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DEF_ECOLI_2_168

Peptide deformylase [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer
A1 (DEF_ECOLI):42:47, 51, 87:92, 95, 96, 98, 126, 129, 130, 133, 134, 13742:47, 51, 87:92, 95, 96, 98, 126, 129, 130, 133, 134, 137
Metals (Me):Co/Ni/Zn

Full PDB list

1bs4, 1bs5, 1bs6, 1bs7, 1bs8, 1bsj, 1bsk, 1bsz, 1dff, 1g27, 1g2a, 1icj, 1lru, 1xem, 1xen, 1xeo, 2ai8, 2w3t, 2w3u, 3k6l, 4al2, 4al3, 4az4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
E
4
3
G
4
4
I
4
5
G
4
6
Q
5
1
I
8
7
E
8
8
E
8
9
G
9
0
C
9
1
L
9
2
P
9
5
E
9
6
R
9
8
L
1
2
6
I
1
2
9
C
1
3
0
H
1
3
3
E
1
3
4
H
1
3
7
[1]1bs4.c 2pe28 . . . . . . . . . . . . . . . . . . . . Zn
[1]1bs6.b MAS20 . . . . . . . . . . . . . . . . . . . . Ni
[1]1bsj.a mln29 . . . . . . . . . . . . . . . . . . . . Co
[1]1g27.a bb123 . . . . . . . . . . . . . . . . . . . . Ni
[1]1g2a.a bb227 . . . . . . . . . . . . . . . . . . . . Ni
[1]1xeo.a none . . . . . . . . . . . . . . . . . . . . Co
[1]2ai8.a sb713 . . . . . . . . . . . . . . . . . . . . Ni
[1]3k6l.b 2bb24 . . . . . . . . . . . . . . . . . . . . Ni
[1]4al3.a none . . . . . . . . . * . . . . . . . . . . Co
[1]4az4.a none . . . . . . . . . . . . . . . . * . . . Co

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
E
4
2
E
4
3
G
4
4
I
4
5
G
4
6
L
4
7
Q
5
1
I
8
7
E
8
8
E
8
9
G
9
0
C
9
1
L
9
2
P
9
5
E
9
6
R
9
8
L
1
2
6
I
1
2
9
C
1
3
0
H
1
3
3
E
1
3
4
H
1
3
7
[1]1bs4.c . . . . . . . . . . . . . . . * . . . . . . Zn
[1]1bs6.b . . . . . . . . . . . . . . . . . . . . . . Ni
[1]1bsj.a . . . . . . . . . . . . . . . . . . . . . . Co
[1]1g27.a . . . . . . . . . . . . . . . . . . . . . . Ni
[1]1g2a.a . . . . . . . . . . . . . . . . . . . . . . Ni
[1]1xeo.a . . . . . . . . . . . . . . . . . . . . . . Co
[1]2ai8.a . . . . . . . . . . . . . . . * . . . . . . Ni
[1]3k6l.b . . . . . . . . . . . . . . . . . . . . . . Ni
[1]4al3.a . . . . . . . . . . . * . . . . . . . . . . Co
[1]4az4.a . . . . . . . . . . . . . . . . . . * . . . Co

