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PDBsum entry 5iy9
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Top Page protein dna_rna metals Protein-protein interface(s) pores links
Pore analysis for: 5iy9 calculated with MOLE 2.0 PDB id
5iy9
Pores calculated on whole structure Pores calculated excluding ligands
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60 pores, coloured by radius 60 pores, coloured by radius 60 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 1.50 2.02 65.0 -1.77 -0.22 27.1 76 11 9 4 6 6 3 0  
2 1.46 1.47 113.0 -1.73 -0.39 21.5 84 16 8 9 5 3 2 0  MG 2002 A DG 49 Y DA 50 Y DC 51 Y C 4 Z G 5 Z C 6
Z
3 1.21 1.34 122.0 -1.80 -0.33 27.4 85 13 7 4 8 2 1 0  
4 1.86 1.94 129.6 -1.22 -0.29 20.9 83 14 11 8 11 3 2 0  
5 1.49 1.52 129.9 -1.88 -0.44 23.5 85 17 9 10 9 2 2 0  
6 1.56 1.64 147.5 -2.18 -0.36 25.9 79 22 11 10 5 6 4 0  
7 1.14 1.35 146.8 -1.66 -0.44 21.8 82 8 10 8 6 4 0 0  DA 3 X DG 4 X DG 87 Y DC 88 Y DC 89 Y
8 1.65 2.67 170.9 -1.83 -0.30 24.1 78 21 9 7 6 5 7 0  
9 1.73 2.24 173.7 -1.66 -0.31 20.4 78 11 12 8 9 4 6 0  
10 1.18 1.31 187.1 -1.61 -0.42 22.6 84 15 9 6 8 3 1 0  DG 22 X DT 23 X DG 24 X DG 26 X DG 27 X DG 63 Y
DC 67 Y DC 88 Y DC 89 Y
11 1.16 1.30 193.3 -2.03 -0.45 25.6 82 23 11 8 9 4 3 0  
12 1.73 1.87 210.8 -1.99 -0.41 26.9 86 18 13 9 8 2 0 0  DG 22 X DT 23 X DG 24 X DG 26 X DG 27 X DG 63 Y
DC 67 Y DC 88 Y DC 89 Y
13 2.15 2.62 203.6 -2.34 -0.44 29.1 80 20 11 8 5 2 3 0  
14 1.70 1.93 208.5 -2.23 -0.59 26.4 81 21 14 9 5 2 0 0  DG 22 X DT 34 X DT 35 X DT 36 X DT 38 X DT 39 X
DT 40 X DT 41 X DT 42 X DT 45 X DT 50 X DG 52 X D
A 36 Y DG 37 Y DT 38 Y DG 39 Y DT 40 Y DT 41 Y DC
64 Y DG 65 Y DC 66 Y DC 67 Y DC 88 Y DC 89 Y
15 1.00 0.98 243.4 -1.64 -0.40 21.1 82 21 14 15 17 5 8 1  DC 55 X DA 61 X DG 62 X DG 35 Y DA 36 Y
16 1.81 1.98 249.1 -2.21 -0.37 30.6 76 19 23 7 9 7 3 0  
17 1.59 3.05 248.4 -1.76 -0.33 24.8 76 17 19 8 11 4 4 1  DC 88 Y DC 89 Y
18 1.22 2.83 252.0 -1.53 -0.34 21.0 80 22 12 11 13 7 2 1  DA 3 X DG 4 X DG 22 X DT 31 X DT 32 X DT 33 X DT
34 X DT 35 X DT 36 X DT 38 X DT 39 X DC 64 Y DG
65 Y DC 66 Y DC 67 Y DG 87 Y DC 88 Y DC 89 Y
19 1.25 1.54 251.1 -1.70 -0.32 23.4 75 18 18 9 12 6 4 1  DA 3 X DG 4 X DG 87 Y DC 88 Y DC 89 Y
20 1.21 1.48 263.1 -1.55 -0.29 23.2 76 19 15 8 11 9 3 1  DA 3 X DG 4 X DG 87 Y DC 88 Y DC 89 Y
21 1.71 2.74 260.5 -1.58 -0.30 24.5 77 18 16 8 10 7 3 1  DC 88 Y DC 89 Y
22 1.20 1.33 274.2 -1.71 -0.39 16.9 82 22 11 17 11 9 6 0  DT 38 X DT 39 X DT 40 X DT 41 X DT 42 X DT 43 X
DT 45 X DT 40 Y DT 41 Y DC 42 Y DG 43 Y DA 44 Y
DT 45 Y DG 55 Y DG 56 Y DA 57 Y DC 58 Y A 1 Z
23 1.50 1.93 274.4 -1.92 -0.42 25.1 79 30 21 15 12 7 11 1  DC 55 X DG 35 Y DA 36 Y DG 37 Y
24 1.20 1.35 283.2 -1.79 -0.46 19.0 82 13 19 22 15 6 7 0  
