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DEF_PSEAE_1_168

Peptide deformylase [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer
A1 (DEF_PSEAE):44:46, 51, 88:93, 99, 127, 130, 131, 134, 135, 13844:46, 51, 88:93, 99, 127, 130, 131, 134, 135, 138
Metals (Me):Ni/Zn

Full PDB list

1ix1, 1lry, 1n5n, 1s17 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
G
4
4
I
4
5
G
4
6
Q
5
1
Y
8
8
Q
8
9
E
9
0
G
9
1
C
9
2
L
9
3
Y
9
9
V
1
3
0
C
1
3
1
H
1
3
4
E
1
3
5
H
1
3
8
[1]1ix1.a bb227 . . . . . . . . . . . . . . . . Zn
[1]1n5n.a none . . . . . . . . . . . . . . . . Zn
[1]1s17.a gnr16 . . . . . . . . . . . . . . . . Ni

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 Me
G
4
4
I
4
5
G
4
6
Q
5
1
Y
8
8
Q
8
9
E
9
0
G
9
1
C
9
2
L
9
3
Y
9
9
L
1
2
7
V
1
3
0
C
1
3
1
H
1
3
4
E
1
3
5
H
1
3
8
[1]1ix1.a . . . . . . . . . . . . . . . . . Zn
[1]1n5n.a . . . . . . . . . . . . . . . . . Zn
[1]1s17.a . . . . . . . . . . . . . . . . . Ni

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
1ix1.a:bb2
1n5n.a is apo
1s17.a:gnr
[1] 1ix1.a
0
- 0
[1] 1n5n.a 0.9
-
0.5
[1] 1s17.a 0.3 -
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
1ix1.a
1n5n.a
1s17.a
[1] 1ix1.a
0
.05 .02
[1] 1n5n.a .05
0
.04
[1] 1s17.a .02 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1ix1.a
1n5n.a
1s17.a
[1] 1ix1.a
0
0.2 0.2
[1] 1n5n.a 0.2
0
0.2
[1] 1s17.a 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1ix1.a
1n5n.a
1s17.a
[1] 1ix1.a
0
0.6 0.5
[1] 1n5n.a 0.6
0
0.3
[1] 1s17.a 0.5 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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