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PDBsum entry 5iyb
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Top Page protein dna_rna metals Protein-protein interface(s) pores links
Pore analysis for: 5iyb calculated with MOLE 2.0 PDB id
5iyb
Pores calculated on whole structure Pores calculated excluding ligands
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30 pores, coloured by radius 28 pores, coloured by radius 28 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 3.03 4.43 39.3 -1.97 -0.62 28.5 77 4 4 1 5 1 1 0  DC 54 X
2 1.24 1.23 54.2 -0.05 0.03 14.8 70 3 6 1 9 3 1 0  
3 1.27 1.73 67.4 -1.64 -0.44 25.5 85 8 7 6 5 2 0 0  
4 1.41 1.47 80.0 -1.17 -0.45 20.1 78 6 5 4 6 1 1 2  
5 1.38 2.12 91.3 -0.76 -0.25 11.5 77 8 6 6 13 6 2 0  
6 3.06 5.09 90.9 -1.68 -0.51 21.9 83 8 7 5 4 1 1 0  DC 54 X DA 55 X DT 41 Y DC 42 Y
7 2.46 3.68 119.4 -1.98 -0.44 22.9 79 16 8 8 6 3 2 0  DA 48 X DC 54 X DA 55 X DT 41 Y DC 42 Y
8 1.36 2.12 130.0 -1.43 -0.27 18.0 74 13 9 5 14 10 5 0  
9 2.55 4.13 133.1 -1.62 -0.51 19.9 87 10 6 8 5 0 1 0  DG 21 X DT 22 X DG 23 X DT 34 X DT 35 X DC 62 Y
DG 63 Y DG 65 Y DC 66 Y DC 67 Y DC 68 Y DC 70 Y D
A 71 Y DC 72 Y
10 2.44 2.84 133.8 -1.74 -0.58 16.9 83 7 4 9 4 2 2 0  DT 35 X DT 36 X DA 53 X DC 54 X DG 43 Y DA 44 Y
DT 45 Y DC 46 Y
11 2.64 2.98 137.3 -1.33 -0.55 15.3 86 11 2 5 5 0 1 0  DG 21 X DT 22 X DG 23 X DT 34 X DT 39 X DT 40 X
DT 41 X DT 42 X DC 44 X DG 45 X DC 54 X DG 43 Y D
A 44 Y DT 45 Y DC 46 Y DG 47 Y DC 48 Y DG 49 Y DC
62 Y DG 63 Y DC 64 Y DG 65 Y DC 66 Y DC 67 Y DC
68 Y DC 70 Y DA 71 Y DC 72 Y
12 2.07 2.30 137.7 -1.95 -0.62 22.6 85 14 9 8 3 0 1 0  DG 20 X DG 21 X DT 22 X DG 23 X DT 34 X DT 35 X
DC 62 Y DG 63 Y DG 65 Y DC 66 Y DC 67 Y
13 2.64 2.97 140.1 -1.10 -0.60 11.9 83 11 1 4 5 0 1 0  DG 21 X DT 22 X DG 23 X DT 34 X DT 38 X DT 39 X
DT 40 X DT 41 X DA 53 X DC 54 X DG 43 Y DA 44 Y
DT 45 Y DC 46 Y DG 47 Y DC 48 Y DG 49 Y DC 62 Y
DG 63 Y DC 64 Y DG 65 Y DC 66 Y DC 67 Y DC 68 Y
DC 70 Y DA 71 Y DC 72 Y
14 1.86 1.87 139.0 -2.01 -0.54 25.6 83 11 9 10 7 1 1 1  
15 2.16 2.35 141.9 -1.71 -0.65 18.9 84 15 5 5 3 0 1 0  DG 20 X DG 21 X DT 22 X DG 23 X DT 34 X DT 39 X
DT 40 X DT 41 X DT 42 X DC 44 X DG 45 X DC 54 X
DG 43 Y DA 44 Y DT 45 Y DC 46 Y DG 47 Y DC 48 Y
DG 49 Y DC 62 Y DG 63 Y DC 64 Y DG 65 Y DC 66 Y
DC 67 Y
16 2.14 2.34 144.7 -1.48 -0.68 15.8 81 15 4 4 3 0 1 0  DG 20 X DG 21 X DT 22 X DG 23 X DT 34 X DT 38 X
DT 39 X DT 40 X DT 41 X DA 53 X DC 54 X DG 43 Y D
A 44 Y DT 45 Y DC 46 Y DG 47 Y DC 48 Y DG 49 Y DC
62 Y DG 63 Y DC 64 Y DG 65 Y DC 66 Y DC 67 Y
17 1.59 3.90 149.6 -1.58 -0.32 24.1 80 19 13 8 10 4 5 1  
18 1.79 3.90 181.1 -1.59 -0.36 24.4 82 21 14 6 16 4 5 0  
19 1.78 1.80 188.7 -1.87 -0.55 21.5 80 13 10 11 6 3 3 1  DT 35 X DT 36 X DA 53 X DC 54 X DG 43 Y DA 44 Y
DT 45 Y DC 46 Y
20 1.59 2.68 189.6 -2.16 -0.49 28.1 81 19 11 11 9 2 0 0  DG 26 X DG 27 X DC 69 Y
21 1.81 1.80 192.9 -1.74 -0.53 23.1 82 16 10 10 8 1 2 1  DG 21 X DT 22 X DG 23 X DT 34 X DT 35 X DC 62 Y
DG 63 Y DG 65 Y DC 66 Y DC 67 Y DC 68 Y DC 70 Y D
A 71 Y DC 72 Y
22 1.80 1.80 197.5 -1.96 -0.60 24.6 81 20 13 9 6 1 2 1  DG 20 X DG 21 X DT 22 X DG 23 X DT 34 X DT 35 X
DC 62 Y DG 63 Y DG 65 Y DC 66 Y DC 67 Y
23 1.73 3.84 204.6 -2.05 -0.48 26.6 81 22 15 8 10 3 4 0  DC 54 X DG 43 Y
24 2.50 2.55 210.9 -1.87 -0.52 21.3 84 16 10 12 6 2 3 0  DT 35 X DT 36 X DT 38 X DT 40 X DT 42 X DG 47 X D
A 48 X DT 49 X DT 41 Y DC 42 Y DG 43 Y DA 44 Y DT
45 Y DC 46 Y
25 2.40 3.46 237.2 -1.98 -0.49 21.5 82 22 11 14 8 4 4 0  DT 35 X DT 36 X DT 38 X DT 40 X DT 42 X DG 47 X D
A 48 X DT 49 X DT 41 Y DC 42 Y DG 43 Y DA 44 Y DT
45 Y DC 46 Y
26 1.25 1.73 257.4 -1.68 -0.47 21.7 87 20 16 16 12 3 1 0  DG 25 X DG 26 X DG 27 X DT 34 X DT 35 X DC 62 Y
DG 63 Y DG 65 Y DC 66 Y
27 2.17 2.17 255.0 -1.54 -0.49 20.9 82 22 15 9 13 1 1 1  DG 20 X DG 21 X DT 22 X DG 23 X DG 24 X DG 25 X
DG 26 X DC 66 Y DC 67 Y
28 1.67 3.83 325.6 -1.87 -0.49 23.6 81 31 21 16 14 4 6 0  DT 35 X DT 36 X DT 38 X DT 40 X DT 42 X DC 44 X
DG 45 X DT 45 Y DC 46 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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