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END4_THEMA_1_286

Probable endonuclease 4 [AP endonuclease 2 family]

Composition of the binding site

Protein chains monomer
A1 (END4_THEMA):72, 109, 228:23072, 109, 228:230
Metals (Me):Cd/Mn/Zn

Full PDB list

2x7v, 2x7w, 4hno (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
H
1
0
9
D
2
2
8
R
2
2
9
H
2
3
0
[1]2x7w.a bcn11 . . . . Cd,Zn
[1]4hno.a none . . . . Mn,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
Y
7
2
H
1
0
9
D
2
2
8
R
2
2
9
H
2
3
0
[1]2x7w.a . . . . . Cd,Zn
[1]4hno.a . . . . . Mn,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
2x7w.a:bcn
4hno.a is apo
[1] 2x7w.a
0
-
[1] 4hno.a 0.2
-
[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
2x7w.a
4hno.a
[1] 2x7w.a
0
.04
[1] 4hno.a .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
2x7w.a
4hno.a
[1] 2x7w.a
0
0.3
[1] 4hno.a 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

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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
2x7w.a
4hno.a
[1] 2x7w.a
0
2.7
[1] 4hno.a 2.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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