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ERAP2_HUMAN_1_960

Endoplasmic reticulum aminopeptidase 2 [Peptidase M1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ERAP2_HUMAN):R: Substrate binding (334:337)
177, 198, 200, 201, 332, 333, 345, 347, 348, 359, 360, 363, 367, 370, 371, 374, 392, 393, 397, 447, 450:452, 455, 456, 756, 792, 822, 825, 826, 857, 858, 861, 864, 892, 895, 896
177, 198, 200, 201, 332:337, 345, 347, 348, 359, 360, 363, 367, 370, 371, 374, 392, 393, 397, 447, 450:452, 455, 456, 756, 792, 822, 825, 826, 857, 858, 861, 864, 892, 895, 896
Metals (Me):Zn

Full PDB list

3se6, 4e36, 4jbs, 5ab0, 5ab2, 5cu5, 5j6s, 5k1v

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
1
9
8
E
2
0
0
P
2
0
1
A
3
3
2
P
3
3
3
G
3
3
4
A
3
3
5
M
3
3
6
E
3
3
7
R
3
4
5
T
3
4
7
S
3
4
8
D
3
6
0
W
3
6
3
V
3
6
7
H
3
7
0
E
3
7
1
H
3
7
4
K
3
9
2
E
3
9
3
Q
4
4
7
F
4
5
0
D
4
5
1
E
4
5
2
Y
4
5
5
K
7
5
6
K
7
9
2
N
8
2
2
L
8
2
5
Y
8
2
6
A
8
5
7
L
8
5
8
A
8
6
1
R
8
6
4
Y
8
9
2
M
8
9
6
[1]3se6.a K10 . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . . . . Zn
[1]4e36.a K10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4jbs.a p5235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]5ab0.a 2x0.7gaKHHAFSFlyn93 . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . . . . Zn
[1]5ab2.a GPGRAF42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]5cu5.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5j6s.b 6ga23 . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . . . . Zn
[1]5k1v.a 6px35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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

[download in TSV format]
   
PDB.ch
A1 Me
E
1
7
7
D
1
9
8
E
2
0
0
P
2
0
1
A
3
3
2
P
3
3
3
G
3
3
4
A
3
3
5
M
3
3
6
E
3
3
7
R
3
4
5
T
3
4
7
S
3
4
8
S
3
5
9
D
3
6
0
W
3
6
3
V
3
6
7
H
3
7
0
E
3
7
1
H
3
7
4
K
3
9
2
E
3
9
3
K
3
9
7
Q
4
4
7
F
4
5
0
D
4
5
1
E
4
5
2
Y
4
5
5
N
4
5
6
K
7
5
6
K
7
9
2
N
8
2
2
L
8
2
5
Y
8
2
6
A
8
5
7
L
8
5
8
A
8
6
1
R
8
6
4
Y
8
9
2
R
8
9
5
M
8
9
6
[1]3se6.a . . . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . . . . . . . Zn
[1]4e36.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4jbs.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]5ab0.a . . . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . . . . . . . Zn
[1]5ab2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . Zn
[1]5cu5.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . .
[1]5j6s.b . . . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . . . . . . . Zn
[1]5k1v.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
3se6.a:K
4e36.a:K
4jbs.a:p52
5ab0.a:2x0.7gaKHHAFSFlyn
5ab2.a:GPGRAF
5cu5.a is apo
5j6s.b:6ga
5k1v.a:6px
[1] 3se6.a
0
0 0.3 0.9 0.2 - 0.2 0.8
[1] 4e36.a 0.1
0
0.3 0.7 0.3 - 0.1 0.5
[1] 4jbs.a 0 0
0
0.4 0.2 - 0 0.4
[1] 5ab0.a 0 0 0.1
0
0.2 - 0.3 0.6
[1] 5ab2.a 0 0.1 0.1 3.6
0
- 0.4 0.4
[1] 5cu5.a 0.1 0 1.5 2.1 1.7
-
1.0 2.6
[1] 5j6s.b 0.1 0.1 0.3 0.7 0.3 -
0.1
0.6
[1] 5k1v.a 0 0 0.3 0.4 0.1 - 0.2
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
3se6.a
4e36.a
4jbs.a
5ab0.a
5ab2.a
5cu5.a
5j6s.b
5k1v.a
[1] 3se6.a
0
.02 .03 .02 .10 .08 .03 .03
[1] 4e36.a .02
0
.02 .02 .10 .08 .02 .02
[1] 4jbs.a .03 .02
0
.02 .10 .08 .03 .03
[1] 5ab0.a .02 .02 .02
0
.10 .09 .02 .02
[1] 5ab2.a .10 .10 .10 .10
0
.16 .11 .10
[1] 5cu5.a .08 .08 .08 .09 .16
0
.08 .09
[1] 5j6s.b .03 .02 .03 .02 .11 .08
0
.03
[1] 5k1v.a .03 .02 .03 .02 .10 .09 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
3se6.a
4e36.a
4jbs.a
5ab0.a
5ab2.a
5cu5.a
5j6s.b
5k1v.a
[1] 3se6.a
0
0.2 0.3 0.4 0.4 0.6 0.3 0.3
[1] 4e36.a 0.2
0
0.3 0.4 0.4 0.6 0.4 0.3
[1] 4jbs.a 0.3 0.3
0
0.3 0.3 0.7 0.4 0.3
[1] 5ab0.a 0.4 0.4 0.3
0
0.3 0.7 0.4 0.4
[1] 5ab2.a 0.4 0.4 0.3 0.3
0
0.6 0.4 0.3
[1] 5cu5.a 0.6 0.6 0.7 0.7 0.6
0
0.6 0.6
[1] 5j6s.b 0.3 0.4 0.4 0.4 0.4 0.6
0
0.3
[1] 5k1v.a 0.3 0.3 0.3 0.4 0.3 0.6 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
3se6.a
4e36.a
4jbs.a
5ab0.a
5ab2.a
5cu5.a
5j6s.b
5k1v.a
[1] 3se6.a
0
0.5 0.6 0.9 1.2 1.2 0.8 0.9
[1] 4e36.a 0.5
0
0.5 0.9 1.2 1.1 0.8 0.9
[1] 4jbs.a 0.6 0.5
0
0.8 1.2 1.1 0.8 0.9
[1] 5ab0.a 0.9 0.9 0.8
0
1.2 1.2 0.7 0.8
[1] 5ab2.a 1.2 1.2 1.2 1.2
0
1.4 1.1 1.1
[1] 5cu5.a 1.2 1.1 1.1 1.2 1.4
0
1.1 1.1
[1] 5j6s.b 0.8 0.8 0.8 0.7 1.1 1.1
0
0.8
[1] 5k1v.a 0.9 0.9 0.9 0.8 1.1 1.1 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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