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ERAP1_HUMAN_39_529

Endoplasmic reticulum aminopeptidase 1 [Peptidase M1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ERAP1_HUMAN):R: Substrate binding (317:320)
181, 183, 184, 316, 349, 350, 353, 354, 357, 376, 380, 383, 432:434, 438
181, 183, 184, 316:320, 349, 350, 353, 354, 357, 376, 380, 383, 432:434, 438
Metals (Me):Zn

Full PDB list

2yd0, 3mdj, 3qnf (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
1
8
1
E
1
8
3
S
3
1
6
G
3
1
7
A
3
1
8
M
3
1
9
E
3
2
0
H
3
5
3
E
3
5
4
H
3
5
7
E
3
7
6
K
3
8
0
E
3
8
3
F
4
3
3
Y
4
3
8
[1]2yd0.a bes22 . . . . . . . . . . . . . . . Zn
[1]3qnf.b none . . . . . . . . . . . . . . . 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
Q
1
8
1
E
1
8
3
P
1
8
4
S
3
1
6
G
3
1
7
A
3
1
8
M
3
1
9
E
3
2
0
M
3
4
9
T
3
5
0
H
3
5
3
E
3
5
4
H
3
5
7
E
3
7
6
K
3
8
0
E
3
8
3
M
4
3
2
F
4
3
3
D
4
3
4
Y
4
3
8
[1]2yd0.a . . . . . . . . . . . . . . . . . . . . Zn
[1]3qnf.b . . . . . . . . . . . . . . . . . . . . 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
2yd0.a:bes
3qnf.b is apo
[1] 2yd0.a
0.4
-
[1] 3qnf.b 0.6
-
[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
2yd0.a
3qnf.b
[1] 2yd0.a
0
.03
[1] 3qnf.b .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
2yd0.a
3qnf.b
[1] 2yd0.a
0
1.9
[1] 3qnf.b 1.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
2yd0.a
3qnf.b
[1] 2yd0.a
0
2.0
[1] 3qnf.b 2.0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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