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PDBsum entry 3v6d
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Top Page protein dna_rna Protein-protein interface(s) pores links
Pore analysis for: 3v6d calculated with MOLE 2.0 PDB id
3v6d
Pores calculated on whole structure Pores calculated excluding ligands
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22 pores, coloured by radius 22 pores, coloured by radius 22 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 2.94 3.54 29.8 -1.57 -0.31 22.4 72 4 3 1 2 4 1 0  DG 719 T DG 720 T
2 1.22 1.22 35.4 -0.22 0.10 8.2 76 1 1 1 4 3 2 0  DG 720 E DG 721 E DA 722 E DC 803 F DA 804 F
3 1.68 3.52 38.2 -0.97 -0.21 13.7 73 2 4 0 2 4 2 0  DT 813 P DC 814 P DG 710 T DG 719 T DG 720 T
4 1.24 2.62 38.6 -2.90 -0.54 31.6 75 7 4 2 1 2 0 0  
5 1.70 2.87 50.4 -1.27 -0.51 19.5 78 5 5 0 2 2 1 0  DG 710 E DG 719 E DG 720 E DA 804 F DT 813 F DC
814 F
6 3.20 3.42 52.5 -1.83 -0.39 24.9 75 7 5 2 2 3 2 0  
7 1.70 2.87 53.9 -1.53 -0.48 20.1 77 4 5 0 1 2 1 0  DG 710 E DC 712 E DC 713 E DG 714 E DC 809 F DT
810 F DG 811 F DT 812 F DT 813 F DC 814 F DG 815 F
8 2.01 2.01 55.3 -1.59 -0.55 22.9 80 6 4 0 2 0 0 0  DG 710 E DC 712 E DC 713 E DG 714 E DG 719 E DG
720 E DC 809 F DT 810 F DG 811 F DT 812 F DT 813
F DC 814 F DG 815 F
9 2.03 2.03 58.3 -0.89 -0.63 12.1 71 2 1 0 1 0 0 0  DA 706 E DG 707 E DG 708 E DC 709 E DG 710 E DC
711 E DC 712 E DC 713 E DG 714 E DA 715 E DC 809
F DT 810 F DG 811 F DT 812 F DT 813 F DC 814 F DG
815 F DG 816 F MRG 817 F DC 818 F
10 2.38 2.50 63.8 -0.95 -0.66 14.3 75 4 3 0 2 0 0 0  DT 813 P DC 814 P DG 815 P DG 816 P MRG 817 P DC
818 P DA 706 T DG 707 T DG 708 T DC 709 T DA 715
T DA 716 T DG 719 T DG 720 T
11 1.59 1.59 65.6 -1.63 -0.48 17.7 80 4 1 3 0 1 1 0  DC 803 P DA 804 P DG 805 P DT 806 P DC 807 P DG
720 T DG 721 T DA 722 T DC 723 T DT 724 T DG 725 T
12 1.66 3.55 68.7 -0.99 -0.33 12.7 70 2 3 0 2 4 2 0  DC 814 P DG 815 P DG 816 P MRG 817 P DC 818 P DA
706 T DG 707 T DG 708 T DC 709 T DG 710 T DC 711
T DA 715 T DA 716 T
13 1.69 2.87 70.9 -1.01 -0.49 15.0 76 3 4 0 2 2 1 0  DA 706 E DG 707 E DG 708 E DC 709 E DG 710 E DC
711 E DC 713 E DG 714 E DA 715 E DT 813 F DC 814
F DG 815 F DG 816 F MRG 817 F DC 818 F
14 1.86 2.09 71.4 -2.10 -0.58 17.8 69 4 4 4 0 5 2 0  DG 720 T DG 721 T
15 2.21 2.21 73.7 -1.22 -0.59 18.3 75 5 5 0 3 1 0 0  DA 706 E DG 707 E DG 708 E DC 713 E DG 714 E DA
715 E DG 719 E DG 720 E DT 813 F DC 814 F DG 815
F DG 816 F MRG 817 F DC 818 F
16 1.19 1.27 84.2 -1.27 -0.26 12.9 76 3 4 5 4 5 2 0  
17 1.41 1.80 94.7 -1.55 -0.20 23.0 79 9 5 3 2 2 4 0  
18 1.38 2.63 100.0 -2.21 -0.34 22.2 70 5 5 3 0 6 0 0  
19 2.32 2.50 103.8 -1.83 -0.47 19.6 77 10 4 5 4 3 2 0  DT 813 P DC 814 P DG 710 T DC 711 T DC 712 T DC
713 T DG 714 T DG 719 T DG 720 T
20 2.29 2.29 159.9 -1.20 -0.18 20.8 73 8 5 1 4 2 4 0  DG 816 P MRG 817 P DC 818 P DG 819 P DC 820 P DC
821 P DG 703 T DG 704 T DA 705 T DA 706 T DA 715
T DA 716 T
21 1.40 1.58 175.8 -1.54 -0.29 23.2 78 12 6 2 3 0 5 0  DG 816 P MRG 817 P DC 818 P DG 819 P DC 820 P DC
821 P DG 703 T DG 704 T DA 705 T DA 706 T DA 715
T DA 716 T
22 1.19 1.39 351.6 -1.38 -0.40 18.4 78 27 16 5 12 5 10 0  DT 813 P DC 814 P DG 815 P DG 816 P DC 818 P DG
819 P DC 820 P DC 821 P DG 703 T DG 704 T DA 705
T DA 706 T DG 707 T DG 708 T DC 709 T DG 719 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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