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AMPN_PIG_63_963

Aminopeptidase N [Peptidase M1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMPN_PIG):R: Metalloprotease (206, 208, 209, 345:350, 358, 361, 375, 376, 379, 380, 383, 384, 387, 406, 410, 413, 414, 429, 432:434, 436, 437, 440, 444, 464, 467, 472, 473, 564, 660, 664, 689, 693, 694, 697, 698, 752, 854, 891:894, 940)
R: Substrate binding (347:350)
206, 208, 209, 345:350, 358, 361, 375, 376, 379, 380, 383, 384, 387, 406, 410, 413, 414, 429, 432:434, 436, 437, 440, 444, 464, 467, 472, 473, 564, 660, 664, 689, 693, 694, 697, 698, 752, 854, 891:894, 940
Metals (Me):Zn

Full PDB list

4f5c, 4fke, 4fkh, 4fkk, 4hom, 4naq, 4nz8, 4ou3, 5lds, 5lg6, 6buy, 6bv0, 6bv1, 6bv2, 6bv3, 6bv4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
2
0
6
Q
2
0
8
S
2
0
9
N
3
4
5
A
3
4
6
G
3
4
7
A
3
4
8
M
3
4
9
E
3
5
0
A
3
6
1
E
3
7
5
R
3
7
6
T
3
7
9
V
3
8
0
H
3
8
3
E
3
8
4
H
3
8
7
E
4
0
6
S
4
1
0
E
4
1
3
Y
4
1
4
L
4
2
9
P
4
3
2
G
4
3
3
D
4
3
4
Y
4
3
6
R
4
3
7
A
4
4
0
L
4
4
4
S
4
6
4
F
4
6
7
Y
4
7
2
S
4
7
3
L
5
6
4
Y
6
6
0
N
6
6
4
Q
6
9
3
S
6
9
7
S
6
9
8
[1]4fkh.a A6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4fkk.a bes22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4hom.a RPKPQQFFGLM95 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4naq.a AAAAAAA36 . . . . . . . . . . . . . . . Q . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4nz8.a A,AAAAAA36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4ou3.a CNGRCG40 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]5lds.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]5lg6.a none . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6buy.a G5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv0.a R12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv1.a D9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv2.a I9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv3.a L9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv4.a M9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
Q
2
0
6
Q
2
0
8
S
2
0
9
N
3
4
5
A
3
4
6
G
3
4
7
A
3
4
8
M
3
4
9
E
3
5
0
R
3
5
8
A
3
6
1
E
3
7
5
R
3
7
6
T
3
7
9
V
3
8
0
H
3
8
3
E
3
8
4
H
3
8
7
E
4
0
6
S
4
1
0
E
4
1
3
Y
4
1
4
L
4
2
9
P
4
3
2
G
4
3
3
D
4
3
4
Y
4
3
6
R
4
3
7
A
4
4
0
L
4
4
4
S
4
6
4
F
4
6
7
Y
4
7
2
S
4
7
3
L
5
6
4
Y
6
6
0
N
6
6
4
Y
6
8
9
Q
6
9
3
A
6
9
4
S
6
9
7
S
6
9
8
N
7
5
2
Q
8
5
4
G
8
9
1
S
8
9
2
F
8
9
3
S
8
9
4
K
9
4
0
