If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

TRY2_RAT_22_246

Anionic trypsin-2 [Peptidase S1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (TRY2_RAT):D: Peptidase S1 (63, 101:104, 175, 177, 178, 194:200, 214:220, 227:229)63, 101:104, 175, 177, 178, 194:200, 214:220, 227:229

Full PDB list

1amh, 1anb, 1anc, 1and, 1ane, 1bra, 1brb, 1brc, 1co7, 1dpo, 1ezs, 1ezu, 1f5r, 1f7z, 1fy8, 1j14, 1j15, 1j16, 1j17, 1k9o, 1ql9, 1slu, 1slv, 1slw, 1slx, 1trm, 1ykt, 1ylc, 1yld, 2trm, 3fp6, 3fp7, 3fp8, 3tgi, 3tgj, 3tgk (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
6
3
K
1
0
2
T
1
0
3
L
1
0
4
Y
1
7
5
G
1
7
7
K
1
7
8
D
1
9
4
S
1
9
5
C
1
9
6
Q
1
9
7
G
1
9
8
D
1
9
9
S
2
0
0
V
2
1
4
S
2
1
5
W
2
1
6
G
2
1
7
Y
2
1
8
G
2
1
9
C
2
2
0
G
2
2
7
V
2
2
8
Y
2
2
9
[1]1amh.b none . . . . . . . S . . . . . . . . . . . . . . . .
[1]1and.a ben9 . . . . . . . . . . . . . . . . . . . . . . . .
[1]1bra.a ben9 . . . . . . . G . . . . . . . . . . . . . D . .
[1]1brb.e GPCK26 . . . . . . . G . . . . . . . . . . . . . D . .
[1]1brc.e PCR24 . . . . . . . G . . . . . . . . . . . . . D . .
[1]1dpo.a ben9 . . . . . . . . . . . . . C . . . . . . . . . .
[1]1ezs.c VSTR31 . . . . . . . . . . . . . . . . . . . . . . . .
[1]1j14.a ben9 . E . Y . . . . . . . . . . . . . . . . . . . .
[1]1j16.a ben9 . E . Y S F I . A . . . . . . . . . . . . . . .
[1]1k9o.e IVPK31 . . . . . . . . . . . . . A . . . . . . . . . .
[1]1slu.b R-VSTM39 . . . . . . . . . . . . . . . . . . . . . . . .
[1]1slw.b VSTM28 . . . . . . . . . . . . . . . . . . . . . . . .
[1]1trm.a ben9 . . . . . . . . . . . . . . . . . . . . . . . .
[1]3fp6.e GPCK26 . . . . . . . . . . . . . . . . . . . . . . . .
[1]3fp7.e GPCK27 . . . . . . . . . . . . . A . . . . . . . . . .
[1]3tgk.e GPCK26 . . . . . . . . . . . . N . . . . . . . . . . .
[2]1j17.t zen34 . E . Y S F I . A . . . . . . . . . . . . . . .
[2]1ql9.a zen34 . E . Y . . . . . . . . . . . . . . . . . . . .
[3]1anb.a ben9 . . . . . . . . . . . . . . . E . . . . . . . .
[3]1anc.a ben9 . . . . . . . . . . . . . . . K . . . . . . . .

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
H
6
3
R
1
0
1
K
1
0
2
T
1
0
3
L
1
0
4
Y
1
7
5
G
1
7
7
K
1
7
8
D
1
9
4
S
1
9
5
C
1
9
6
Q
1
9
7
G
1
9
8
D
1
9
9
S
2
0
0
V
2
1
4
S
2
1
5
W
2
1
6
G
2
1
7
Y
2
1
8
G
2
1
9
C
2
2
0
G
2
2
7
V
2
2
8
Y
2
2
9
[1]1amh.b . . . . . . . . S . . . . . * . . . . . . . . . .
[1]1and.a * H . . . . . . . . . * . . . . . . . . . . . . .
[1]1bra.a . . . . . . . . G . . * . . . . . . . . . . D . .
[1]1brb.e . . . . . . . . G . . * . . . . . . . * . . D . .
[1]1brc.e . . . . . . . . G . . * . . . . . . . * . . D . .
[1]1dpo.a . . . . . . . * . . . * . . C . . . . . . . . . .
[1]1ezs.c . . . . * . . . . . . * . . . . . . . . . . . . .
[1]1j14.a . . E . Y . . . . . . * . . . . . . . . . . . . .
[1]1j16.a . . E . Y S F I . A . * . . . . . . . . . . . . .
[1]1k9o.e . . . . . . . . . . . * . . A . . . . . . . . . .
[1]1slu.b . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1slw.b . . . . . . . . . . . * . . . . . . . . . . . . .
[1]1trm.a * . . . . . . . . . . * . . * . . . . . . . . . .
[1]3fp6.e . . . . . . . . . . . * . . . . . . . * . . . . .
[1]3fp7.e . . . . . . . . . . . * . . A . . . . * . . . . .
[1]3tgk.e . . . . . . . . . . . * . N . . . . . * . . . . .
[2]1j17.t . . E . Y S F I . A . . . . . . . . . . . . . . .
[2]1ql9.a . . E . Y . . . . . . . . . . . . . . * . . . . .
[3]1anb.a . . . . . . . . . . . * . . * . E * . . . . . . .
[3]1anc.a . . . . . . . . . . . * . . * . K * . . . . . . .

