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PDBsum entry 3d1n
Go to PDB code: 
Top Page protein dna_rna Protein-protein interface(s) pores links
Pore analysis for: 3d1n calculated with MOLE 2.0 PDB id
3d1n
Pores calculated on whole structure Pores calculated excluding ligands
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27 pores, coloured by radius 24 pores, coloured by radius 24 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 1.62 1.62 27.3 -0.04 -0.20 5.9 79 1 0 2 2 3 1 0  DT 5 C DA 6 C DC 13 D
2 1.22 1.40 29.0 1.08 0.16 4.3 82 1 1 1 3 2 0 0  DT 4 D DT 5 D MSE 267 K
3 1.31 2.51 32.0 0.07 -0.10 7.5 81 1 2 2 2 3 0 0  DA 6 C DA 7 C DA 8 C DT 9 C DA 3 D DT 4 D
4 1.50 2.78 43.0 0.41 0.46 4.7 72 1 0 0 7 2 1 0  DA 14 C DA 3 D DT 4 D DT 5 D MSE 172 I
5 2.10 2.13 48.3 -1.89 -0.78 14.9 89 3 2 5 0 0 0 0  DA 4 C DT 5 C DT 7 D DT 8 D MSE 224 L
6 1.64 2.33 54.4 0.40 0.26 4.2 70 1 1 0 6 3 1 0  DA 13 A DA 14 A DT 1 B DT 2 B DA 3 B DT 4 B DT 5
B DT 1 D DT 2 D DA 3 D DT 4 D MSE 172 K
7 1.33 1.39 61.7 -1.59 -0.60 11.3 90 4 1 7 1 0 0 0  DA 4 E DT 5 E DA 6 E DT 12 E DT 7 F DT 8 F DT 9 F
DT 14 F MSE 224 N
8 1.23 1.23 65.6 -1.36 -0.59 12.6 83 3 2 6 2 3 0 0  DT 5 C DA 6 C DA 7 C DT 7 D DT 8 D MSE 224 L
9 1.31 2.41 67.5 0.92 0.59 5.1 75 2 1 0 14 5 0 0  DA 13 A DA 14 A DT 1 B DA 14 C MSE 172 I MSE 172 K
10 2.10 2.11 76.0 -1.09 -0.54 10.4 88 4 0 5 2 0 1 0  DA 4 C DT 5 C DA 14 C DA 3 D DT 4 D DT 5 D DA 6 D
DT 7 D DT 8 D
11 1.48 2.79 78.3 -0.95 -0.25 12.7 74 4 2 3 7 2 2 0  DT 12 C DA 13 C DA 14 C DT 5 D DA 6 D DT 7 D MSE
172 I MSE 224 L
12 1.71 2.54 92.5 -0.88 -0.28 16.4 77 4 4 3 6 3 1 0  DA 13 A DA 14 A DT 12 C MSE 172 K MSE 224 L
13 1.69 2.64 105.1 -0.63 -0.34 12.6 82 5 3 3 7 3 1 0  DA 13 A DA 14 A DA 4 C DT 5 C DT 12 C DT 7 D DT 8
D MSE 172 K
14 1.37 1.39 110.5 -1.60 -0.74 12.9 85 6 2 4 0 0 2 0  DA 4 E DT 5 E DA 6 E DT 12 E DA 6 F DT 7 F DT 8 F
DT 9 F DT 14 F DT 12 G DA 13 G DT 5 H DA 6 H
15 2.48 2.49 122.0 -1.50 -0.63 15.6 83 8 3 5 1 0 2 0  DT 12 E DA 6 F DT 7 F DT 8 F DT 12 G DA 13 G DT 5
H DA 6 H MSE 224 N
16 1.18 1.25 128.1 -0.36 -0.18 11.0 78 5 4 3 10 6 1 0  DA 13 A DA 14 A DT 5 C DA 6 C DA 7 C DT 12 C DT 7
D DT 8 D MSE 172 K
17 2.07 2.07 129.5 -2.07 -0.76 19.1 81 6 5 8 0 0 2 0  DT 12 A DA 6 B DT 7 B DT 8 B DT 12 C MSE 224 J MS
E 224 L
18 1.61 2.42 147.6 -1.10 -0.26 13.1 79 9 4 11 9 3 1 0  DT 12 A DA 14 A DT 5 B DA 6 B DT 7 B DT 8 B MSE
224 J MSE 172 K
19 1.34 2.27 154.9 -1.43 -0.40 16.2 82 8 5 9 10 2 1 0  DT 12 A DA 13 A DA 14 A DT 1 B DA 6 B DT 7 B DT 8
B DA 14 C MSE 172 I MSE 224 J
20 1.97 1.98 182.2 -1.76 -0.67 16.1 85 10 6 11 3 0 2 0  DT 12 A DA 6 B DT 7 B DT 8 B DA 4 C DT 5 C DT 12
C DT 7 D DT 8 D MSE 224 J
21 2.14 2.15 185.2 -1.66 -0.62 16.2 82 10 6 9 4 0 3 0  DT 12 A DA 6 B DT 7 B DT 8 B DT 12 C DA 13 C DA
14 C DA 3 D DT 4 D DT 5 D DA 6 D DT 7 D MSE 224 J
22 1.20 1.74 224.9 -0.76 -0.11 11.4 77 9 5 11 14 6 1 0  DT 12 A DA 14 A DT 5 B DA 6 B DT 7 B DT 8 B DA 4
G DT 5 G DT 7 H DT 8 H MSE 224 J MSE 172 K MSE
172 P MSE 224 P
23 1.59 2.95 245.2 -1.02 -0.35 11.6 79 11 4 12 10 3 1 0  DT 12 A DA 14 A DT 5 B DA 6 B DT 7 B DT 8 B DA 4
G DT 5 G DT 12 G DA 13 G DT 5 H DA 6 H DT 7 H DT
8 H MSE 224 J MSE 172 K MSE 224 P
24 2.19 2.54 33.0 -2.92 -0.64 27.7 74 2 5 2 1 1 1 0  MSE 267 I

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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