[1]4fkh.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4fkk.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4hom.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4naq.a . . . . . . . . . . . . . . . . Q . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4nz8.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4ou3.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]5lds.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . * * . . Zn
[1]5lg6.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . * . . . . . . . Zn
[1]6buy.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv0.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv3.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]6bv4.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
4fkh.a:A
4fkk.a:bes
4hom.a:RPKPQQFFGLM
4naq.a:AAAAAAA
4nz8.a:A,AAAAAA
4ou3.a:CNGRCG
5lds.a is apo
5lg6.a is apo
6buy.a:G
6bv0.a:R
6bv1.a:D
6bv2.a:I
6bv3.a:L
6bv4.a:M
[1] 4fkh.a
0
0.2 0.3 0.6 0.4 0.2 - - 0.1 0 0.1 0.4 0.1 0.1
[1] 4fkk.a 0
0
0.4 0.5 0.2 0.1 - - 0 0 0 0.4 0 0
[1] 4hom.a 0.1 0.2
0.2
0.6 0.3 0.2 - - 0.1 0.1 0.1 0.4 0.2 0.1
[1] 4naq.a 0 0.2 0.5
0.8
0.5 0.2 - - 0.1 0 0.1 0.4 0.2 0.1
[1] 4nz8.a 0.1 0.2 0.6 0.6
0.5
0.2 - - 0.1 0.1 0.1 0.4 0.2 0.1
[1] 4ou3.a 0 0.2 0.3 0.7 0.5
0.1
- - 0 0 0 0.3 0.2 0
[1] 5lds.a 0.2 1.3 7.2 0.8 1.0 5.8
-
- 0.1 1.2 0.4 0.4 0.2 1.2
[1] 5lg6.a 0.3 0.7 5.2 1.2 1.3 1.8 -
-
0.1 0.3 0.3 0.5 0.2 0.3
[1] 6buy.a 0 0.2 0.6 0.8 0.4 0.2 - -
0.1
0.1 0.1 0.4 0.2 0.1
[1] 6bv0.a 0.1 0.2 0.2 0.7 0.4 0.1 - - 0.1
0.1
0.1 0.4 0.1 0.1
[1] 6bv1.a 0 0.2 0.5 0.7 0.4 0.2 - - 0.1 0
0.1
0.4 0.2 0.1
[1] 6bv2.a 0 0.2 0.5 0.6 0.4 0.1 - - 0 0 0
0.3
0.1 0
[1] 6bv3.a 0 0.2 0.7 0.6 0.3 0.1 - - 0.1 0 0.1 0.2
0.1
0
[1] 6bv4.a 0 0.2 0.5 0.5 0.4 0.1 - - 0.1 0.1 0.1 0.3 0.2
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
4fkh.a
4fkk.a
4hom.a
4naq.a
4nz8.a
4ou3.a
5lds.a
5lg6.a
6buy.a
6bv0.a
6bv1.a
6bv2.a
6bv3.a
6bv4.a
[1] 4fkh.a
0
.01 .01 .01 .01 .01 .20 .14 .01 .01 0 .01 .02 .01
[1] 4fkk.a .01
0
.01 .02 .01 .02 .20 .14 .02 .01 .01 .01 .02 .01
[1] 4hom.a .01 .01
0
.01 .01 .01 .21 .14 .01 0 0 .01 .02 .01
[1] 4naq.a .01 .02 .01
0
.02 .01 .21 .14 .01 .01 .01 .01 .02 .02
[1] 4nz8.a .01 .01 .01 .02
0
.02 .21 .14 .02 .01 .01 .01 .02 .01
[1] 4ou3.a .01 .02 .01 .01 .02
0
.20 .14 .01 0 .01 .01 .02 .01
[1] 5lds.a .20 .20 .21 .21 .21 .20
0
.13 .21 .21 .21 .21 .20 .20
[1] 5lg6.a .14 .14 .14 .14 .14 .14 .13
0
.14 .14 .14 .14 .14 .14
[1] 6buy.a .01 .02 .01 .01 .02 .01 .21 .14
0
.01 .01 .01 .02 .01
[1] 6bv0.a .01 .01 0 .01 .01 0 .21 .14 .01
