PDBsum entry 3ndk

Tunnel analysis for: 3ndk calculated with

MOLE 2.0

PDB id

3ndk

Tunnels calculated on whole structure

Tunnels calculated excluding ligands

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MOLEonline 2.0 manipulation
and
visualization
with HETATM:

without HETATM:

4 tunnels, coloured by tunnel radius

9 tunnels, coloured by tunnel radius

9 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

1.13

1.19

32.0

-1.65

-0.43

23.9

80

5

4

1

5

1

1

0

DCP 904 A CA 905 A

2

1.13

1.19

40.8

-0.30

0.17

10.2

84

4

1

4

7

3

1

0

DCP 904 A DA 114 P DOC 115 P DG 4 T DG 5 T

3

1.13

1.19

41.0

-0.54

-0.13

6.5

84

1

0

1

4

2

1

0

DCP 904 A DC 111 P DT 112 P DT 113 P DA 114 P DOC
115 P DT 1 T DA 3 T DG 4 T DG 5 T DT 6 T

4

1.13

1.19

56.9

-1.30

-0.33

16.1

81

4

3

2

4

3

1

0

DCP 904 A DT 113 P DA 114 P DOC 115 P DT 1 T DG 4
T DG 5 T

5

1.14

1.20

69.1

-0.73

-0.02

14.4

79

6

2

3

6

4

2

0

DCP 904 A DT 113 P DA 114 P DOC 115 P DG 4 T DG 5
T

6

1.23

1.49

20.4

0.36

0.09

10.2

85

1

1

2

6

2

0

0

7

1.21

1.49

20.7

0.75

0.23

12.8

86

1

2

1

5

1

0

0

8

1.53

1.74

15.6

-0.76

0.01

16.6

78

2

1

0

4

1

0

0

9

1.54

1.73

15.7

-0.80

0.03

18.3

78

2

3

0

4

1

0

0

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.