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TRY3_HUMAN_81_304

Trypsin-3 [Peptidase S1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (TRY3_HUMAN):D: Peptidase S1 (120, 161, 251:257, 271:274, 276, 277, 284)120, 161, 251:257, 271:274, 276, 277, 284

Full PDB list

1h4w, 2r9p, 3l33, 3l3t, 3p92, 3p95, 4dg4, 4u30, 4u32, 5c67, 5jbt, 5tp0 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
1
2
0
L
1
6
1
D
2
5
1
S
2
5
2
C
2
5
3
Q
2
5
4
R
2
5
5
D
2
5
6
S
2
5
7
V
2
7
1
S
2
7
2
W
2
7
3
G
2
7
4
G
2
7
6
C
2
7
7
G
2
8
4
[1]1h4w.a ben9 . . . . . . . . . . . . . . . .
[1]2r9p.a K9 . . . . . . . . A . . . . . . .
[1]2r9p.c CK15 . . . . . . . . A . . . . . . .
[1]3l33.b CR17 . . . . . . . . A . . . . . . .
[1]3p95.a R11 . . . . . . . . A . . . . . . .
[1]5tp0.a brn11 . . . . . . . . . . . . . . . .

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
H
1
2
0
L
1
6
1
D
2
5
1
S
2
5
2
C
2
5
3
Q
2
5
4
R
2
5
5
D
2
5
6
S
2
5
7
V
2
7
1
S
2
7
2
W
2
7
3
G
2
7
4
G
2
7
6
C
2
7
7
G
2
8
4
[1]1h4w.a . . . . . . . . * . . . . . . .
[1]2r9p.a . . . . . . . . A . . . . . . .
[1]2r9p.c . . . . . . . . A . . . . . . .
[1]3l33.b . . . . . . . . A . . . . . . .
[1]3p95.a . . . . . . . . A . . . . . . .
[1]5tp0.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
1h4w.a:ben
2r9p.a:K
2r9p.c:CK
3l33.b:CR
3p95.a:R
5tp0.a:brn
[1] 1h4w.a
0
0.8 1.0 1.0 0.7 0.3
[1] 2r9p.a 0.1
0
0.1 0.2 0.1 0.1
[1] 2r9p.c 0.1 0
0
0.1 0.2 0.1
[1] 3l33.b 0.1 0.1 0.1
0.1
0.1 0.1
[1] 3p95.a 0.1 0.1 0.2 0.2
0
0.2
[1] 5tp0.a 0 0.4 0.6 0.6 0.5
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
1h4w.a
2r9p.a
2r9p.c
3l33.b
3p95.a
5tp0.a
[1] 1h4w.a
0
.08 .09 .07 .08 .04
[1] 2r9p.a .08
0
.01 .01 .03 .05
[1] 2r9p.c .09 .01
0
.02 .03 .06
[1] 3l33.b .07 .01 .02
0
.01 .04
[1] 3p95.a .08 .03 .03 .01
0
.05
[1] 5tp0.a .04 .05 .06 .04 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1h4w.a
2r9p.a
2r9p.c
3l33.b
3p95.a
5tp0.a
[1] 1h4w.a
0
0.3 0.3 0.3 0.3 0.1
[1] 2r9p.a 0.3
0
0.2 0.1 0.2 0.3
[1] 2r9p.c 0.3 0.2
0
0.2 0.2 0.3
[1] 3l33.b 0.3 0.1 0.2
0
0.2 0.3
[1] 3p95.a 0.3 0.2 0.2 0.2
0
0.3
[1] 5tp0.a 0.1 0.3 0.3 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
1h4w.a
2r9p.a
2r9p.c
3l33.b
3p95.a
5tp0.a
[1] 1h4w.a
0
1.2 1.2 1.1 0.8 0.7
[1] 2r9p.a 1.2
0
0.2 0.2 0.6 1.4
[1] 2r9p.c 1.2 0.2
0
0.2 0.6 1.4
[1] 3l33.b 1.1 0.2 0.2
0
0.6 1.3
[1] 3p95.a 0.8 0.6 0.6 0.6
0
1.1
[1] 5tp0.a 0.7 1.4 1.4 1.3 1.1
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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