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DEF_ENTFA_1_187

Peptide deformylase [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer
A1 (DEF_ENTFA):56:60, 65, 108, 110:115, 150, 153, 154, 157, 158, 161, 18756:60, 65, 108, 110:115, 150, 153, 154, 157, 158, 161, 187
Metals (Me):Ni

Full PDB list

2os0, 2os1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
R
5
6
G
5
7
G
5
8
V
5
9
G
6
0
Q
6
5
L
1
0
8
E
1
1
0
G
1
1
1
E
1
1
2
G
1
1
3
C
1
1
4
L
1
1
5
Y
1
5
0
I
1
5
3
V
1
5
4
H
1
5
7
E
1
5
8
H
1
6
1
.
1
8
7
A
[1]2os0.a none . . D . . . . . . . . . . . . . . . . L Ni
[1]2os1.a bb227 . . . . . . . . . . . . . . . . . . . L 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
R
5
6
G
5
7
G
5
8
V
5
9
G
6
0
Q
6
5
L
1
0
8
E
1
1
0
G
1
1
1
E
1
1
2
G
1
1
3
C
1
1
4
L
1
1
5
Y
1
5
0
I
1
5
3
V
1
5
4
H
1
5
7
E
1
5
8
H
1
6
1
.
1
8
7
A
[1]2os0.a . . D . . . . . . . . . . . . . . . . L Ni
[1]2os1.a . . . . . . . . . . . . . . . . . . . L 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
2os0.a is apo
2os1.a:bb2
[1] 2os0.a
-
1.0
[1] 2os1.a -
0.1
[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
2os0.a
2os1.a
[1] 2os0.a
0
.05
[1] 2os1.a .05
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
2os0.a
2os1.a
[1] 2os0.a
0
0.3
[1] 2os1.a 0.3
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
2os0.a
2os1.a
[1] 2os0.a
0
0.6
[1] 2os1.a 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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