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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1amh.b is apo
1and.a:ben
1bra.a:ben
1brb.e:GPCK
1brc.e:PCR
1dpo.a:ben
1ezs.c:VSTR
1j14.a:ben
1j16.a:ben
1k9o.e:IVPK
1slu.b:R-VSTM
1slw.b:VSTM
1trm.a:ben
3fp6.e:GPCK
3fp7.e:GPCK
3tgk.e:GPCK
1j17.t:zen
1ql9.a:zen
1anb.a:ben
1anc.a:ben
[1] 1amh.b
-
0.5 0.9 1.2 1.5 0.5 1.1 0.5 0.7 0.8 1.3 1.1 0.5 0.9 0.6 0.8 0.9 1.2 0.6 0.5
[1] 1and.a -
0
0.1 1.5 1.5 0 1.6 0 0 1.2 2.5 1.8 0 1.4 1.7 1.7 2.6 2.8 0.1 0
[1] 1bra.a - 0.4
0.1
0.6 0.6 0.5 0.8 0.5 0.4 0.8 1.1 0.7 0.4 0.7 0.9 0.5 3.0 3.1 0.7 0.4
[1] 1brb.e - 0.2 0.2
0
0.2 0.2 2.9 0.2 0.2 0.2 3.1 2.7 0.2 0.1 0.4 0 2.1 2.3 0.7 0.2
[1] 1brc.e - 0.2 0 0.1
0
0.2 1.9 0.2 0.1 0.1 2.6 2.7 0.2 0.1 0.2 0.1 1.6 1.6 0.4 0.2
[1] 1dpo.a - 0 0.1 1.2 1.3
0
1.5 0 0 1.0 2.2 2.2 0 1.3 1.0 1.3 2.4 2.9 0.1 0
[1] 1ezs.c - 0.1 0.2 0.1 0.2 0
0
0 0.1 0.8 0.4 0.6 0.1 0.1 0 0.1 2.4 2.7 0.1 0.1
[1] 1j14.a - 0 0.3 2.4 2.2 0 2.0
0
0 1.3 2.3 2.0 0 2.0 2.3 2.4 2.6 2.7 0 0
[1] 1j16.a - 0 0.2 1.4 1.4 0 1.8 0
0
1.2 2.3 1.9 0 2.0 2.0 1.6 2.4 2.4 0.2 0
[1] 1k9o.e - 0.2 0.1 0.3 0.4 0.1 0.5 0 0.1
0.1
1.1 0.8 0.2 0.2 0.3 0.3 2.2 2.2 0.1 0.2
[1] 1slu.b - 0.1 0.1 0.1 0.2 0 0.2 0 0.1 0.4
0.1
0.2 0.2 0.2 0.2 0.1 0.8 0.9 0 0.1
[1] 1slw.b - 0.2 0.1 0.1 0.3 0.2 0.3 0.1 0.2 0.4 0.1
0.1
0.2 0.2 0.1 0.1 1.2 1.2 0.2 0.2
[1] 1trm.a - 0 0.2 1.2 1.1 0 1.7 0 0 1.1 1.8 1.5
0.1
1.4 1.5 1.3 2.1 2.3 0.1 0.1
[1] 3fp6.e - 0.1 0.1 0.2 0.1 0 2.3 0 0.1 0.6 2.9 3.0 0.1
0.1
0.2 0.2 2.2 2.2 0.1 0.1
[1] 3fp7.e - 0.2 0.1 0.2 0.3 0.1 2.7 0.1 0.2 0.5 3.0 2.9 0.2 0.2
0
0.3 2.6 2.6 0.1 0.2
[1] 3tgk.e - 0.1 0.1 0.1 0.2 0.1 2.7 0.1 0.1 0.3 2.7 2.7 0 0.1 0.1
0.1
2.0 1.9 0.1 0
[2] 1j17.t - 0 0.1 1.9 1.8 0 2.8 0 0 1.1 2.9 2.9 0 2.2 1.9 1.7
0
0 0 0
[2] 1ql9.a - 0 0.2 1.8 1.9 0 4.6 0.1 0 1.7 4.9 5.3 0 1.9 2.2 1.9 0
0
0 0
[3] 1anb.a - 0 0.2 5.7 5.3 0 5.0 0 0 5.0 5.8 5.0 0 5.3 5.4 5.7 5.7 5.5
0
0
[3] 1anc.a - 0 0.1 5.1 4.9 0 4.4 0 0 4.4 4.6 4.6 0 5.0 5.0 5.4 5.7 5.3 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1amh.b
1and.a
1bra.a
1brb.e
1brc.e
1dpo.a
1ezs.c
1j14.a
1j16.a
1k9o.e
1slu.b
1slw.b
1trm.a
3fp6.e
3fp7.e
3tgk.e
1j17.t
1ql9.a
1anb.a
1anc.a
