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PDBsum entry 4j8u
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Top Page protein dna_rna ligands metals Protein-protein interface(s) pores links
Pore analysis for: 4j8u calculated with MOLE 2.0 PDB id
4j8u
Pores calculated on whole structure Pores calculated excluding ligands
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21 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 2.99 2.99 25.2 -1.09 -0.77 12.9 73 2 1 0 0 0 0 0  DT -36 I DT -35 I DG -
34 I DA 39 I DC 40 I DA 50 I DG 51 I DT 52 I DA
53 I DT -50 J DA -49 J DC -48 J DC -47 J DA -
46 J DA -45 J DA -
44 J DT 30 J DT 31 J DT 32 J DA 39 J DC 40 J
2 3.02 3.03 41.6 -1.42 -0.51 15.7 79 4 1 0 1 1 0 0  DT -36 I DT -35 I DG -
34 I DA 36 I DA 37 I DT 38 I DA 39 I DC 40 I DT -
41 J DT -39 J DA 39 J DC 40 J
3 2.45 2.97 44.4 -1.78 -0.78 22.2 80 5 2 1 0 0 0 0  DA -45 I DA -44 I DT -35 I DG -
34 I DT 31 I DA 39 I DC 40 I DA 50 I DG 51 I DT
52 I DA 53 I DT -50 J DA -49 J DC -48 J DC -
47 J DA -46 J DA -45 J DA -44 J DT -35 J DG -
34 J DT 30 J DT 31 J DT 32 J DA 39 J
4 3.61 3.78 47.7 -1.58 -0.76 16.2 93 4 1 5 0 0 0 0  DC -24 I DT 49 I DC 58 I DA 59 I DG 60 I DC -
64 J DC -63 J DC -61 J DC -60 J DG -55 J DT 19 J
5 1.24 1.24 49.3 -1.58 -0.68 17.8 87 2 0 0 0 0 0 0  DC -26 I DT -25 I DC -
24 I DT 46 I DG 47 I DG 48 I DT 49 I DA 50 I DG
51 I DC -47 J DA -46 J DA -45 J DA -44 J DA -43 J
6 1.43 1.43 50.7 -0.82 -0.68 10.1 86 3 0 0 1 0 0 0  DA -16 I DG -15 I DG -14 I DC -13 I DA -
12 I DG 60 I DG 61 I DC -57 J DA -
56 J DC 15 J DT 16 J DT 18 J DT 19 J DG 20 J
7 3.76 3.83 50.7 -1.35 -0.70 15.2 77 2 0 0 0 0 0 0  DA -16 I DG -15 I DG -
14 I DC 58 I DA 59 I DG 60 I DG 61 I DT 62 I DA -
66 J DT -65 J DC -64 J DC -63 J DC -61 J DC -
60 J DC -57 J DG 20 J
8 2.07 2.07 54.0 -1.35 -0.68 11.8 89 4 1 6 1 0 0 0  DC -24 I DA -22 I DT -21 I DC -20 I DT 49 I DG -
55 J DT 19 J DG 20 J DA 25 J
9 1.43 1.43 56.2 -1.17 -0.74 13.6 92 4 1 3 1 0 0 0  DC -24 I DG -15 I DG -14 I DC -13 I DA -
12 I DT 49 I DG 60 I DG -
55 J DC 15 J DT 16 J DT 18 J DT 19 J
10 1.61 2.27 56.8 -1.44 -0.69 17.2 88 6 1 3 1 0 0 0  DA -66 I DT -65 I DG -
55 I DA 11 I DT 12 I DG 13 I DC 14 I DT 19 I DC -
26 J DT -25 J DC -24 J DG -14 J DC -
13 J DA 50 J DG 51 J DG 60 J DG 61 J
11 2.42 2.98 60.8 -1.86 -0.64 22.4 81 7 2 1 1 1 0 0  DA -45 I DA -44 I DT -35 I DG -
34 I DT 31 I DA 36 I DA 37 I DT 38 I DA 39 I DC
40 I DT -41 J DT -39 J DT -35 J DG -34 J DA 39 J
12 2.69 3.19 63.0 -1.72 -0.50 22.1 84 5 2 4 2 1 0 0  ELJ 1102 D DT -36 I DT -35 I DG -34 I DC -
24 I DA 39 I DC 40 I DT 49 I DA 50 I DA -
44 J DA 28 J DA 39 J DC 40 J
13 2.07 2.07 63.2 -1.03 -0.70 9.1 85 3 1 4 1 0 0 0  DA -22 I DT -21 I DC -20 I DA -
16 I DG 60 I DG 61 I DC -57 J DA -56 J DG -
55 J DT 19 J DG 20 J DA 25 J
14 2.68 3.19 71.3 -2.36 -0.33 30.1 83 8 1 4 3 2 0 0  ELJ 1102 D DG -34 I DC -
24 I DA 36 I DA 37 I DT 38 I DA 39 I DC 40 I DA
