PDBsum entry 3vdb

Tunnel analysis for: 3vdb calculated with

MOLE 2.0

PDB id

3vdb

Tunnels calculated on whole structure

Tunnels calculated excluding ligands

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MOLEonline 2.0 manipulation
and
visualization
with HETATM:

without HETATM:

10 tunnels, coloured by tunnel radius

11 tunnels, coloured by tunnel radius

11 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

1.32

1.44

29.1

-1.01

-0.33

17.0

75

2

2

3

3

2

1

1

2

1.33

1.44

34.4

-1.24

-0.35

17.7

75

3

2

2

3

3

1

0

3

1.32

1.43

37.3

-1.99

-0.54

21.4

83

6

6

3

4

1

1

0

DMS 8018 A

4

1.33

1.44

43.9

-0.91

-0.43

12.0

72

1

3

4

3

2

4

1

5

1.32

1.43

44.8

-1.69

-0.59

12.0

72

3

2

4

1

3

4

0

6

1.33

1.44

53.6

-1.68

-0.61

16.9

75

2

5

3

2

1

4

1

7

1.34

1.46

58.0

-1.97

-0.62

19.8

80

6

6

4

4

1

4

0

DMS 8001 D

8

1.20

1.46

21.4

-1.77

-0.42

4.2

87

1

0

8

1

2

0

0

9

1.18

1.34

26.4

-1.69

-0.34

4.2

87

1

0

8

1

2

0

0

10

1.29

1.41

22.5

-1.69

-0.34

3.7

87

1

0

8

1

2

0

0

11

1.13

3.14

29.8

-0.90

-0.05

9.2

67

3

0

4

3

3

1

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

Tunnels were calculated by

MOLE 2.0 program version 2.5.13.11.08 and visualized using Pymol 0.97rc.