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PDBsum entry 3d5c
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Top Page protein dna_rna metals Protein-protein interface(s) tunnels links
Tunnel analysis for: 3d5c calculated with MOLE 2.0 PDB id
3d5c
Tunnels calculated on whole structure Tunnels calculated excluding ligands
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13 tunnels, coloured by tunnel radius 24 tunnels, coloured by tunnel radius 24 tunnels, coloured as in
list below
Tunnels are interior spaces connected with the protein surrounding. Only channels longer than 15 Å are shown.
Tunnels
Free R
Length
HPathy
HPhob
Polar
Rel Mut
Residue..type
Ligands
Radius
1 1.18 1.18 65.7 -0.84 -0.60 10.0 84 6 0 1 2 2 0 0  C 136 A i:B C 136 A i:A U 950 A G 951 A G 971 A C
972 A G 973 A A 974 A A 975 A G 976 A A 977 A A
978 A C 980 A U 1358 A C 1359 A A 1360 A G 1361 A
A 1363 A G 1365 A C 1366 A
2 1.34 1.70 67.9 -0.91 -0.65 12.2 86 3 2 1 2 1 0 0  G 951 A U 952 A G 953 A G 954 A U 955 A U 956 A U
957 A A 959 A U 960 A U 961 A C 962 A G 971 A C
972 A G 973 A A 974 A A 975 A G 976 A C 985 A A
986 A C 1223 A G 1224 A U 1358 A G 1365 A C 1366
A MG 1884 A MG 1892 A MG 1898 A
3 1.36 1.67 79.6 -0.98 -0.60 11.1 82 7 0 2 3 2 0 0  C 136 A i:B A 949 A U 950 A G 951 A G 971 A C 972
A G 973 A A 974 A A 975 A G 976 A A 977 A G 1224
A U 1307 A G 1311 A G 1312 A C 1320 A C 1321 A G
1323 A A 1324 A C 1325 A U 1358 A A 1363 A G 1365
A C 1366 A MG 1672 A
4 1.36 1.36 87.4 -0.68 -0.69 7.0 87 5 0 2 2 1 0 0  C 136 A i:B C 136 A i:A A 949 A U 950 A G 951 A G
971 A C 972 A G 973 A A 974 A A 975 A G 976 A A
977 A G 1224 A G 1258 A C 1259 A C 1260 A C 1270
A G 1271 A G 1272 A C 1314 A U 1315 A G 1316 A A
1324 A C 1325 A U 1358 A G 1361 A A 1363 A U 1364
A G 1365 A C 1366 A
5 1.42 1.42 89.2 -0.63 -0.57 9.7 79 4 2 1 6 2 0 0  G 951 A U 952 A G 953 A G 954 A U 955 A U 961 A C
962 A G 963 A A 964 A A 965 A G 971 A C 972 A G
973 A A 974 A A 975 A G 976 A C 1223 A G 1224 A U
1358 A G 1365 A C 1366 A MG 1698 A MG 1884 A MG
1892 A MG 1898 A G 29 Y
6 1.34 1.49 96.5 -1.69 -0.56 19.1 79 9 2 1 2 2 0 0  C 136 A i:B A 949 A U 950 A G 951 A G 971 A C 972
A G 973 A A 974 A A 975 A G 976 A A 977 A G 1224
A C 1243 A C 1244 A A 1245 A C 1267 A G 1305 A U
1307 A U 1308 A A 1324 A C 1325 A C 1326 A C 1327
A C 1328 A A 1329 A U 1330 A G 1331 A U 1358 A A
1363 A G 1365 A C 1366 A MG 1554 A MG 1930 A
7 1.35 1.66 122.1 -0.42 -0.63 6.4 83 3 1 1 3 2 0 0  C 924 A G 925 A G 926 A G 928 A G 929 A C 931 A G
951 A U 952 A G 953 A G 954 A U 955 A U 961 A C
962 A G 963 A A 964 A A 965 A G 966 A C 967 A G
971 A C 972 A G 973 A A 974 A A 975 A G 976 A C
1195 A U 1196 A G 1197 A G 1198 A C 1223 A G 1224
A U 1358 A G 1365 A C 1366 A U 1381 A C 1382 A C
1383 A G 1385 A G 1386 A C 1399 A C 1400 A MG
1698 A MG 1830 A MG 1884 A MG 1891 A MG 1892 A MG
