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APX1_PEA_2_250_ascorbate

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

Composition of the binding site

Protein chains monomer
A1 (APX1_PEA):30:32, 34, 35, 76, 79, 80, 169, 17230:32, 34, 35, 76, 79, 80, 169, 172
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

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PDB.ch
   
ligand
A1 cF Me
K
3
0
K
3
1
C
3
2
P
3
4
L
3
5
I
7
6
L
8
0
H
1
6
9
R
1
7
2
[1]1apx.b none . . . . . . . . . hem Fe,K
[1]1oaf.a asc12 . R . . . . . . . hem Fe,Na
[1]2vcf.x isz10 . R . . . . . . . hem Fe,Na
[1]2y6b.a none . R . . . . . . . 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

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PDB.ch
A1 cF Me
K
3
0
K
3
1
C
3
2
P
3
4
L
3
5
I
7
6
R
7
9
L
8
0
H
1
6
9
R
1
7
2
[1]1apx.b . . . . . . . . . . hem Fe,K
[1]1oaf.a * R . . . . . . . . hem Fe,Na
[1]2vcf.x . R . . . . . . . . hem Fe,Na
[1]2y6b.a . R . . . . . . . . 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.b is apo
1oaf.a:asc
2vcf.x:isz
2y6b.a is apo
[1] 1apx.b
-
0 0 -
[1] 1oaf.a -
0
1.2 -
[1] 2vcf.x - 0
0
-
[1] 2y6b.a - 0 0.1
-
[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.b
1oaf.a
2vcf.x
2y6b.a
[1] 1apx.b
0
.12 0 .01
[1] 1oaf.a .12
0
.12 .11
[1] 2vcf.x 0 .12
0
.01
[1] 2y6b.a .01 .11 .01
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
1apx.b
1oaf.a
2vcf.x
2y6b.a
[1] 1apx.b
0
0.4 0.4 0.4
[1] 1oaf.a 0.4
0
0.1 0.2
[1] 2vcf.x 0.4 0.1
0
0.2
[1] 2y6b.a 0.4 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.b
1oaf.a
2vcf.x
2y6b.a
[1] 1apx.b
0
1.3 1.1 1.2
[1] 1oaf.a 1.3
0
0.8 0.8
[1] 2vcf.x 1.1 0.8
0
0.6
[1] 2y6b.a 1.2 0.8 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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