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DEF1_BACCR_1_156

Peptide deformylase 1 [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer
A1 (DEF1_BACCR):43:46, 51, 88:91, 97, 125, 128, 129, 132, 133, 13643:46, 51, 88:91, 97, 125, 128, 129, 132, 133, 136
Metals (Me):Ni

Full PDB list

1ws0, 1ws1

Pocket contact map

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PDB.ch
   
ligand
A1 Me
D
4
3
G
4
4
V
4
5
G
4
6
Q
5
1
E
8
8
G
8
9
C
9
0
L
9
1
Y
9
7
F
1
2
5
R
1
2
8
A
1
2
9
H
1
3
2
E
1
3
3
H
1
3
6
[1]1ws0.a none . . . . . . . . . . . . . . . . Ni
[1]1ws1.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

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PDB.ch
A1 Me
D
4
3
G
4
4
V
4
5
G
4
6
Q
5
1
E
8
8
G
8
9
C
9
0
L
9
1
Y
9
7
F
1
2
5
R
1
2
8
A
1
2
9
H
1
3
2
E
1
3
3
H
1
3
6
[1]1ws0.a . . . . . . . . . . . . . . . . Ni
[1]1ws1.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1ws0.a is apo
1ws1.a:bb2
[1] 1ws0.a
-
0.7
[1] 1ws1.a -
0.1
[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
1ws0.a
1ws1.a
[1] 1ws0.a
0
.04
[1] 1ws1.a .04
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
1ws0.a
1ws1.a
[1] 1ws0.a
0
0.3
[1] 1ws1.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

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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
1ws0.a
1ws1.a
[1] 1ws0.a
0
0.6
[1] 1ws1.a 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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