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DBP5_YEAST_295_482

ATP-dependent RNA helicase DBP5 [DEAD box helicase family. DDX19/DBP5 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DBP5_YEAST):D: Helicase ATP-binding (139:146, 180, 181, 184)
D: Helicase C-terminal (395, 429, 430)
94, 110, 112, 114:116, 119
94, 110, 112, 114:116, 119, 139:146, 180, 181, 184, 395, 429, 430

Full PDB list

3gfp, 3peu, 3pev, 3pew, 3pey, 3rrm, 5elx (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
9
4
M
1
1
0
F
1
1
2
K
1
1
4
Q
1
1
9
Q
1
3
9
S
1
4
0
G
1
4
1
T
1
4
2
G
1
4
3
K
1
4
4
T
1
4
5
A
1
4
6
E
1
8
4
D
3
9
5
R
4
2
9
F
4
3
0
[1]3gfp.a none - - - - - - - - - - - - - - . . .
[1]3pew.a adp,mg28 . . . . . . . . . . . . . . . . .
[1]5elx.a m2a,mg38 . . . . . . . . . . . . . . . . .
[2]3rrm.a adp27 - . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
F
9
4
M
1
1
0
F
1
1
2
K
1
1
4
P
1
1
5
S
1
1
6
Q
1
1
9
Q
1
3
9
S
1
4
0
G
1
4
1
T
1
4
2
G
1
4
3
K
1
4
4
T
1
4
5
A
1
4
6
E
1
8
0
V
1
8
1
E
1
8
4
D
3
9
5
R
4
2
9
F
4
3
0
[1]3gfp.a - - - - - - - - - - - - - - - - - - . . *
[1]3pew.a . . . . . . . . . . . . . * . . * . . . .
[1]5elx.a . . . . . . . . . . . . . * . . * . . . .
[2]3rrm.a - . . . . . * * . * * . . . . . . . . . *

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3gfp.a is apo
3pew.a:adp,mg
5elx.a:m2a,mg
3rrm.a:adp
[1] 3gfp.a
-
1.5 1.4 0.1
[1] 3pew.a -
0
0.1 3.7
[1] 5elx.a - 0
0
3.5
[2] 3rrm.a - 11 11
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3gfp.a
3pew.a
5elx.a
3rrm.a
[1] 3gfp.a
0
.23 .21 .52
[1] 3pew.a .23
0
.01 .65
[1] 5elx.a .21 .01
0
.66
[2] 3rrm.a .52 .65 .66
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 4.9 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3gfp.a
3pew.a
5elx.a
3rrm.a
[1] 3gfp.a
0
5.4 5.4 3.4
[1] 3pew.a 5.4
0
0.2 5.1
[1] 5elx.a 5.4 0.2
0
5.0
[2] 3rrm.a 3.4 5.1 5.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 4.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3gfp.a
3pew.a
5elx.a
3rrm.a
[1] 3gfp.a
0
6.8 6.8 4.4
[1] 3pew.a 6.8
0
0.9 5.4
[1] 5elx.a 6.8 0.9
0
5.4
[2] 3rrm.a 4.4 5.4 5.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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