1898 A MG 1911 A A 12 V A 13 V
8 1.42 1.42 126.4 -0.41 -0.64 6.2 86 3 1 1 4 2 0 0  U 920 A U 921 A G 922 A A 923 A C 924 A G 951 A U
952 A G 953 A G 954 A U 955 A U 961 A C 962 A G
963 A A 964 A A 965 A G 966 A C 967 A G 971 A C
972 A G 973 A A 974 A A 975 A G 976 A U 1194 A C
1195 A U 1196 A G 1197 A G 1198 A C 1223 A G 1224
A U 1358 A G 1365 A C 1366 A G 1386 A G 1387 A C
1388 A C 1389 A U 1390 A U 1391 A C 1399 A C 1400
A MG 1698 A MG 1884 A MG 1892 A MG 1898 A MG 1921
A
9 1.34 1.34 133.5 -0.61 -0.60 8.6 83 7 1 2 4 3 0 0  U 534 A G 951 A U 952 A G 953 A G 954 A U 955 A U
961 A C 962 A G 963 A A 964 A A 965 A G 966 A C
967 A G 971 A C 972 A G 973 A A 974 A A 975 A G
976 A U 1194 A C 1195 A U 1196 A G 1197 A G 1198
A C 1223 A G 1224 A U 1358 A G 1365 A C 1366 A C
1397 A A 1398 A C 1399 A C 1400 A MG 1698 A MG
1884 A MG 1892 A MG 1898 A A 23 V
10 1.33 1.70 157.8 -0.62 -0.68 7.9 79 6 2 1 4 3 0 0  C 924 A G 933 A C 934 A A 935 A G 951 A U 952 A G
953 A G 954 A U 955 A U 961 A C 962 A G 963 A A
964 A A 965 A G 966 A C 967 A A 968 A G 971 A C
972 A G 973 A A 974 A A 975 A G 976 A C 1063 A G
1064 A U 1065 A C 1066 A G 1175 A G 1181 A G 1182
A A 1183 A G 1185 A G 1186 A G 1187 A C 1195 A U
1196 A G 1197 A G 1198 A C 1223 A G 1224 A G 1343
A C 1344 A U 1345 A A 1346 A U 1358 A G 1365 A C
1366 A G 1385 A G 1386 A C 1399 A C 1400 A MG
1698 A MG 1878 A MG 1884 A MG 1892 A MG 1898 A
11 1.50 1.50 25.9 -0.40 -0.80 3.4 0 0 0 0 0 0 0 0  G 7 Z U 8 Z U 47 Z C 48 Z G 49 Z U 50 Z C 51 Z G
52 Z G 53 Z A 58 Z A 59 Z U 60 Z MG 80 Z MG 126 Z
MG 270 Z
12 1.49 1.49 28.2 -0.40 -0.80 3.4 0 0 0 0 0 0 0 0  G 4 Z G 5 Z G 6 Z G 7 Z U 8 Z C 17 Z C 48 Z G 49
Z U 50 Z A 59 Z U 60 Z C 61 Z C 62 Z G 63 Z MG 77
Z MG 78 Z MG 264 Z MG 270 Z MG 426 Z
13 1.49 1.49 30.6 -0.40 -0.80 3.4 0 0 0 0 0 0 0 0  G 2 Z C 3 Z G 4 Z G 5 Z G 6 Z G 7 Z U 8 Z C 48 Z
G 49 Z U 50 Z A 59 Z U 60 Z C 61 Z C 62 Z G 63 Z
G 64 Z C 65 Z MG 77 Z MG 78 Z MG 108 Z MG 264 Z
MG 270 Z
14 1.34 1.98 16.8 1.33 0.31 10.5 71 1 2 0 5 0 0 0  
15 1.23 1.95 17.0 3.27 0.85 0.5 81 0 0 0 10 0 0 0  
16 1.24 2.36 18.0 2.59 0.68 3.8 77 0 1 0 7 0 0 0  
17 1.09 2.36 16.1 1.66 0.66 6.0 91 1 1 0 5 1 0 0  A 684 A
18 1.26 2.41 20.7 2.88 0.87 0.8 78 0 0 0 10 3 0 0  
19 1.54 1.54 15.3 -0.61 -0.66 6.5 98 1 0 1 2 0 0 0  A 76 Y
20 1.57 1.85 18.4 -2.23 -0.67 25.6 90 2 1 2 0 0 0 0  C 1 Y G 2 Y A 73 Y C 74 Y
21 1.57 1.60 18.8 -2.37 -0.69 24.0 90 2 1 2 0 0 0 0  C 1 Y G 2 Y A 73 Y C 74 Y
22 1.09 1.18 18.6 -0.76 -0.44 10.8 76 3 0 1 2 0 1 0  C 948 A A 949 A A 1227 A U 1307 A
23 1.10 1.17 19.0 -0.85 -0.49 9.7 76 3 0 1 2 0 1 0  C 948 A A 949 A A 1227 A U 1307 A
24 1.16 2.27 18.4 1.09 0.50 4.7 71 0 2 0 5 2 1 1  

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
Tunnels were calculated by MOLE 2.0 program version 2.5.13.11.08 and visualized using Pymol 0.97rc.
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