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PDBsum entry 5b40
Go to PDB code: 
Top Page protein dna_rna Protein-protein interface(s) pores links
Pore analysis for: 5b40 calculated with MOLE 2.0 PDB id
5b40
Pores calculated on whole structure Pores calculated excluding ligands
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30 pores, coloured by radius 30 pores, coloured by radius 30 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 1.22 1.28 25.8 -1.23 -0.44 15.4 77 2 0 0 2 0 2 0  DT 6 I DT 80 I DG 81 I DA 82 I DA 83 I DA 213 J
DG 214 J DC 215 J DT 216 J DA 291 J
2 3.48 3.56 28.9 -1.21 -0.46 17.0 86 6 1 3 1 1 0 0  DT 38 I DT 48 I DA 113 I DC 114 I DT 123 I DA 175
J DG 249 J
3 2.08 2.28 29.0 -1.72 -0.51 17.9 74 3 0 0 0 1 0 0  DC 84 I DT 92 I DT 93 I DG 94 I DA 95 I DA 201 J
DA 202 J DA 203 J DG 205 J DC 206 J DG 280 J DG
281 J
4 2.96 3.21 36.3 -0.59 -0.62 6.2 81 1 0 2 1 0 0 0  DG 18 I DT 90 I DT 91 I DT 92 I DT 93 I DG 94 I D
A 95 I DT 198 J DC 199 J DA 200 J DA 201 J DA 202
J DA 203 J DG 205 J DG 280 J DG 281 J
5 2.09 2.11 40.3 -2.04 -0.51 21.1 87 5 1 4 1 1 0 0  DG 18 I DC 26 I DC 84 I DT 92 I DC 193 J DT 194 J
DC 195 J DC 206 J DG 271 J DA 272 J DG 280 J
6 3.19 3.19 40.4 -1.21 -0.72 11.7 93 2 1 4 1 0 0 0  DG 18 I DC 26 I DT 92 I DT 93 I DG 94 I DA 95 I
DC 193 J DT 194 J DC 195 J DA 201 J DA 202 J DA
203 J DG 205 J DC 206 J DG 271 J DA 272 J DG 280 J
7 3.39 3.39 47.4 -0.90 -0.74 9.9 72 3 0 0 0 0 0 0  DC 26 I DA 27 I DA 28 I DA 102 I DG 103 I DT 104
I DT 105 I DG 185 J DA 188 J DA 189 J DC 190 J DT
191 J DC 193 J DG 271 J DA 272 J
8 2.10 2.11 51.3 -1.80 -0.48 18.7 76 4 1 3 2 1 0 0  DG 18 I DC 84 I DT 90 I DT 91 I DT 92 I DT 93 I
DT 198 J DC 199 J DA 200 J DC 206 J DG 280 J
9 2.87 2.89 54.1 -0.81 -0.42 11.6 93 4 0 5 2 0 0 0  DT 20 I DT 21 I DC 22 I DT 23 I DG 100 I DA 102 I
DT 104 I DA 188 J DA 189 J DC 190 J DT 191 J DC
195 J DT 269 J DA 270 J
10 3.23 3.23 56.4 -1.49 -0.74 18.0 75 4 2 0 0 0 0 0  DA 28 I DT 37 I DT 38 I DG 100 I DA 102 I DG 103
I DT 104 I DA 113 I DC 114 I DT 184 J DG 185 J DA
188 J DA 189 J DC 190 J DT 191 J DC 260 J DA 261 J
11 3.12 3.36 58.7 -1.34 -0.62 13.3 89 5 1 6 2 0 0 0  DG 18 I DT 92 I DT 93 I DG 94 I DA 95 I DA 102 I
DT 104 I DA 188 J DA 189 J DC 190 J DT 191 J DC
195 J DA 201 J DA 202 J DA 203 J DG 205 J DC 206
J DG 280 J
12 3.11 3.11 58.9 0.33 -0.16 5.5 70 2 0 0 3 1 0 1  DA 7 I DC 69 I DC 79 I DT 80 I DG 81 I DA 82 I DA
83 I DC 84 I DC 206 J DA 207 J DT 208 J DG 209 J
DT 210 J DA 218 J DA 219 J DT 220 J
13 1.69 2.01 61.4 -2.17 -0.54 24.6 85 12 2 6 1 2 0 0  DT 38 I DA 113 I DC 114 I
14 2.99 3.11 63.9 -0.93 -0.61 8.6 89 3 0 6 2 0 0 0  DG 18 I DT 90 I DT 91 I DT 92 I DT 93 I DA 102 I
DT 104 I DA 188 J DA 189 J DC 190 J DT 191 J DC
195 J DC 196 J DT 198 J DC 199 J DA 200 J
15 1.22 1.23 67.1 -1.48 -0.62 14.7 81 5 0 2 0 1 0 0  DA 5 I DT 6 I DA 7 I DT 8 I DC 9 I DC 10 I DT 92
