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APX1_PEA_2_250_SHA

L-ascorbate peroxidase, cytosolic [Peroxidase family. Ascorbate peroxidase subfamily]

Composition of the binding site

Protein chains monomer
A1 (APX1_PEA):38, 41, 42, 69, 70, 72, 132:134, 172, 17338, 41, 42, 69, 70, 72, 132:134, 172, 173
Cofactors (cF):hem
Metals (Me):Fe/Na/K

Full PDB list

1apx, 1oaf, 1oag, 1v0h, 2ghh, 2ghk, 2vcf, 2xi6, 2xif, 2xih, 2xj6, 2y6a, 2y6b, 5jpr, 5jqr (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
R
3
8
W
4
1
H
4
2
G
6
9
A
7
0
N
7
2
P
1
3
2
D
1
3
3
A
1
3
4
R
1
7
2
S
1
7
3
[1]1apx.a none . . . . . . . . . . . hem Fe,K
[1]1oaf.a none . . . S . . . . . . . hem Fe,Na
[1]1v0h.x sha11 . . . S . . . . . . . hem Fe,Na
[1]2vcf.x isz10 . . . S . . . . . . . hem Fe,Na
[1]2y6a.a none A . . S . . . . . . . Fe
[1]2y6b.a none K . . S . . . . . . . Fe

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 cF Me
R
3
8
W
4
1
H
4
2
G
6
9
A
7
0
N
7
2
P
1
3
2
D
1
3
3
A
1
3
4
R
1
7
2
S
1
7
3
[1]1apx.a . . . . . . . . . . . hem Fe,K
[1]1oaf.a . . . S . . . . . . . hem Fe,Na
[1]1v0h.x . . . S . . . . . . . hem Fe,Na
[1]2vcf.x . . . S . . . . . . . hem Fe,Na
[1]2y6a.a A . . S . * . . . . . Fe
[1]2y6b.a K . . S . . . . . . . Fe

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
1apx.a is apo
1oaf.a is apo
1v0h.x:sha
2vcf.x:isz
2y6a.a is apo
2y6b.a is apo
[1] 1apx.a
-
- 0 0 - -
[1] 1oaf.a -
-
0 0 - -
[1] 1v0h.x - -
0
0 - -
[1] 2vcf.x - - 0
0
- -
[1] 2y6a.a - - 0 1.1
-
-
[1] 2y6b.a - - 0 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
1apx.a
1oaf.a
1v0h.x
2vcf.x
2y6a.a
2y6b.a
[1] 1apx.a
0
0 0 0 .10 0
[1] 1oaf.a 0
0
0 0 .10 0
[1] 1v0h.x 0 0
0
0 .10 0
[1] 2vcf.x 0 0 0
0
.10 0
[1] 2y6a.a .10 .10 .10 .10
0
.10
[1] 2y6b.a 0 0 0 0 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1apx.a
1oaf.a
1v0h.x
2vcf.x
2y6a.a
2y6b.a
[1] 1apx.a
0
0.2 0.3 0.2 0.4 0.3
[1] 1oaf.a 0.2
0
0.2 0.1 0.3 0.2
[1] 1v0h.x 0.3 0.2
0
0.2 0.4 0.3
[1] 2vcf.x 0.2 0.1 0.2
0
0.3 0.2
[1] 2y6a.a 0.4 0.3 0.4 0.3
0
0.2
[1] 2y6b.a 0.3 0.2 0.3 0.2 0.2
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
1apx.a
1oaf.a
1v0h.x
2vcf.x
2y6a.a
2y6b.a
[1] 1apx.a
0
0.4 0.4 0.4 0.9 0.4
[1] 1oaf.a 0.4
0
0.3 0.1 0.8 0.4
[1] 1v0h.x 0.4 0.3
0
0.3 0.8 0.5
[1] 2vcf.x 0.4 0.1 0.3
0
0.7 0.4
[1] 2y6a.a 0.9 0.8 0.8 0.7
0
0.8
[1] 2y6b.a 0.4 0.4 0.5 0.4 0.8
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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