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
1bs4.c:2pe
1bs6.b:MAS
1bsj.a:mln
1g27.a:bb1
1g2a.a:bb2
1xeo.a is apo
2ai8.a:sb7
3k6l.b:2bb
4al3.a is apo
4az4.a is apo
[1] 1bs4.c
0.1
0.3 0.4 0.9 1.1 - 0.2 1.5 - -
[1] 1bs6.b 0.3
0.2
0.4 1.0 0.5 - 0.1 1.4 - -
[1] 1bsj.a 0.2 0.2
0
0.3 0.2 - 0.1 0.5 - -
[1] 1g27.a 0.1 0.1 0.1
0.1
0.2 - 0.2 0.4 - -
[1] 1g2a.a 0.2 0.1 0.1 0.4
0.2
- 0.1 0.2 - -
[1] 1xeo.a 0.2 0.3 0.2 0.3 0.1
-
0.3 0.6 - -
[1] 2ai8.a 0.8 0.3 1.1 1.0 1.4 -
0.2
1.5 - -
[1] 3k6l.b 0.7 0.2 0.6 0.5 0.5 - 0.2
0.1
- -
[1] 4al3.a 0.2 0.3 0.4 0.7 0.7 - 0.5 0.7
-
-
[1] 4az4.a 0.2 0.2 0.5 0.4 0.7 - 0.3 0.5 -
-
[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
1bs4.c
1bs6.b
1bsj.a
1g27.a
1g2a.a
1xeo.a
2ai8.a
3k6l.b
4al3.a
4az4.a
[1] 1bs4.c
0
.02 .08 .08 .09 .08 .02 .10 .10 .07
[1] 1bs6.b .02
0
.06 .06 .07 .06 .04 .10 .09 .05
[1] 1bsj.a .08 .06
0
.03 .02 .03 .08 .07 .04 .03
[1] 1g27.a .08 .06 .03
0
.03 .02 .09 .08 .03 .03
[1] 1g2a.a .09 .07 .02 .03
0
.03 .09 .06 .03 .04
[1] 1xeo.a .08 .06 .03 .02 .03
0
.08 .08 .03 .02
[1] 2ai8.a .02 .04 .08 .09 .09 .08
0
.11 .11 .07
[1] 3k6l.b .10 .10 .07 .08 .06 .08 .11
0
.10 .09
[1] 4al3.a .10 .09 .04 .03 .03 .03 .11 .10
0
.04
[1] 4az4.a .07 .05 .03 .03 .04 .02 .07 .09 .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
1bs4.c
1bs6.b
1bsj.a
1g27.a
1g2a.a
1xeo.a
2ai8.a
3k6l.b
4al3.a
4az4.a
[1] 1bs4.c
0
0.3 0.6 0.4 0.3 0.4 0.2 0.8 0.4 0.4
[1] 1bs6.b 0.3
0
0.5 0.3 0.3 0.4 0.4 0.8 0.4 0.5
[1] 1bsj.a 0.6 0.5
0
0.4 0.5 0.4 0.7 0.8 0.5 0.5
[1] 1g27.a 0.4 0.3 0.4
0
0.3 0.3 0.5 0.8 0.4 0.5
[1] 1g2a.a 0.3 0.3 0.5 0.3
0
0.3 0.3 0.8 0.3 0.4
[1] 1xeo.a 0.4 0.4 0.4 0.3 0.3
0
0.5 0.8 0.2 0.3
[1] 2ai8.a 0.2 0.4 0.7 0.5 0.3 0.5
0
0.8 0.5 0.5
[1] 3k6l.b 0.8 0.8 0.8 0.8 0.8 0.8 0.8
0
0.8 0.8
[1] 4al3.a 0.4 0.4 0.5 0.4 0.3 0.2 0.5 0.8
0
0.3
[1] 4az4.a 0.4 0.5 0.5 0.5 0.4 0.3 0.5 0.8 0.3
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
1bs4.c
1bs6.b
1bsj.a
1g27.a
1g2a.a
1xeo.a
2ai8.a
3k6l.b
4al3.a
4az4.a
[1] 1bs4.c
0
0.7 0.9 0.8 0.8 0.7 0.6 1.3 0.8 1.1
[1] 1bs6.b 0.7
0
0.8 0.8 0.8 0.8 0.8 1.2 1.0 1.1
[1] 1bsj.a 0.9 0.8
0
0.7 0.7 0.8 0.9 1.2 0.9 1.1
[1] 1g27.a 0.8 0.8 0.7
0
0.6 0.8 0.8 1.1 1.0 0.9
[1] 1g2a.a 0.8 0.8 0.7 0.6
0
0.8 0.8 1.1 0.8 1.0
[1] 1xeo.a 0.7 0.8 0.8 0.8 0.8
0
0.7 1.2 0.7 1.0
[1] 2ai8.a 0.6 0.8 0.9 0.8 0.8 0.7
0
1.2 1.0 1.0
[1] 3k6l.b 1.3 1.2 1.2 1.1 1.1 1.2 1.2
0
1.4 1.3
[1] 4al3.a 0.8 1.0 0.9 1.0 0.8 0.7 1.0 1.4
0
1.2
[1] 4az4.a 1.1 1.1 1.1 0.9 1.0 1.0 1.0 1.3 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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