.34 -0.56 13.6 84 3 8 10 3 4 3 0  UNK 216 r UNK 224 r UNK 227 r UNK 228 r UNK 243 r
UNK 244 r UNK 245 r UNK 246 r UNK 247 r UNK 248 r
UNK 249 r UNK 258 r UNK 261 r UNK 262 r UNK 278 r
UNK 281 r
48 1.46 1.46 114.4 -1.00 -0.25 19.9 81 6 8 4 8 1 0 0  UNK 200 r UNK 212 r UNK 226 r UNK 227 r UNK 228 r
UNK 229 r UNK 230 r UNK 231 r UNK 240 r UNK 241 r
UNK 243 r UNK 244 r UNK 245 r UNK 261 r UNK 262 r
UNK 265 r UNK 274 r UNK 277 r UNK 278 r UNK 280 r
UNK 281 r UNK 284 r
49 1.32 2.74 115.2 -1.27 -0.25 20.1 84 8 8 11 11 4 2 0  
50 1.51 1.51 117.5 -1.19 -0.42 16.9 78 4 6 6 7 2 0 0  UNK 216 r UNK 224 r UNK 227 r UNK 228 r UNK 243 r
UNK 244 r UNK 245 r UNK 246 r UNK 247 r UNK 248 r
UNK 249 r UNK 258 r UNK 261 r UNK 262 r UNK 278 r
UNK 280 r UNK 281 r UNK 284 r
51 1.54 1.54 123.3 -1.32 -0.54 13.3 84 3 8 10 3 4 3 0  UNK 200 r UNK 212 r UNK 226 r UNK 227 r UNK 228 r
UNK 229 r UNK 230 r UNK 231 r UNK 240 r UNK 241 r
UNK 243 r UNK 244 r UNK 245 r UNK 261 r UNK 262 r
UNK 265 r UNK 274 r UNK 277 r UNK 278 r UNK 281 r
52 1.53 1.98 125.3 -1.20 -0.41 16.2 78 4 6 6 7 2 0 0  UNK 200 r UNK 212 r UNK 226 r UNK 227 r UNK 228 r
UNK 229 r UNK 230 r UNK 231 r UNK 240 r UNK 241 r
UNK 243 r UNK 244 r UNK 245 r UNK 261 r UNK 262 r
UNK 265 r UNK 274 r UNK 277 r UNK 278 r UNK 280 r
UNK 281 r UNK 284 r
53 1.33 2.87 136.1 -0.76 -0.22 11.3 86 10 6 15 11 5 1 0  ADP 1500 X
54 1.25 1.50 149.0 -0.52 -0.13 14.2 83 13 6 14 18 5 3 0  
55 1.26 1.78 155.9 -1.08 -0.20 17.8 81 7 9 10 11 7 3 0  UNK 121 r UNK 122 r
56 1.21 1.33 158.0 -0.95 -0.27 15.7 80 8 10 12 12 6 1 0  UNK 280 r UNK 281 r UNK 284 r
57 1.31 2.03 175.0 -0.89 0.06 15.8 76 16 6 8 14 13 2 1  ADP 1500 X UNK 121 r UNK 122 r
58 1.39 2.83 200.4 -1.35 -0.48 20.4 84 10 10 9 8 3 1 0  UNK 216 r UNK 224 r UNK 227 r UNK 228 r UNK 231 r
UNK 238 r UNK 240 r UNK 241 r UNK 243 r UNK 244 r
UNK 246 r UNK 247 r UNK 261 r UNK 262 r UNK 265 r
UNK 266 r UNK 269 r UNK 270 r UNK 274 r UNK 275 r
UNK 278 r
59 1.31 2.74 215.4 -1.85 -0.49 22.9 84 14 12 13 8 3 1 0  UNK 238 r UNK 242 r UNK 245 r UNK 274 r UNK 276 r
UNK 277 r UNK 280 r UNK 281 r UNK 284 r UNK 310 r
UNK 313 r UNK 316 r
60 2.82 2.82 26.0 -1.58 -0.72 16.5 94 2 0 1 0 0 0 0  U 107 P U 108 P U 112 P U 113 P G 114 P C 141 P
61 3.37 3.38 28.4 -0.08 -0.29 10.5 81 2 1 0 1 0 0 0  U 113 P G 114 P U 124 P G 125 P C 131 P U 132 P A
133 P U 134 P
62 1.28 2.08 38.2 -1.18 -0.44 13.7 88 3 2 4 4 1 1 0  
63 1.27 2.08 40.9 -0.09 -0.01 10.3 89 2 1 4 6 2 0 0  U 155 P U 156 P G 157 P C 158 P U 159 P A 160 P
64 1.48 1.53 41.9 -0.81 -0.45 14.1 94 2 1 3 3 0 0 0  U 106 P U 107 P G 114 P
65 2.44 2.94 46.9 -1.30 -0.86 14.8 87 1 3 2 0 0 0 0  U 94 P C 95 P U 96 P G 98 P U 99 P U 100 P U 101
P U 102 P U 103 P G 104 P G 105 P U 106 P U 107 P
U 108 P G 114 P
66 2.56 2.58 58.6 -1.85 -0.63 24.6 89 5 4 2 1 0 0 0  U 107 P U 108 P U 112 P U 113 P G 114 P C 141 P U
153 P C 154 P U 155 P U 156 P G 157 P C 158 P U
159 P A 160 P
67 2.57 2.56 64.9 -1.87 -0.52 26.9 85 6 3 1 1 0 1 0  U 112 P U 113 P C 154 P U 155 P U 156 P G 157 P C
158 P U 159 P A 160 P C 177 P
68 1.29 2.15 67.9 -1.30 -0.54 16.3 90 4 4 4 4 1 0 0  U 107 P U 108 P U 112 P U 113 P G 114 P C 141 P U
153 P C 154 P
69 2.41 2.50 88.7 -1.90 -0.56 23.2 80 5 6 4 3 1 0 0  G 105 P U 106 P U 107 P U 113 P G 114 P G 115 P A
133 P U 134 P
70 2.00 2.27 92.7 -1.28 -0.51 20.3 86 5 6 3 5 0 0 0  G 105 P U 106 P U 107 P G 114 P G 115 P
71 1.36 1.60 27.6 1.66 0.43 1.5 77 0 1 2 7 5 0 1  

Residue-type_colouring
Positive Negative Neutral Aliphatic Aromatic Pro & Gly Cysteine
H,K,R D,E S,T,N,Q A,V,L,I,M F,Y,W P,G C

Acknowledgement
Pores were calculated by MOLE 2.0 program version 2.5.13.11.08 and visualized using Pymol 0.97rc.
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