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DEFM_HUMAN_62_243

Peptide deformylase, mitochondrial [Polypeptide deformylase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DEFM_HUMAN):R: Hydrophobic dimerization interface (169:173)
108:110, 115, 143, 145, 179, 207, 210, 211, 214, 215, 218
108:110, 115, 143, 145, 169:173, 179, 207, 210, 211, 214, 215, 218
Metals (Me):Co

Full PDB list

3g5k, 3g5p

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
C
1
0
8
V
1
0
9
G
1
1
0
Q
1
1
5
R
1
4
3
P
1
6
9
E
1
7
0
G
1
7
1
C
1
7
2
E
1
7
3
L
1
7
9
W
2
0
7
R
2
1
0
I
2
1
1
H
2
1
4
E
2
1
5
H
2
1
8
[1]3g5k.c bb227 . . . . . . . . . . . . . . . . . Co
[1]3g5p.b 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
C
1
0
8
V
1
0
9
G
1
1
0
Q
1
1
5
R
1
4
3
M
1
4
5
P
1
6
9
E
1
7
0
G
1
7
1
C
1
7
2
E
1
7
3
L
1
7
9
W
2
0
7
R
2
1
0
I
2
1
1
H
2
1
4
E
2
1
5
H
2
1
8
[1]3g5k.c . . . . . . . . . . . . . . . . . . Co
[1]3g5p.b . . . . . . . . . . . . . . . . . . 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
3g5k.c:bb2
3g5p.b is apo
[1] 3g5k.c
0
-
[1] 3g5p.b 0.3
-
[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
3g5k.c
3g5p.b
[1] 3g5k.c
0
.02
[1] 3g5p.b .02
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
3g5k.c
3g5p.b
[1] 3g5k.c
0
0.3
[1] 3g5p.b 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3g5k.c
3g5p.b
[1] 3g5k.c
0
0.6
[1] 3g5p.b 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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