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PDBsum entry 9fd2
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Top Page protein dna_rna metals Protein-protein interface(s) pores links
Pore analysis for: 9fd2 calculated with MOLE 2.0 PDB id
9fd2
Pores calculated on whole structure Pores calculated excluding ligands
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28 pores, coloured by radius 27 pores, coloured by radius 27 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 3.44 4.74 25.2 -2.94 -0.69 34.6 79 5 5 2 2 0 1 0  
2 2.37 2.37 45.4 -1.25 -0.77 13.2 88 3 4 2 1 0 0 0  DT 9 N DT 42 T DG 43 T DG 44 T DC 45 T DA 47 T DT
48 T
3 3.42 4.00 46.5 -2.88 -0.50 30.9 81 6 3 3 2 0 3 0  DT 9 N DA 47 T DT 48 T
4 1.34 2.29 47.3 -0.84 -0.47 17.6 78 2 4 0 4 1 0 0  DT 2 N DA 3 N DG 4 N DT 5 N DA 55 T
5 1.54 2.00 49.0 0.28 0.12 11.2 74 3 2 1 7 5 0 0  
6 1.85 1.98 55.5 -1.46 -0.16 22.0 79 9 4 5 5 5 2 0  
7 1.53 1.93 82.8 -2.07 -0.51 20.2 82 8 5 9 4 1 1 1  
8 3.28 3.35 85.5 -2.14 -0.54 21.6 85 10 7 6 2 4 3 0  
9 3.32 4.08 87.9 -2.06 -0.72 20.0 88 7 8 10 3 1 2 0  A 1 M DG 40 T DA 41 T DT 42 T DG 43 T
10 2.77 2.76 95.6 -2.15 -0.57 18.1 82 13 5 9 6 2 4 0  DT 22 T DC 23 T
11 2.28 2.41 123.3 -1.60 -0.34 20.1 74 11 9 6 6 5 2 2  DA 15 N
12 3.02 4.18 122.4 -2.51 -0.60 27.3 82 12 7 7 6 0 3 0  DA 30 N DG 31 N DG 32 N DA 33 N DG 34 N DT 22 T
DC 23 T DC 24 T DT 25 T DT 26 T DC 27 T DT 28 T
DC 29 T DC 30 T DC 31 T
13 2.67 2.66 139.4 -2.34 -0.68 26.1 82 18 8 7 4 1 3 0  A 1 M C 3 M G 4 M A 5 M DA 30 N DG 31 N DG 32 N D
A 33 N DG 34 N DT 22 T DC 23 T DC 24 T DT 25 T DT
26 T DC 27 T DT 28 T DC 29 T DC 30 T DC 31 T DC
35 T DT 36 T DC 37 T DT 38 T DC 39 T DG 40 T
14 2.22 2.21 144.2 -1.75 -0.54 17.1 86 13 5 15 6 4 2 0  A 1 M C 3 M G 4 M A 5 M A 10 M DA 32 T DT 33 T DC
35 T DT 36 T DC 37 T DT 38 T DC 39 T DG 40 T
15 1.37 2.92 149.6 -2.04 -0.45 25.4 78 16 13 8 7 6 2 2  
16 2.66 2.83 155.5 -2.37 -0.53 24.4 83 14 6 10 4 2 2 0  DA 30 N DG 31 N DG 32 N DA 33 N DG 34 N DC 24 T
DT 25 T DT 26 T DC 27 T DT 28 T DC 29 T DC 30 T
DC 31 T
17 1.66 1.99 160.0 -1.90 -0.52 21.2 83 16 9 16 7 5 1 0  
18 2.60 2.60 176.0 -2.37 -0.62 27.9 80 23 11 8 6 1 3 0  A 1 M C 3 M G 4 M A 5 M DT 9 N DA 30 N DG 31 N DG
32 N DA 33 N DG 34 N DT 22 T DC 23 T DC 24 T DT
25 T DT 26 T DC 27 T DT 28 T DC 29 T DC 30 T DC
31 T DC 35 T DT 36 T DC 37 T DT 38 T DC 39 T DG
40 T DA 41 T DA 47 T DT 48 T
19 3.61 3.62 175.2 -1.82 -0.55 20.1 82 22 12 14 9 3 1 1  DA 36 N DA 39 N DG 40 N DC 41 N DT 17 T DT 19 T
DG 20 T DC 21 T DT 22 T
20 1.22 2.40 184.7 -1.19 -0.29 16.0 84 14 11 10 14 8 4 0  A 1 M DG 40 T DA 41 T DT 42 T DG 43 T
21 1.68 1.99 182.3 -2.18 -0.64 22.5 84 22 14 16 8 2 4 0  DT 22 T DC 23 T
22 1.25 3.18 184.7 -2.15 -0.51 28.1 83 21 13 10 13 0 2 0  DC 21 T DT 22 T
23 1.27 1.49 192.5 -1.94 -0.42 25.6 77 18 17 9 11 7 2 2  
24 1.45 3.09 191.4 -2.11 -0.52 26.1 81 20 16 9 5 3 3 0  
25 1.23 3.16 193.6 -2.02 -0.54 23.0 82 21 14 12 3 3 4 0  A 1 M C 3 M G 4 M A 5 M A 10 M DA 32 T DT 33 T DC
35 T DT 36 T DC 37 T DT 38 T DC 39 T DG 40 T
26 2.72 2.78 212.4 -1.87 -0.54 21.2 81 24 13 14 10 5 1 1  DA 39 N DG 40 N DC 24 T DT 25 T DT 26 T
27 1.31 3.46 236.0 -2.12 -0.49 28.4 83 23 14 7 12 0 2 0  DA 30 N DG 31 N DG 32 N DA 33 N DG 34 N DA 35 N D
A 36 N DG 20 T DC 21 T DT 22 T DC 23 T DC 24 T DT
25 T DT 26 T DC 27 T DT 28 T DC 29 T DC 30 T DC
31 T

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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