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BAPA_SPHXN_30_402

Beta-peptidyl aminopeptidase BapA [Peptidase S58 family]

Composition of the binding site

Protein chains homodimer
A1 (BAPA_SPHXN):105, 106, 129, 162:164, 166, 167, 236, 275:279, 316, 317105, 106, 129, 162:164, 166, 167, 236, 275:279, 316, 317
A3 (BAPA_SPHXN):113, 121, 153, 154, 156, 157113, 121, 153, 154, 156, 157

Full PDB list

3n2w, 3n33, 3n5i, 3ndv, 3nfb

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A3
T
1
0
5
G
1
0
6
T
1
2
9
E
1
6
2
T
1
6
3
L
1
6
4
N
1
6
6
R
1
6
7
N
2
3
6
S
2
7
9
L
3
1
6
S
3
1
7
L
1
1
3
F
1
5
3
S
1
5
4
L
1
5
6
L
1
5
7
[1]3n2w.a none . . . . . . . . . . . . . . . . .
[1]3n33.d aes13 . . . . . . . . . . . . . . . . .
[1]3ndv.a aic24 . . . . . . . . . . . . . . . . .
[1]3nfb.a oae25 . . . . . . . . . . . . . . . . .
[2]3n5i.d none . . . . . . . . . A . . . . . . .

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 A3
T
1
0
5
G
1
0
6
T
1
2
9
E
1
6
2
T
1
6
3
L
1
6
4
N
1
6
6
R
1
6
7
N
2
3
6
Q
2
7
5
D
2
7
6
K
2
7
7
N
2
7
8
S
2
7
9
L
3
1
6
S
3
1
7
L
1
1
3
L
1
2
1
F
1
5
3
S
1
5
4
L
1
5
6
L
1
5
7
[1]3n2w.a . . . . . . . . . - - - - . . . . . . . . .
[1]3n33.d . . . . . . . . . - - - - . . . . . . . . .
[1]3ndv.a . . . . . . . . . - - - - . . . . . . . . .
[1]3nfb.a . . . . . . . . . - - - - . . . . . . . . .
[2]3n5i.d . . . . . . . . . . * * * A . . . . . . . .

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
3n2w.a is apo
3n33.d:aes
3ndv.a:aic
3nfb.a:oae
3n5i.d is apo
[1] 3n2w.a
-
0 0.4 0.5 -
[1] 3n33.d -
0
0.5 0.9 -
[1] 3ndv.a - 0
0.1
0.3 -
[1] 3nfb.a - 0 0.1
0.1
-
[2] 3n5i.d - 0 9.3 7.7
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
3n2w.a
3n33.d
3ndv.a
3nfb.a
3n5i.d
[1] 3n2w.a
0
.05 .03 .02 .46
[1] 3n33.d .05
0
.04 .04 .48
[1] 3ndv.a .03 .04
0
.01 .45
[1] 3nfb.a .02 .04 .01
0
.45
[2] 3n5i.d .46 .48 .45 .45
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
3n2w.a
3n33.d
3ndv.a
3nfb.a
3n5i.d
[1] 3n2w.a
0
0.2 0.3 0.4 0.2
[1] 3n33.d 0.2
0
0.2 0.3 0.2
[1] 3ndv.a 0.3 0.2
0
0.2 0.3
[1] 3nfb.a 0.4 0.3 0.2
0
0.3
[2] 3n5i.d 0.2 0.2 0.3 0.3
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
3n2w.a
3n33.d
3ndv.a
3nfb.a
3n5i.d
[1] 3n2w.a
0
1.2 0.9 1.1 0.9
[1] 3n33.d 1.2
0
0.8 0.9 1.3
[1] 3ndv.a 0.9 0.8
0
0.9 1.0
[1] 3nfb.a 1.1 0.9 0.9
0
0.8
[2] 3n5i.d 0.9 1.3 1.0 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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