0
0 .01 .02 .01
[1] 6bv1.a 0 .01 0 .01 .01 .01 .21 .14 .01 0
0
.01 .02 .01
[1] 6bv2.a .01 .01 .01 .01 .01 .01 .21 .14 .01 .01 .01
0
.01 .01
[1] 6bv3.a .02 .02 .02 .02 .02 .02 .20 .14 .02 .02 .02 .01
0
.02
[1] 6bv4.a .01 .01 .01 .02 .01 .01 .20 .14 .01 .01 .01 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
4fkh.a
4fkk.a
4hom.a
4naq.a
4nz8.a
4ou3.a
5lds.a
5lg6.a
6buy.a
6bv0.a
6bv1.a
6bv2.a
6bv3.a
6bv4.a
[1] 4fkh.a
0
0.3 0.3 0.3 0.3 0.3 4.5 4.4 0.2 0.2 0.2 0.2 0.3 0.1
[1] 4fkk.a 0.3
0
0.5 0.4 0.4 0.3 4.3 4.3 0.4 0.3 0.4 0.3 0.2 0.3
[1] 4hom.a 0.3 0.5
0
0.5 0.4 0.4 4.6 4.6 0.2 0.3 0.2 0.4 0.5 0.2
[1] 4naq.a 0.3 0.4 0.5
0
0.2 0.4 4.4 4.4 0.3 0.4 0.4 0.3 0.4 0.3
[1] 4nz8.a 0.3 0.4 0.4 0.2
0
0.4 4.5 4.4 0.3 0.3 0.3 0.3 0.4 0.3
[1] 4ou3.a 0.3 0.3 0.4 0.4 0.4
0
4.3 4.3 0.3 0.2 0.3 0.3 0.3 0.3
[1] 5lds.a 4.5 4.3 4.6 4.4 4.5 4.3
0
0.5 4.5 4.4 4.4 4.5 4.3 4.5
[1] 5lg6.a 4.4 4.3 4.6 4.4 4.4 4.3 0.5
0
4.5 4.4 4.4 4.4 4.3 4.5
[1] 6buy.a 0.2 0.4 0.2 0.3 0.3 0.3 4.5 4.5
0
0.2 0.2 0.2 0.4 0.2
[1] 6bv0.a 0.2 0.3 0.3 0.4 0.3 0.2 4.4 4.4 0.2
0
0.2 0.1 0.2 0.2
[1] 6bv1.a 0.2 0.4 0.2 0.4 0.3 0.3 4.4 4.4 0.2 0.2
0
0.2 0.3 0.1
[1] 6bv2.a 0.2 0.3 0.4 0.3 0.3 0.3 4.5 4.4 0.2 0.1 0.2
0
0.2 0.2
[1] 6bv3.a 0.3 0.2 0.5 0.4 0.4 0.3 4.3 4.3 0.4 0.2 0.3 0.2
0
0.3
[1] 6bv4.a 0.1 0.3 0.2 0.3 0.3 0.3 4.5 4.5 0.2 0.2 0.1 0.2 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
4fkh.a
4fkk.a
4hom.a
4naq.a
4nz8.a
4ou3.a
5lds.a
5lg6.a
6buy.a
6bv0.a
6bv1.a
6bv2.a
6bv3.a
6bv4.a
[1] 4fkh.a
0
0.3 0.3 0.5 0.5 0.8 4.7 4.5 0.3 0.3 0.2 0.2 0.3 0.2
[1] 4fkk.a 0.3
0
0.5 0.6 0.5 0.8 4.6 4.4 0.4 0.3 0.4 0.3 0.3 0.3
[1] 4hom.a 0.3 0.5
0
0.6 0.5 0.8 4.8 4.6 0.3 0.4 0.2 0.4 0.5 0.3
[1] 4naq.a 0.5 0.6 0.6
0
0.3 0.9 4.6 4.5 0.6 0.6 0.5 0.5 0.6 0.5
[1] 4nz8.a 0.5 0.5 0.5 0.3
0
0.9 4.7 4.5 0.5 0.5 0.5 0.5 0.6 0.5
[1] 4ou3.a 0.8 0.8 0.8 0.9 0.9
0
4.6 4.4 0.8 0.8 0.8 0.8 0.8 0.8
[1] 5lds.a 4.7 4.6 4.8 4.6 4.7 4.6
0
1.0 4.7 4.6 4.7 4.7 4.6 4.7
[1] 5lg6.a 4.5 4.4 4.6 4.5 4.5 4.4 1.0
0
4.5 4.4 4.5 4.5 4.4 4.5
[1] 6buy.a 0.3 0.4 0.3 0.6 0.5 0.8 4.7 4.5
0
0.3 0.3 0.3 0.4 0.2
[1] 6bv0.a 0.3 0.3 0.4 0.6 0.5 0.8 4.6 4.4 0.3
0
0.2 0.2 0.2 0.2
[1] 6bv1.a 0.2 0.4 0.2 0.5 0.5 0.8 4.7 4.5 0.3 0.2
0
0.2 0.3 0.2
[1] 6bv2.a 0.2 0.3 0.4 0.5 0.5 0.8 4.7 4.5 0.3 0.2 0.2
0
0.2 0.2
[1] 6bv3.a 0.3 0.3 0.5 0.6 0.6 0.8 4.6 4.4 0.4 0.2 0.3 0.2
0
0.3
[1] 6bv4.a 0.2 0.3 0.3 0.5 0.5 0.8 4.7 4.5 0.2 0.2 0.2 0.2 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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