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AMPL_BOVIN_33_518

Cytosol aminopeptidase [Peptidase M17 family]

Composition of the binding site

Protein chains monomer
A1 (AMPL_BOVIN):282, 287, 294, 301, 302, 305, 362, 364:366, 368, 391:395, 397, 398, 453, 454, 456, 457, 460, 483, 486282, 287, 294, 301, 302, 305, 362, 364:366, 368, 391:395, 397, 398, 453, 454, 456, 457, 460, 483, 486
Metals (Me):Mg/Na/Zn

Full PDB list

1bll, 1bpm, 1bpn, 1lam, 1lan, 1lap, 1lcp, 2ewb, 2j9a (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
K
2
8
2
D
2
8
7
K
2
9
4
M
3
0
2
D
3
0
5
N
3
6
2
D
3
6
4
A
3
6
5
E
3
6
6
R
3
6
8
T
3
9
1
L
3
9
2
T
3
9
3
G
3
9
4
A
3
9
5
D
3
9
7
I
3
9
8
I
4
5
3
G
4
5
4
Y
4
5
6
R
4
5
7
G
4
6
0
A
4
8
3
[1]1bll.e l2oVVD33 . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1bpm.a none . . . . . . . . . . . . . . . . . . . . . . . Mg,Zn
[1]1lan.a L9 . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1lcp.a plu10 . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]2ewb.a zed21 . . . . . . . . . . . . . . . . . . . . . . . Na,Zn
[1]2j9a.a ahyAmleYY52 . . . . . . . . . . . . . . . . . . . . . . . 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
K
2
8
2
D
2
8
7
K
2
9
4
L
3
0
1
M
3
0
2
D
3
0
5
N
3
6
2
D
3
6
4
A
3
6
5
E
3
6
6
R
3
6
8
T
3
9
1
L
3
9
2
T
3
9
3
G
3
9
4
A
3
9
5
D
3
9
7
I
3
9
8
I
4
5
3
G
4
5
4
Y
4
5
6
R
4
5
7
G
4
6
0
A
4
8
3
M
4
8
6
[1]1bll.e . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1bpm.a . . . . . . . . . . . . . . . . . . . . . . . . . Mg,Zn
[1]1lan.a . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]1lcp.a . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]2ewb.a . . . . . . . . . . . . . . . . . . . . . . . . . Na,Zn
[1]2j9a.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
1bll.e:l2oVVD
1bpm.a is apo
1lan.a:L
1lcp.a:plu
2ewb.a:zed
2j9a.a:ahyAmleYY
[1] 1bll.e
0.3
- 0.1 0.1 0.6 0.4
[1] 1bpm.a 0.1
-
0.1 0.2 0.4 0.2
[1] 1lan.a 0.2 -
0
0 0.2 0.1
[1] 1lcp.a 0.2 - 0
0
0.1 0.3
[1] 2ewb.a 0.6 - 0.2 0.2
0.1
0.5
[1] 2j9a.a 0.2 - 0 0.1 0.8
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
1bll.e
1bpm.a
1lan.a
1lcp.a
2ewb.a
2j9a.a
[1] 1bll.e
0
.02 .03 .04 .04 .06
[1] 1bpm.a .02
0
.02 .03 .03 .04
[1] 1lan.a .03 .02
0
.01 .03 .04
[1] 1lcp.a .04 .03 .01
0
.03 .04
[1] 2ewb.a .04 .03 .03 .03
0
.06
[1] 2j9a.a .06 .04 .04 .04 .06
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
1bll.e
1bpm.a
1lan.a
1lcp.a
2ewb.a
2j9a.a
[1] 1bll.e
0
0.4 0.4 0.3 0.4 0.3
[1] 1bpm.a 0.4
0
0.3 0.3 0.3 0.3
[1] 1lan.a 0.4 0.3
0
0.2 0.2 0.2
[1] 1lcp.a 0.3 0.3 0.2
0
0.2 0.2
[1] 2ewb.a 0.4 0.3 0.2 0.2
0
0.2
[1] 2j9a.a 0.3 0.3 0.2 0.2 0.2
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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1bll.e
1bpm.a
1lan.a
1lcp.a
2ewb.a
2j9a.a
[1] 1bll.e
0
0.6 1.3 1.4 0.9 1.0
[1] 1bpm.a 0.6
0
1.2 1.3 0.8 1.0
[1] 1lan.a 1.3 1.2
0
0.5 0.4 1.1
[1] 1lcp.a 1.4 1.3 0.5
0
0.5 1.2
[1] 2ewb.a 0.9 0.8 0.4 0.5
0
0.6
[1] 2j9a.a 1.0 1.0 1.1 1.2 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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