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DEF1A_ARATH_78_268

Peptide deformylase 1A, chloroplastic/mitochondrial [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DEF1A_ARATH):R: Substrate binding (123:126)
R: Dimerization (195)
131, 147, 161, 186:189, 223, 226, 227, 230, 231, 234
123:126, 131, 147, 161, 186:189, 195, 223, 226, 227, 230, 231, 234
Metals (Me):Zn

Full PDB list

1zxz, 1zy0, 1zy1, 4je6, 4je7, 4je8 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
P
1
2
3
G
1
2
4
V
1
2
5
G
1
2
6
Q
1
3
1
Y
1
4
7
R
1
6
1
E
1
8
6
G
1
8
7
C
1
8
8
L
1
8
9
R
1
9
5
W
2
2
3
R
2
2
6
I
2
2
7
H
2
3
0
E
2
3
1
H
2
3
4
[1]1zxz.b none . . . . . . . . . . . . . . . . . . Zn
[1]1zy1.a MAS20 . . . . . . . . . . . . . . . . . . Zn
[1]4je6.a none . C . . . . . . . . E . . . . . . . Zn
[1]4je7.a bb227 . C . . . . . . . . E . . . . . . . Zn
[1]4je8.a MAS19 . C . . . . . . . . E . . . . . . . Zn

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
P
1
2
3
G
1
2
4
V
1
2
5
G
1
2
6
Q
1
3
1
Y
1
4
7
R
1
6
1
E
1
8
6
G
1
8
7
C
1
8
8
L
1
8
9
R
1
9
5
W
2
2
3
R
2
2
6
I
2
2
7
H
2
3
0
E
2
3
1
H
2
3
4
[1]1zxz.b . . . . . . . . . . . . . . . . . . Zn
[1]1zy1.a . . . . . . . . . . . . . . . . . . Zn
[1]4je6.a . C . . . . . . . . E . . . . . . . Zn
[1]4je7.a . C . . . . . . . . E . . . . . . . Zn
[1]4je8.a . C . . . . . . . . E . . . . . . . Zn

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
1zxz.b is apo
1zy1.a:MAS
4je6.a is apo
4je7.a:bb2
4je8.a:MAS
[1] 1zxz.b
-
0.1 - 0.9 0
[1] 1zy1.a -
0.3
- 0.9 0
[1] 4je6.a - 0.3
-
0.7 0
[1] 4je7.a - 0.3 -
0.1
0
[1] 4je8.a - 0.4 - 1.4
0
[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
1zxz.b
1zy1.a
4je6.a
4je7.a
4je8.a
[1] 1zxz.b
0
.07 .04 .04 .06
[1] 1zy1.a .07
0
.09 .08 .12
[1] 4je6.a .04 .09
0
.02 .08
[1] 4je7.a .04 .08 .02
0
.07
[1] 4je8.a .06 .12 .08 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1zxz.b
1zy1.a
4je6.a
4je7.a
4je8.a
[1] 1zxz.b
0
0.4 0.3 0.4 0.3
[1] 1zy1.a 0.4
0
0.4 0.4 0.4
[1] 4je6.a 0.3 0.4
0
0.2 0.2
[1] 4je7.a 0.4 0.4 0.2
0
0.3
[1] 4je8.a 0.3 0.4 0.2 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1zxz.b
1zy1.a
4je6.a
4je7.a
4je8.a
[1] 1zxz.b
0
0.8 0.7 0.7 0.8
[1] 1zy1.a 0.8
0
0.7 0.7 0.7
[1] 4je6.a 0.7 0.7
0
0.6 0.8
[1] 4je7.a 0.7 0.7 0.6
0
0.9
[1] 4je8.a 0.8 0.7 0.8 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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