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PDBsum entry 5lj3
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Top Page protein dna_rna ligands metals Protein-protein interface(s) pores links
Pore analysis for: 5lj3 calculated with MOLE 2.0 PDB id
5lj3
Pores calculated on whole structure Pores calculated excluding ligands
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33 pores, coloured by radius 33 pores, coloured by radius 33 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 1.28 75.6 -1.46 -0.56 14.7 86 4 6 4 5 1 1 0  G 119 Z G 120 Z U 1151 Z
2 3.49 3.49 79.8 -1.15 -0.48 14.8 84 7 4 2 7 1 1 0  G 120 Z G 143 Z G 144 Z G 1089 Z U 1148 Z
3 1.25 1.28 99.3 -1.43 -0.62 14.1 86 9 5 6 6 0 1 0  G 119 Z G 144 Z G 1089 Z G 1094 Z U 1095 Z C 1096
Z G 1097 Z A 1147 Z U 1148 Z G 1149 Z U 1150 Z U
1151 Z
4 2.93 3.44 127.5 -1.59 -0.52 14.0 85 11 2 12 5 3 3 0  C 37 U U 39 U C 40 U A 41 U A 42 U C 64 U C 107 U
C 108 U
5 1.56 1.62 131.5 -1.57 -0.50 14.0 83 12 5 15 8 4 4 0  G 32 U U 33 U C 34 U A 35 U A 36 U C 37 U C 124 U
C 125 U A 126 U U 127 U U 3 V
6 1.93 1.93 147.0 -1.49 -0.48 16.6 84 11 5 10 4 4 1 0  C 64 U U 65 U A 66 U U 67 U A 68 U A 167 U U 168
U U 169 U U 170 U U 171 U U 172 U U 173 U
7 1.35 1.61 154.0 -1.07 -0.51 14.1 83 4 10 6 8 5 1 0  A 110 Z C 111 Z A 112 Z U 113 Z C 1128 Z U 1129 Z
8 1.84 1.84 170.5 -1.65 -0.54 20.2 82 14 8 11 5 5 0 0  A 30 U G 31 U A 71 U C 72 U G 117 U C 124 U C 125
U A 126 U U 127 U C 142 U U 143 U A 167 U U 168 U
U 169 U U 170 U U 171 U U 172 U U 173 U U 3 V
9 1.20 1.22 182.4 -1.07 -0.39 15.0 86 13 5 15 14 1 4 0  A 91 V UNK 88 x UNK 89 x UNK 90 x
10 1.07 1.26 190.3 -0.85 -0.37 11.6 87 9 6 16 19 2 5 0  A 91 V UNK 88 x UNK 89 x UNK 90 x
11 1.07 0.94 191.4 -0.81 -0.10 16.3 87 8 10 17 15 8 0 0  
12 1.24 1.45 199.0 -0.62 -0.44 10.0 88 7 3 10 12 2 5 0  U 89 V U 90 V A 91 V C 92 V A 93 V A 94 V A 95 V
G 96 V A 97 V G 98 V A 99 V U 102 V G 3 Z A 4 Z A
5 Z U 6 Z C 7 Z U 8 Z C 9 Z G 13 Z C 14 Z C 15 Z
UNK 76 x UNK 77 x UNK 80 x
13 1.88 1.81 214.5 0.37 0.03 10.8 79 12 10 8 29 7 4 1  C 4 U U 145 U A 167 U U 168 U U 169 U U 170 U U
171 U U 172 U U 173 U
14 1.54 1.54 212.5 -0.66 -0.05 19.3 76 14 11 2 18 6 2 0  
15 1.12 1.33 228.4 -0.70 -0.24 13.8 82 9 10 14 17 5 2 2  U -16 E A -15 E
16 1.46 1.82 225.2 0.31 0.18 11.1 76 11 8 4 27 8 3 1  A 30 U G 31 U C 124 U C 125 U A 126 U U 3 V
