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DEF_STAAU_1_183

Peptide deformylase [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer
A1 (DEF_STAAU):-6:-1, 45, 56:60, 65, 78, 105, 109:112, 147, 150, 151, 154, 155, 158, 185-6:-1, 45, 56:60, 65, 78, 105, 109:112, 147, 150, 151, 154, 155, 158, 185
Metals (Me):Fe/Zn

Full PDB list

1lm4, 1lmh, 1lqw, 1q1y, 2ai9, 3u7k, 3u7l, 3u7m, 3u7n (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
4
5
R
5
6
S
5
7
G
5
8
V
5
9
G
6
0
Q
6
5
P
7
8
L
1
0
5
E
1
0
9
G
1
1
0
C
1
1
1
L
1
1
2
Y
1
4
7
I
1
5
0
V
1
5
1
H
1
5
4
E
1
5
5
H
1
5
8
.
1
8
5
[1]1lm4.b none . . . . . . . . . . . * . . . . . . . - Fe
[1]1lqw.a none . . . . . . . . . . . . . . . . . . . - Zn
[1]1q1y.a bb227 . . . . . . . . . . . * . . . . . . . E Zn
[1]3u7k.a mdb31 . . . . . . . . . . . * . . . . . . . E Zn
[1]3u7l.a udb31 . . . . . . . . . . . * . . . . . . . E Zn
[1]3u7m.a fhf27 . . . . . . . . . . . * . . . . . . . E Zn
[1]3u7n.a uhf27 . . . . . . . . . . . * . . . . . . . E Zn
[2]1lm4.a none . . . . . . . . . . . * . . . . . . . - Fe

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

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PDB.ch
A1 Me
.
-
6
.
-
5
.
-
4
.
-
3
.
-
2
.
-
1
Q
4
5
R
5
6
S
5
7
G
5
8
V
5
9
G
6
0
Q
6
5
P
7
8
L
1
0
5
E
1
0
9
G
1
1
0
C
1
1
1
L
1
1
2
Y
1
4
7
I
1
5
0
V
1
5
1
H
1
5
4
E
1
5
5
H
1
5
8
.
1
8
5
[1]1lm4.b - - - - - - . . . . . . . . . . . * . . . . . . . - Fe
[1]1lqw.a - - - - - - . . . . . . . . . . . . . . . . . . . - Zn
[1]1q1y.a - - - - - - . . . . . . . . . . . * . . . . . . . E Zn
[1]3u7k.a - - - - - - . . . . . . . . . . . * . . . . . . . E Zn
[1]3u7l.a - - - - - - . . . . . . . . . . . * . . . . . . . E Zn
[1]3u7m.a - - - - - - . . . . . . . . . . . * . . . . . . . E Zn
[1]3u7n.a - - - - - - . . . . . . . . . . . * . . . . . . . E Zn
[2]1lm4.a G S D K I H . . . . . . . . . . . * . . . . . . . - Fe

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
1lm4.b is apo
1lqw.a is apo
1q1y.a:bb2
3u7k.a:mdb
3u7l.a:udb
3u7m.a:fhf
3u7n.a:uhf
1lm4.a is apo
[1] 1lm4.b
-
- 0.4 1.0 0.9 0.5 0.6 -
[1] 1lqw.a -
-
0.1 0.7 0.4 0.3 0.4 -
[1] 1q1y.a - -
0
0.4 0.4 0.1 0.3 -
[1] 3u7k.a - - 0.2
0.1
0.1 0.1 0.2 -
[1] 3u7l.a - - 0.2 0.1
0.1
0.1 0.2 -
[1] 3u7m.a - - 0.1 0.4 0.4
0.2
0.3 -
[1] 3u7n.a - - 0 0.4 0.3 0.1
0.2
-
[2] 1lm4.a - - 16 16 17 15 16
-
[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
1lm4.b
1lqw.a
1q1y.a
3u7k.a
3u7l.a
3u7m.a
3u7n.a
1lm4.a
[1] 1lm4.b
0
.02 .02 .03 .03 .02 .02 .75
[1] 1lqw.a .02
0
.01 .02 .02 .01 .01 .75
[1] 1q1y.a .02 .01
0
.01 .01 0 0 .74
[1] 3u7k.a .03 .02 .01
0
0 .01 .01 .74
[1] 3u7l.a .03 .02 .01 0
0
.01 .01 .74
[1] 3u7m.a .02 .01 0 .01 .01
0
0 .74
[1] 3u7n.a .02 .01 0 .01 .01 0
0
.74
[2] 1lm4.a .75 .75 .74 .74 .74 .74 .74
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1lm4.b
1lqw.a
1q1y.a
3u7k.a
3u7l.a
3u7m.a
3u7n.a
1lm4.a
[1] 1lm4.b
0
0.4 0.4 0.6 0.5 0.3 0.4 0.3
[1] 1lqw.a 0.4
0
0.3 0.5 0.4 0.3 0.3 0.4
[1] 1q1y.a 0.4 0.3
0
0.5 0.4 0.3 0.3 0.3
[1] 3u7k.a 0.6 0.5 0.5
0
0.3 0.5 0.5 0.4
[1] 3u7l.a 0.5 0.4 0.4 0.3
0
0.4 0.4 0.4
[1] 3u7m.a 0.3 0.3 0.3 0.5 0.4
0
0.2 0.3
[1] 3u7n.a 0.4 0.3 0.3 0.5 0.4 0.2
0
0.2
[2] 1lm4.a 0.3 0.4 0.3 0.4 0.4 0.3 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
1lm4.b
1lqw.a
1q1y.a
3u7k.a
3u7l.a
3u7m.a
3u7n.a
1lm4.a
[1] 1lm4.b
0
0.9 0.8 0.8 0.8 0.8 0.8 0.8
[1] 1lqw.a 0.9
0
0.5 0.7 0.6 0.6 0.6 0.6
[1] 1q1y.a 0.8 0.5
0
1.1 0.5 0.5 0.3 0.4
[1] 3u7k.a 0.8 0.7 1.1
0
1.3 1.1 1.1 0.6
[1] 3u7l.a 0.8 0.6 0.5 1.3
0
0.7 0.5 0.5
[1] 3u7m.a 0.8 0.6 0.5 1.1 0.7
0
0.4 0.5
[1] 3u7n.a 0.8 0.6 0.3 1.1 0.5 0.4
0
0.4
[2] 1lm4.a 0.8 0.6 0.4 0.6 0.5 0.5 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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