If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

DEF_HAEI8_1_169

Peptide deformylase [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer
A1 (DEF_HAEI8):43:46, 51, 87:92, 98, 126, 129, 130, 133, 134, 13743:46, 51, 87:92, 98, 126, 129, 130, 133, 134, 137
Metals (Me):Ni

Full PDB list

4wxk, 4wxl

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
K
4
3
G
4
4
I
4
5
G
4
6
Q
5
1
I
8
7
E
8
8
E
8
9
G
9
0
C
9
1
L
9
2
R
9
8
I
1
2
9
C
1
3
0
H
1
3
3
E
1
3
4
H
1
3
7
[1]4wxk.a none . . . . . . . . . . . . . . . . . Ni
[1]4wxl.a bb227 . . . . . . . . . . . . . . . . . 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
K
4
3
G
4
4
I
4
5
G
4
6
Q
5
1
I
8
7
E
8
8
E
8
9
G
9
0
C
9
1
L
9
2
R
9
8
L
1
2
6
I
1
2
9
C
1
3
0
H
1
3
3
E
1
3
4
H
1
3
7
[1]4wxk.a . . . . . . . . . . . * . . . . . . Ni
[1]4wxl.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
4wxk.a is apo
4wxl.a:bb2
[1] 4wxk.a
-
1.4
[1] 4wxl.a -
0.3
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4wxk.a
4wxl.a
[1] 4wxk.a
0
.06
[1] 4wxl.a .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
4wxk.a
4wxl.a
[1] 4wxk.a
0
0.3
[1] 4wxl.a 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
4wxk.a
4wxl.a
[1] 4wxk.a
0
0.9
[1] 4wxl.a 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...