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PDBsum entry 8s09
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Top Page protein dna_rna ligands metals Protein-protein interface(s) pores links
Pore analysis for: 8s09 calculated with MOLE 2.0 PDB id
8s09
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 1.25 1.53 48.2 -0.05 0.14 16.4 77 4 5 2 13 1 2 0  
2 1.33 1.46 65.8 -0.16 -0.04 17.6 78 4 7 2 10 3 1 0  
3 1.19 1.20 71.6 -0.26 -0.09 18.6 90 4 4 5 12 1 0 0  
4 1.25 1.52 75.8 -0.65 -0.11 17.2 80 5 8 5 13 1 3 0  
5 2.34 2.32 109.5 -1.77 -0.61 17.7 90 5 10 12 8 0 1 0  DA 28 X DT 29 X DA -25 Y
6 1.16 1.59 134.1 0.03 -0.12 8.5 79 6 4 9 17 4 1 1  DA 28 X DT 29 X DC -26 Y DA -25 Y
7 1.16 1.55 132.9 0.36 -0.02 11.2 84 6 9 8 21 5 0 1  
8 1.32 1.48 163.4 -1.19 -0.34 20.9 80 14 10 7 19 6 2 0  DA 28 X DG 30 X DC 31 X DC -34 Y DA -33 Y DT -32 Y
9 1.25 1.60 168.8 -0.60 -0.22 17.6 83 12 15 11 26 3 3 0  
10 1.39 1.56 177.7 -1.43 -0.37 16.1 81 14 10 13 8 8 2 3  ADP 901 B
11 1.24 3.82 183.3 -1.32 -0.36 19.6 81 11 14 9 22 1 2 1  DA 21 X DT 22 X DT 23 X DT 25 X DG 26 X DT -
21 Y DG -20 Y DC -19 Y DA -18 Y DT -17 Y
12 1.19 1.82 186.1 -1.31 -0.46 15.4 86 18 12 14 13 5 2 0  ADP 901 3 MG 902 3 DA -39 Y
13 1.67 1.81 191.0 -2.03 -0.43 23.6 79 21 11 10 8 7 4 0  
14 1.24 1.83 187.7 -1.52 -0.59 15.5 87 11 11 13 10 2 4 0  DG 30 X DC 31 X DT 33 X DG 34 X DC 35 X DC 37 X D
A -39 Y DT -38 Y DC -36 Y DG -35 Y DC -34 Y DA -
33 Y
15 1.16 1.18 197.4 -1.15 -0.38 18.0 84 15 11 5 17 1 4 0  DC 37 X DA 38 X DT 39 X DG 40 X DC 41 X DA 42 X
DG -45 Y DC -44 Y DT -42 Y DC -40 Y
16 1.63 1.79 202.0 -1.58 -0.46 19.9 85 19 10 15 18 1 2 1  DC 12 X DT 14 X DT 22 X DT 23 X DT 25 X DG 26 X
DT -21 Y DG -20 Y DC -19 Y DA -18 Y
17 1.23 2.39 226.0 -1.09 -0.20 15.4 79 17 13 16 19 9 4 3  ADP 901 3
18 1.36 1.37 224.4 -1.35 -0.49 16.5 85 20 12 17 16 4 2 0  ADP 901 3 MG 902 3 DA 28 X DG 30 X DC 31 X DT 33
X DG 34 X DC 35 X DA -39 Y DT -38 Y DC -36 Y DG -
35 Y DC -34 Y DA -33 Y DT -32 Y
19 1.16 1.23 236.8 -0.93 -0.26 16.2 84 14 18 19 32 5 2 1  
20 1.19 1.50 271.8 -0.83 -0.17 16.0 79 25 11 13 21 8 4 3  
21 1.14 1.39 278.1 -0.60 -0.19 12.5 81 17 13 19 27 13 1 4  ADP 901 3
22 1.39 1.30 272.8 -1.39 -0.37 21.1 83 27 14 15 28 7 3 0  DC 12 X DT 14 X DT 22 X DT 23 X DA 24 X DT 25 X
DG 26 X DC 27 X DA 28 X DG 30 X DC 31 X DC -
34 Y DA -33 Y DT -32 Y DT -24 Y DA -23 Y DT -
21 Y DG -20 Y DC -19 Y DA -18 Y
23 1.27 2.25 276.9 -1.30 -0.44 19.4 87 21 18 16 20 5 1 1  ADP 901 3 MG 902 3 DT 43 X DG 44 X DC 45 X DG -
45 Y DC -44 Y DA -43 Y DT -42 Y DG -41 Y DC -
40 Y DA -39 Y
24 1.38 1.87 293.6 -1.68 -0.50 20.3 87 15 16 20 17 3 2 1  DG 30 X DC 31 X DT 33 X DG 34 X DC 35 X DC 37 X
DC 45 X DG -45 Y DC -44 Y DA -43 Y DT -42 Y DG -
41 Y DA -39 Y DT -38 Y DC -36 Y DG -35 Y DC -
34 Y DA -33 Y
25 1.56 1.64 314.0 -1.55 -0.39 17.1 84 24 21 27 24 9 3 3  ADP 901 3
26 2.23 3.48 319.3 -1.96 -0.47 23.2 82 37 21 19 12 5 6 2  
27 1.39 1.86 322.4 -1.74 -0.52 21.6 84 20 17 20 18 3 7 1  DC 45 X DG -45 Y DC -44 Y DA -43 Y DT -42 Y DG -
41 Y
28 1.27 2.23 336.9 -1.09 -0.23 17.0 81 21 17 21 31 8 4 3  DT 33 X DG 34 X DC 45 X DG -45 Y DC -44 Y DA -
43 Y DT -42 Y DG -41 Y DA -39 Y
29 0.95 1.09 358.3 -1.52 -0.41 19.9 85 29 16 19 27 2 5 0  DC 12 X DT 14 X DT 22 X DT 23 X DA 24 X DT 25 X
DG 26 X DC 27 X DA 28 X DG 30 X DC 31 X DT 33 X
DG 34 X DC 35 X DC 37 X DA 38 X DT 39 X DG 40 X
DC 41 X DA 42 X DG -45 Y DC -44 Y DT -42 Y DC -
40 Y DA -39 Y DT -38 Y DC -36 Y DG -35 Y DC -
34 Y DA -33 Y DT -32 Y DT -24 Y DA -23 Y DT -
21 Y DG -20 Y DC -19 Y DA -18 Y
30 1.30 2.25 416.9 -1.63 -0.44 20.7 86 33 16 25 27 3 3 1  DC 12 X DT 14 X DT 22 X DT 23 X DA 24 X DT 25 X
DG 26 X DC 27 X DA 28 X DG 30 X DC 31 X DT 33 X
DG 34 X DC 35 X DC 37 X DC 45 X DG -45 Y DC -
44 Y DA -43 Y DT -42 Y DG -41 Y DA -39 Y DT -
38 Y DC -36 Y DG -35 Y DC -34 Y DA -33 Y DT -
32 Y DT -24 Y DA -23 Y DT -21 Y DG -20 Y DC -
19 Y DA -18 Y

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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