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DEF1B_ARATH_80_272_actinonin

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

Composition of the binding site

Protein chains monomer
A1 (DEF1B_ARATH):120:125, 128, 167:172, 178, 206, 209, 210, 213, 214, 217120:125, 128, 167:172, 178, 206, 209, 210, 213, 214, 217
Metals (Me):Zn

Full PDB list

3cpm, 3m6o, 3m6p, 3m6q, 3m6r, 3o3j, 3pn2, 3pn3, 3pn4, 3pn5, 3pn6 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
1
2
0
G
1
2
1
I
1
2
2
G
1
2
3
Q
1
2
8
F
1
6
7
D
1
6
8
E
1
6
9
G
1
7
0
C
1
7
1
L
1
7
2
Y
1
7
8
L
2
0
6
R
2
0
9
I
2
1
0
H
2
1
3
E
2
1
4
H
2
1
7
[1]3cpm.a none . . . . . . . . . . . . . . . . . . Zn
[1]3m6q.a bb227 . Q . . . . . . . . . . . . . . . . Zn
[1]3m6r.d bb227 . M . . . . . . . . . . . . . . . . Zn
[1]3o3j.a bb415 . . . . . . . . . . . . . . . . . . Zn
[1]3pn3.a zn1 . . . . . . . . . . . . . . . . . . Zn
[1]3pn4.a bb227 . . . . . . . . . . . . . . . . . . Zn
[1]3pn5.a zn1 . Q . . . . . . . . . . . . . . . . Zn
[1]3pn6.b none . M . . . . . . . . . . . . . . . . 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

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PDB.ch
A1 Me
D
1
2
0
G
1
2
1
I
1
2
2
G
1
2
3
L
1
2
4
S
1
2
5
Q
1
2
8
F
1
6
7
D
1
6
8
E
1
6
9
G
1
7
0
C
1
7
1
L
1
7
2
Y
1
7
8
L
2
0
6
R
2
0
9
I
2
1
0
H
2
1
3
E
2
1
4
H
2
1
7
[1]3cpm.a . . . . . . . . . . . . . . . . . . . . Zn
[1]3m6q.a . Q . . . . . . . . . . . . . . . . . . Zn
[1]3m6r.d . M . . . . . . . . . . . . . . . . . . Zn
[1]3o3j.a . . . . . . . . . . . . . . . . . . . . Zn
[1]3pn3.a . . . . . . . . . . . . . . . . . . * . Zn
[1]3pn4.a . . . . . . . . . . . . . . . . . . . . Zn
[1]3pn5.a . Q . . . . . . . . . . . . . . * . * . Zn
[1]3pn6.b . M . . . . . . . . . . . . . . . . . . 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
3cpm.a is apo
3m6q.a:bb2
3m6r.d:bb2
3o3j.a:bb4
3pn3.a:zn
3pn4.a:bb2
3pn5.a:zn
3pn6.b is apo
[1] 3cpm.a
-
0.5 1.4 0.2 0.1 1.1 0 -
[1] 3m6q.a -
0.4
0.5 0.6 0.4 1.6 0.1 -
[1] 3m6r.d - 0
0.1
0.2 0.1 0.6 0 -
[1] 3o3j.a - 0.7 1.0
0.2
0.1 0.9 0 -
[1] 3pn3.a - 1.0 1.8 0.6
0.5
1.2 0.2 -
[1] 3pn4.a - 0.2 0.4 0.1 0.1
0.2
0 -
[1] 3pn5.a - 3.0 2.7 1.7 0.8 2.5
0.3
-
[1] 3pn6.b - 1.0 1.5 0.6 0.1 2.2 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
3cpm.a
3m6q.a
3m6r.d
3o3j.a
3pn3.a
3pn4.a
3pn5.a
3pn6.b
[1] 3cpm.a
0
.11 .10 .06 .06 .07 .20 .10
[1] 3m6q.a .11
0
.07 .09 .12 .10 .14 .08
[1] 3m6r.d .10 .07
0
.06 .10 .05 .15 .11
[1] 3o3j.a .06 .09 .06
0
.07 .05 .19 .10
[1] 3pn3.a .06 .12 .10 .07
0
.07 .14 .14
[1] 3pn4.a .07 .10 .05 .05 .07
0
.20 .12
[1] 3pn5.a .20 .14 .15 .19 .14 .20
0
.20
[1] 3pn6.b .10 .08 .11 .10 .14 .12 .20
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
3cpm.a
3m6q.a
3m6r.d
3o3j.a
3pn3.a
3pn4.a
3pn5.a
3pn6.b
[1] 3cpm.a
0
0.6 0.6 0.5 1.4 0.4 1.2 0.4
[1] 3m6q.a 0.6
0
0.5 0.4 1.0 0.4 0.8 0.6
[1] 3m6r.d 0.6 0.5
0
0.6 1.2 0.5 0.9 0.7
[1] 3o3j.a 0.5 0.4 0.6
0
1.2 0.4 1.1 0.5
[1] 3pn3.a 1.4 1.0 1.2 1.2
0
1.3 0.7 1.4
[1] 3pn4.a 0.4 0.4 0.5 0.4 1.3
0
1.1 0.4
[1] 3pn5.a 1.2 0.8 0.9 1.1 0.7 1.1
0
1.3
[1] 3pn6.b 0.4 0.6 0.7 0.5 1.4 0.4 1.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
3cpm.a
3m6q.a
3m6r.d
3o3j.a
3pn3.a
3pn4.a
3pn5.a
3pn6.b
[1] 3cpm.a
0
1.1 1.2 1.1 1.6 0.8 1.6 1.1
[1] 3m6q.a 1.1
0
0.9 0.9 1.3 1.0 1.3 0.8
[1] 3m6r.d 1.2 0.9
0
1.1 1.6 1.1 1.5 1.1
[1] 3o3j.a 1.1 0.9 1.1
0
1.5 0.8 1.4 0.9
[1] 3pn3.a 1.6 1.3 1.6 1.5
0
1.5 0.9 1.6
[1] 3pn4.a 0.8 1.0 1.1 0.8 1.5
0
1.5 0.9
[1] 3pn5.a 1.6 1.3 1.5 1.4 0.9 1.5
0
1.6
[1] 3pn6.b 1.1 0.8 1.1 0.9 1.6 0.9 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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