25 1.22 1.57 292.1 -1.56 -0.43 18.8 81 19 15 18 14 8 6 0  DA 3 X DG 4 X DG 22 X DT 34 X DT 35 X DT 36 X DT
37 X DT 39 X DC 66 Y DC 67 Y DG 87 Y DC 88 Y DC
89 Y
26 1.19 1.28 305.7 -1.66 -0.44 17.6 82 18 12 19 10 7 6 0  DT 23 X DG 24 X DG 26 X DG 27 X DT 34 X DT 35 X
DT 36 X DT 37 X DT 39 X DG 63 Y DC 66 Y DC 67 Y
27 1.25 1.44 306.6 -1.57 -0.41 20.9 82 25 18 15 19 8 3 0  DA 3 X DG 4 X DG 22 X DT 34 X DT 35 X DT 36 X DT
38 X DT 39 X DT 40 X DT 41 X DT 42 X DT 45 X DT
50 X DG 52 X DA 61 X DG 62 X DA 36 Y DG 37 Y DT
38 Y DG 39 Y DT 40 Y DT 41 Y DC 64 Y DG 65 Y DC
66 Y DC 67 Y DG 87 Y DC 88 Y DC 89 Y
28 1.18 1.26 416.2 -1.75 -0.44 19.5 82 18 24 24 21 7 6 0  
29 1.64 3.17 405.5 -1.89 -0.48 25.0 81 37 25 14 17 5 6 0  DG 22 X DT 34 X DT 35 X DT 36 X DT 38 X DT 39 X
DT 40 X DT 41 X DT 42 X DT 45 X DT 49 X DT 50 X
DC 51 X DG 52 X DT 40 Y DT 41 Y DC 64 Y DG 65 Y
DC 66 Y DC 67 Y DC 88 Y DC 89 Y
30 1.24 1.45 417.3 -1.68 -0.39 21.1 79 23 20 15 17 7 4 1  DA 3 X DG 4 X DG 87 Y DC 88 Y DC 89 Y
31 1.19 1.33 26.6 -1.97 -0.24 22.0 69 2 2 1 1 2 1 0  
32 1.42 1.61 27.2 0.37 0.22 15.0 74 3 2 1 4 2 1 1  
33 1.26 1.48 27.2 -0.14 0.18 10.0 77 3 0 2 4 3 1 0  
34 1.34 1.60 28.7 0.24 0.21 9.4 81 3 1 1 4 2 0 0  
35 1.35 1.59 29.6 0.05 0.06 8.9 77 3 1 1 4 2 0 0  
36 1.28 1.43 39.0 -0.50 -0.32 13.7 85 4 3 2 5 1 0 0  
37 1.31 3.48 72.8 -0.67 0.24 20.0 76 6 2 1 5 2 1 1  
38 1.46 1.47 82.0 -1.02 -0.29 11.1 87 5 3 8 7 2 1 0  DC 72 X DC 19 Y DA 20 Y DC 21 Y DG 22 Y DT 23 Y
39 1.57 1.65 111.8 -1.78 -0.56 20.9 87 7 8 7 4 3 1 0  
40 1.23 1.49 116.4 -0.77 -0.21 17.5 84 11 6 9 13 5 1 0  
41 1.35 3.02 124.6 -0.51 -0.12 16.6 83 11 8 6 16 4 0 0  
42 1.23 3.39 126.0 -0.47 -0.10 15.9 83 12 7 6 18 4 0 0  
43 1.24 2.93 127.8 -0.60 -0.17 16.8 82 9 7 2 16 4 1 0  
44 1.87 2.03 137.8 -0.77 -0.18 14.2 87 6 7 8 14 1 1 0  DC 72 X DA 20 Y DC 21 Y DG 22 Y DT 23 Y
45 1.35 1.35 143.3 -1.58 -0.44 23.0 85 6 8 3 8 3 1 0  
46 1.44 1.47 147.2 -0.86 -0.19 12.3 86 7 8 10 13 3 1 0  
47 1.33 1.34 158.3 -1.41 -0.38 22.8 83 5 9 4 6 3 1 1  
48 1.55 1.55 163.9 -1.48 -0.30 20.3 85 13 4 8 11 4 0 0  
49 1.31 1.29 176.4 -1.45 -0.43 19.3 85 11 11 7 10 5 2 0  
50 1.29 1.27 200.4 -1.07 -0.29 17.7 82 10 13 6 12 4 2 1  
51 1.99 3.72 211.9 -1.75 -0.33 22.8 85 14 9 8 13 2 1 0  
52 1.29 1.53 29.1 2.66 0.94 0.8 84 0 0 1 11 1 1 0  
53 1.30 1.30 30.2 -0.85 -0.23 12.3 74 3 2 2 4 2 1 0  
54 1.42 1.55 35.8 -0.21 -0.31 11.2 76 4 3 2 9 1 0 0  
55 1.62 1.63 42.2 0.88 0.19 9.2 74 3 0 2 7 0 0 0  
56 1.32 1.85 45.7 1.92 0.80 4.5 70 3 0 0 14 4 2 1  
57 1.28 1.80 46.8 1.20 0.44 8.1 70 3 1 1 10 2 1 0  
58 1.18 1.27 47.8 0.13 -0.01 8.8 66 4 1 1 6 4 1 1  
59 1.32 1.31 74.6 -0.29 -0.35 10.1 82 4 3 6 10 1 1 0  
60 1.65 1.65 26.7 -1.13 -0.38 13.0 80 2 0 2 2 1 2 0  

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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