41 I DC 42 I DT 49 I DA 50 I DA -45 J DA -
44 J DA -43 J DG -42 J DT -41 J DT -39 J DA 28 J
15 2.23 3.61 73.8 -2.63 -0.47 32.4 79 13 5 3 2 2 1 0  ELJ 204 H DA -45 I DA -44 I DT -11 I DT 31 I DG -
34 J DT 16 J
16 1.35 1.34 76.0 -1.55 -0.39 21.1 78 7 0 0 3 0 2 0  DT -11 I DG -10 I DT -9 I DT -8 I DC -7 I DA -
6 I DG -5 I DC -4 I DT -3 I DG -2 I DA -
1 I DA 0 I DT 1 I DA 71 I DT 72 I DG -
2 J DT 0 J DG 7 J DA 8 J DA 11 J DT 12 J DG 13 J
DC 14 J
17 2.09 2.09 79.0 -1.46 -0.70 14.4 85 6 2 6 1 0 0 0  DA -22 I DT -21 I DC -
20 I DC 58 I DA 59 I DG 60 I DC -64 J DC -
63 J DC -61 J DC -60 J DG -
55 J DT 19 J DG 20 J DA 25 J
18 2.76 2.82 84.7 -1.85 -0.60 20.6 90 10 1 8 3 0 0 0  ELJ 204 H DC -63 I DA -62 I DC -61 I DG -
55 I DT 19 I DA 28 I DA 36 I DA -32 J DA -
31 J DC -24 J DC 58 J DA 59 J DG 60 J
19 3.20 3.47 86.1 -1.77 -0.58 20.3 89 9 1 7 3 1 0 0  ELJ 204 H DC -63 I DA -62 I DC -61 I DG -55 I DA -
45 I DA -44 I DT 19 I DA 28 I DT 31 I DT 32 I DG -
34 J DC -24 J DC 58 J DA 59 J DG 60 J
20 1.80 1.80 86.2 -1.62 -0.62 18.6 90 9 1 6 3 0 0 0  ELJ 204 H DA -66 I DT -65 I DG -
55 I DA 11 I DT 12 I DG 13 I DT 19 I DA 28 I DA
36 I DA -32 J DA -31 J DC -24 J DG -14 J DC -
13 J DG 60 J DG 61 J
21 1.80 1.80 87.7 -1.65 -0.59 19.4 88 8 1 5 3 1 0 0  ELJ 204 H DA -66 I DT -65 I DG -55 I DA -45 I DA -
44 I DA 11 I DT 12 I DG 13 I DT 19 I DA 28 I DT
31 I DT 32 I DG -34 J DC -24 J DG -14 J DC -
13 J DG 60 J DG 61 J
22 1.42 1.42 87.5 -1.20 -0.69 12.8 85 5 2 4 2 0 0 0  DA -22 I DT -21 I DC -20 I DG -15 I DG -14 I DC -
13 I DA -12 I DG 60 I DG -
55 J DC 15 J DT 16 J DT 18 J DT 19 J DG 20 J DA
25 J
23 1.97 2.09 94.4 -2.26 -0.47 26.4 78 13 5 3 3 3 1 0  ELJ 204 H DT -11 I DA 28 I DG 29 I DC -26 J DT -
25 J DC -24 J DT 16 J DG 51 J
24 1.90 2.01 106.4 -1.60 -0.52 18.8 79 10 1 1 4 0 2 0  DG -5 I DC -4 I DT -3 I DG -2 I DA -
1 I DA 0 I DT 1 I DC 58 I DA 59 I DG 60 I DT 68 I
DT 69 I DG 70 I DT -65 J DC -64 J DC -63 J DC -
61 J DC -60 J DG -2 J DT 0 J
25 2.21 3.57 108.6 -2.52 -0.44 29.4 80 16 5 5 3 3 1 0  SO4 201 H ELJ 204 H DT -11 I DA 28 I DA 36 I DA -
32 J DA -31 J DT 16 J
26 1.80 1.80 110.8 -2.12 -0.58 23.8 73 8 0 1 1 0 2 0  DA -66 I DT -65 I DC -64 I DC -63 I DG -2 I DA -
1 I DT 1 I DA 11 I DT 12 I DG 13 I DG -14 J DC -
13 J DG -5 J DC -
4 J DT 6 J DA 59 J DG 60 J DG 61 J DT 62 J DT 68
J DT 69 J DG 70 J DT 72 J
27 1.80 1.80 133.2 -2.19 -0.50 25.9 82 16 6 8 5 3 1 0  ELJ 204 H DA -66 I DT -65 I DG -55 I DT -
11 I DA 11 I DT 12 I DG 13 I DT 19 I DA 28 I DC -
24 J DG -14 J DC -13 J DT 16 J DG 60 J DG 61 J
28 1.90 2.12 189.5 -1.82 -0.63 20.8 85 14 3 9 4 1 2 0  ELJ 204 H DC -64 I DC -63 I DG -55 I DA -44 I DT -
36 I DT -35 I DG -2 I DA -
1 I DT 1 I DT 19 I DA 28 I DA 39 I DC 40 I DT -
35 J DG -34 J DC -24 J DG -5 J DC -
4 J DT 6 J DA 39 J DC 40 J DA 59 J DG 60 J DT 68
J DT 69 J DG 70 J DT 72 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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