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DEF_STRPN_1_203

Peptide deformylase [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer
A1 (DEF_STRPN):57, 68:73, 77, 90, 124, 126:131, 166, 169, 170, 173, 174, 17757, 68:73, 77, 90, 124, 126:131, 166, 169, 170, 173, 174, 177
Metals (Me):Fe/Ni

Full PDB list

1lm6, 2ai7, 2aia, 2aie, 3str, 3svj, 3sw8, 4eox

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
5
7
R
6
8
G
6
9
G
7
0
V
7
1
G
7
2
L
7
3
Q
7
7
P
9
0
L
1
2
4
E
1
2
6
G
1
2
7
E
1
2
8
G
1
2
9
C
1
3
0
L
1
3
1
Y
1
6
6
I
1
6
9
V
1
7
0
H
1
7
3
E
1
7
4
H
1
7
7
[1]1lm6.a none . . . . . . . . . . . . . . * . . . . . . . Fe
[1]2ai7.a sb713 . . . . . . . . . . . . . . . . . . . . . . Ni
[1]2aia.a sb821 . . . . . . . . . . . . . . . . . . . . . . Ni
[1]2aie.p sb914 . . . . . . . . . . . . . . . . . . . . . . Ni
[1]3str.p 3li44 . . . . . . . . . . . . . . . . . . . . . . Ni
[1]3svj.p 4li40 . . . . . . . . . . . . . . * . . . . . . . Ni
[1]3sw8.p 5li17 . . . . . . . . . . . . . . . . . . . . . . Ni
[1]4eox.p 0s530 . . . . . . . . . . . . . . . . . . . . . . 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
Q
5
7
R
6
8
G
6
9
G
7
0
V
7
1
G
7
2
L
7
3
Q
7
7
P
9
0
L
1
2
4
E
1
2
6
G
1
2
7
E
1
2
8
G
1
2
9
C
1
3
0
L
1
3
1
Y
1
6
6
I
1
6
9
V
1
7
0
H
1
7
3
E
1
7
4
H
1
7
7
[1]1lm6.a . . . . . . . . . . . . . . * . . . . . . . Fe
[1]2ai7.a . . . . . . . . . . * . . . . . . . . . . . Ni
[1]2aia.a . . . . . . . . . . . . . . . . . . . . . . Ni
[1]2aie.p . . . . . . . . . . . . . . . . . . . . . . Ni
[1]3str.p . . . . . . . . . . . . . . . . . . . . . . Ni
[1]3svj.p . . . . . . . . . . . . . . * . . . . . . . Ni
[1]3sw8.p . . . . . . . . . . . . . . . . . . . . . . Ni
[1]4eox.p . . . . . . . . . . . . . . . . . . . . . . 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
1lm6.a is apo
2ai7.a:sb7
2aia.a:sb8
2aie.p:sb9
3str.p:3li
3svj.p:4li
3sw8.p:5li
4eox.p:0s5
[1] 1lm6.a
-
0.1 1.0 0.2 0.5 0.7 0.2 0.3
[1] 2ai7.a -
0.1
0.6 0.1 1.6 1.6 0.2 0.1
[1] 2aia.a - 0.1
0
0.1 0.5 0.4 0.1 0.2
[1] 2aie.p - 0.2 1.2
0.1
0.4 0.8 0.2 0.1
[1] 3str.p - 0.2 0.7 0.3
0
0 0.3 0.5
[1] 3svj.p - 0.1 0.3 0.2 0.1
0.1
0.2 0.3
[1] 3sw8.p - 0 0.4 0 0.2 0.3
0
0.2
[1] 4eox.p - 0.1 0.4 0.2 0.6 0.4 0.2
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
1lm6.a
2ai7.a
2aia.a
2aie.p
3str.p
3svj.p
3sw8.p
4eox.p
[1] 1lm6.a
0
.07 .05 .03 .08 .05 .05 .04
[1] 2ai7.a .07
0
.08 .05 .12 .09 .10 .07
[1] 2aia.a .05 .08
0
.05 .08 .05 .05 .03
[1] 2aie.p .03 .05 .05
0
.08 .05 .06 .03
[1] 3str.p .08 .12 .08 .08
0
.05 .08 .06
[1] 3svj.p .05 .09 .05 .05 .05
0
.04 .05
[1] 3sw8.p .05 .10 .05 .06 .08 .04
0
.04
[1] 4eox.p .04 .07 .03 .03 .06 .05 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1lm6.a
2ai7.a
2aia.a
2aie.p
3str.p
3svj.p
3sw8.p
4eox.p
[1] 1lm6.a
0
0.3 0.3 0.2 0.3 0.3 0.3 0.3
[1] 2ai7.a 0.3
0
0.1 0.3 0.3 0.3 0.2 0.3
[1] 2aia.a 0.3 0.1
0
0.3 0.3 0.3 0.2 0.3
[1] 2aie.p 0.2 0.3 0.3
0
0.3 0.3 0.3 0.2
[1] 3str.p 0.3 0.3 0.3 0.3
0
0.3 0.3 0.4
[1] 3svj.p 0.3 0.3 0.3 0.3 0.3
0
0.3 0.4
[1] 3sw8.p 0.3 0.2 0.2 0.3 0.3 0.3
0
0.4
[1] 4eox.p 0.3 0.3 0.3 0.2 0.4 0.4 0.4
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
1lm6.a
2ai7.a
2aia.a
2aie.p
3str.p
3svj.p
3sw8.p
4eox.p
[1] 1lm6.a
0
1.2 0.8 0.5 0.8 1.2 1.3 0.7
[1] 2ai7.a 1.2
0
1.2 1.1 1.4 0.9 0.7 1.3
[1] 2aia.a 0.8 1.2
0
0.6 0.6 1.1 1.1 0.5
[1] 2aie.p 0.5 1.1 0.6
0
0.8 1.2 1.2 0.6
[1] 3str.p 0.8 1.4 0.6 0.8
0
1.0 1.2 0.5
[1] 3svj.p 1.2 0.9 1.1 1.2 1.0
0
0.6 1.0
[1] 3sw8.p 1.3 0.7 1.1 1.2 1.2 0.6
0
1.2
[1] 4eox.p 0.7 1.3 0.5 0.6 0.5 1.0 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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