17 1.38 1.47 239.9 -1.72 -0.47 20.4 77 23 10 11 8 6 3 0  U 4 I G 5 I U 6 I C 7 I U 8 I U 63 I U 65 I U 127
U G 1 V U 2 V U 3 V G 30 V G 31 V U 32 V C 33 V A
34 V A 40 V A 41 V A 42 V C 43 V A 44 V A 45 V U
46 V A 47 V C 48 V C 41 Z U 42 Z
18 1.67 1.75 236.9 -0.09 -0.11 13.7 86 14 10 16 24 3 1 2  
19 1.58 1.75 237.4 -0.93 -0.38 15.8 86 14 14 20 12 7 1 1  A 167 U U 168 U U 169 U U 170 U U 171 U U 172 U U
173 U
20 1.40 1.49 237.1 -1.83 -0.49 20.6 80 24 14 17 13 5 7 0  A 75 I U 76 I U 92 U C 107 U G 32 Z G 34 Z
21 1.38 1.47 256.3 -1.66 -0.50 18.7 88 17 12 21 16 1 4 0  U 4 I G 5 I U 6 I C 7 I U 8 I A 10 I U 63 I U 65
I A 42 V C 43 V A 44 V A 45 V U 46 V A 47 V C 48
V C 41 Z U 42 Z
22 0.94 1.27 263.3 -1.14 -0.41 14.9 82 18 10 17 21 6 4 0  G 32 U U 33 U C 34 U A 35 U A 36 U C 37 U C 124 U
C 125 U A 126 U U 3 V A 91 V UNK 88 x UNK 89 x
UNK 90 x
23 2.05 2.05 301.4 -0.22 -0.12 12.8 86 16 10 20 25 3 1 1  C 64 U U 65 U A 66 U U 67 U A 68 U
24 1.58 1.90 313.5 -1.50 -0.43 19.8 84 25 16 24 15 7 1 1  A 30 U G 31 U A 71 U C 72 U G 117 U C 124 U C 125
U A 126 U C 142 U U 143 U U 3 V
25 1.50 1.57 316.6 -1.70 -0.45 19.9 83 34 18 30 17 5 9 1  A 75 I U 76 I G 32 Z G 34 Z
26 1.57 1.71 342.2 -0.55 -0.14 14.8 82 27 20 25 40 7 7 1  U -12 E G -11 E A 75 I U 76 I G 32 Z G 34 Z
27 1.32 1.32 394.2 -1.52 -0.47 19.6 78 25 16 18 22 6 8 0  U 76 I A 93 V A 94 V A 95 V G 96 V A 97 V G 98 V
A 99 V U 102 V G 3 Z A 4 Z A 5 Z U 6 Z C 7 Z U 8
Z C 9 Z U 10 Z U 11 Z U 12 Z G 13 Z C 14 Z C 15 Z
U 17 Z G 32 Z G 34 Z UNK 76 x UNK 79 x UNK 80 x
UNK 83 x UNK 84 x UNK 87 x
28 0.99 0.83 420.9 -0.48 -0.20 12.5 79 17 11 9 29 9 4 0  U 89 V U 90 V A 91 V C 92 V A 93 V A 94 V A 95 V
G 96 V A 97 V G 98 V A 99 V U 102 V G 3 Z A 4 Z A
5 Z U 6 Z C 7 Z U 8 Z C 9 Z G 13 Z C 14 Z C 15 Z
UNK 76 x UNK 77 x UNK 80 x UNK 88 x UNK 89 x
29 1.21 1.94 464.8 -0.46 -0.17 14.4 81 30 21 23 54 9 9 1  U -12 E G -
11 E C 37 U U 39 U C 40 U A 41 U A 42 U U 92 U C
107 U C 108 U A 91 V UNK 88 x UNK 89 x UNK 90 x
30 1.34 1.52 815.9 -1.18 -0.27 19.1 80 58 38 37 58 20 9 0  U 76 I G 32 Z G 34 Z U 118 Z G 120 Z G 143 Z G
144 Z G 1089 Z U 1148 Z
31 1.15 1.16 117.8 -0.31 -0.27 8.9 81 2 5 9 10 4 0 0  
32 1.40 1.40 122.6 0.20 0.01 9.9 79 4 6 7 9 8 1 1  
33 1.32 1.58 39.1 -0.27 -0.01 17.2 67 2 4 0 3 3 0 2  

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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