I DT 93 I DG 94 I DA 95 I DA 201 J DA 202 J DA
203 J DG 205 J DC 206 J DA 279 J DG 280 J DG 281
J DT 282 J DA 287 J DT 288 J DT 289 J DG 290 J DA
291 J
16 1.72 1.72 69.0 -0.48 -0.34 11.1 70 4 0 0 3 1 0 1  DA 7 I DA 73 I DT 74 I DC 79 I DT 80 I DG 81 I DA
82 I DA 83 I DC 84 I DC 206 J DA 207 J DT 208 J
DG 209 J DT 210 J DT 216 J DG 217 J DA 218 J DA
219 J
17 1.62 1.62 77.7 -1.07 -0.73 12.0 86 3 0 1 0 0 0 0  DT 38 I DG 39 I DG 40 I DA 41 I DA 42 I DA 43 I D
A 113 I DC 114 I DA 175 J DT 250 J DT 251 J DT
252 J DC 254 J DA 255 J DA 256 J DA 257 J
18 1.82 3.86 85.7 -2.05 -0.53 23.4 81 13 2 4 2 3 0 0  DC 26 I DA 102 I DG 103 I DC 193 J DT 194 J DC
195 J DG 271 J DA 272 J
19 1.25 1.26 85.6 -1.28 -0.64 11.6 83 5 0 5 1 1 0 0  DA 5 I DT 6 I DA 7 I DT 8 I DC 9 I DC 10 I DG 18
I DT 90 I DT 91 I DT 92 I DT 93 I DT 198 J DC 199
J DA 200 J DA 279 J DG 280 J DA 287 J DT 288 J DT
289 J DG 290 J DA 291 J
20 2.00 3.94 86.0 -2.28 -0.46 26.2 80 14 2 4 2 3 0 0  DG 100 I DA 102 I DT 104 I DA 188 J DA 189 J DC
190 J DT 191 J
21 2.72 2.76 90.0 -1.25 -0.60 16.0 90 6 2 5 2 0 0 0  DT 20 I DT 21 I DC 22 I DT 23 I DA 28 I DT 37 I
DT 38 I DA 102 I DG 103 I DT 104 I DA 113 I DC
114 I DT 184 J DG 185 J DC 195 J DC 260 J DA 261
J DG 267 J DT 269 J DA 270 J
22 1.89 3.97 93.0 -1.99 -0.42 24.7 84 14 2 6 3 3 0 0  DT 20 I DT 21 I DC 22 I DT 23 I DG 267 J DT 269 J
DA 270 J
23 2.72 2.77 96.7 -1.31 -0.69 14.5 87 5 2 6 2 0 0 0  DG 18 I DA 28 I DT 37 I DT 38 I DT 90 I DT 91 I
DT 92 I DT 93 I DA 102 I DG 103 I DT 104 I DA 113
I DC 114 I DT 184 J DG 185 J DC 195 J DC 196 J DT
198 J DC 199 J DA 200 J DC 260 J DA 261 J
24 1.72 1.72 100.3 -1.93 -0.45 26.8 78 11 5 2 5 1 1 0  DA 73 I DT 74 I DG 100 I DC 101 I DA 189 J DT 191
J DT 216 J DG 217 J DA 218 J DA 219 J
25 1.75 2.38 101.6 -1.98 -0.50 23.3 80 9 4 4 4 2 1 0  DA 7 I DT 8 I DC 9 I DC 10 I DA 83 I DC 84 I DC
206 J DA 287 J DT 288 J DT 289 J
26 1.88 3.95 105.2 -1.95 -0.51 22.3 82 13 2 7 3 3 0 0  DG 18 I DT 90 I DT 91 I DT 92 I DT 93 I DC 195 J
DC 196 J DT 198 J DC 199 J DA 200 J
27 1.93 2.41 117.9 -2.11 -0.54 24.7 81 11 4 6 3 1 1 0  DC 9 I DC 10 I DT 92 I DT 93 I DG 94 I DA 95 I DA
201 J DA 202 J DA 203 J DG 205 J DC 206 J DA 279
J DG 280 J DG 281 J DT 282 J DT 288 J
28 1.55 1.92 120.0 -1.94 -0.45 23.1 84 14 3 8 6 1 1 0  DT 38 I DC 69 I DA 113 I DC 114 I DA 218 J DA 219
J DT 220 J
29 1.18 1.21 149.1 -1.92 -0.52 22.3 82 15 2 5 3 3 0 0  DG 40 I DA 41 I DA 42 I DA 43 I DG 249 J DT 250 J
DT 252 J DC 253 J DC 254 J DA 255 J DA 256 J DA
257 J
30 1.64 1.77 217.7 -1.82 -0.49 21.2 82 19 3 7 8 2 1 0  DG 40 I DA 41 I DA 42 I DA 43 I DA 73 I DT 74 I
DT 216 J DG 217 J DA 218 J DA 219 J DG 249 J DT
250 J DT 252 J DC 253 J DC 254 J DA 255 J DA 256
J DA 257 J

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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