[1] 1amh.b
0
.24 .18 .26 .22 .16 .16 .22 .21 .15 .10 .10 .18 .22 .24 .21 .20 .29 .33 .32
[1] 1and.a .24
0
.11 .28 .28 .11 .14 .13 .14 .11 .19 .18 .08 .23 .22 .25 .28 .38 .31 .26
[1] 1bra.a .18 .11
0
.19 .20 .08 .13 .12 .14 .09 .15 .14 .14 .19 .17 .20 .26 .36 .28 .24
[1] 1brb.e .26 .28 .19
0
.07 .26 .18 .27 .28 .19 .23 .21 .24 .07 .08 .06 .33 .22 .42 .40
[1] 1brc.e .22 .28 .20 .07
0
.24 .18 .27 .28 .18 .19 .18 .23 .07 .08 .05 .32 .22 .39 .38
[1] 1dpo.a .16 .11 .08 .26 .24
0
.13 .12 .13 .10 .15 .14 .13 .20 .20 .21 .27 .38 .25 .21
[1] 1ezs.c .16 .14 .13 .18 .18 .13
0
.12 .12 .06 .10 .08 .09 .14 .17 .16 .20 .30 .28 .28
[1] 1j14.a .22 .13 .12 .27 .27 .12 .12
0
.03 .12 .18 .17 .15 .23 .21 .24 .16 .26 .30 .27
[1] 1j16.a .21 .14 .14 .28 .28 .13 .12 .03
0
.13 .18 .16 .16 .22 .22 .24 .17 .25 .32 .28
[1] 1k9o.e .15 .11 .09 .19 .18 .10 .06 .12 .13
0
.11 .09 .09 .13 .15 .14 .22 .32 .29 .26
[1] 1slu.b .10 .19 .15 .23 .19 .15 .10 .18 .18 .11
0
.02 .13 .20 .22 .18 .16 .26 .31 .30
[1] 1slw.b .10 .18 .14 .21 .18 .14 .08 .17 .16 .09 .02
0
.12 .17 .20 .16 .19 .28 .30 .28
[1] 1trm.a .18 .08 .14 .24 .23 .13 .09 .15 .16 .09 .13 .12
0
.20 .21 .21 .26 .36 .29 .27
[1] 3fp6.e .22 .23 .19 .07 .07 .20 .14 .23 .22 .13 .20 .17 .20
0
.02 .02 .31 .20 .36 .35
[1] 3fp7.e .24 .22 .17 .08 .08 .20 .17 .21 .22 .15 .22 .20 .21 .02
0
.04 .33 .22 .35 .33
[1] 3tgk.e .21 .25 .20 .06 .05 .21 .16 .24 .24 .14 .18 .16 .21 .02 .04
0
.30 .20 .37 .35
[2] 1j17.t .20 .28 .26 .33 .32 .27 .20 .16 .17 .22 .16 .19 .26 .31 .33 .30
0
.20 .44 .41
[2] 1ql9.a .29 .38 .36 .22 .22 .38 .30 .26 .25 .32 .26 .28 .36 .20 .22 .20 .20
0
.54 .51
[3] 1anb.a .33 .31 .28 .42 .39 .25 .28 .30 .32 .29 .31 .30 .29 .36 .35 .37 .44 .54
0
.05
[3] 1anc.a .32 .26 .24 .40 .38 .21 .28 .27 .28 .26 .30 .28 .27 .35 .33 .35 .41 .51 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
1amh.b
1and.a
1bra.a
1brb.e
1brc.e
1dpo.a
1ezs.c
1j14.a
1j16.a
1k9o.e
1slu.b
1slw.b
1trm.a
3fp6.e
3fp7.e
3tgk.e
1j17.t
1ql9.a
1anb.a
1anc.a
[1] 1amh.b
0
1.0 1.0 1.0 0.9 1.1 1.1 1.0 2.0 1.1 1.0 1.0 1.0 1.0 1.0 1.0 1.4 1.1 1.0 1.0
[1] 1and.a 1.0
0
0.3 0.4 0.5 0.2 0.5 0.2 1.8 0.3 0.6 0.6 0.3 0.4 0.3 0.4 1.0 0.5 0.3 0.3
[1] 1bra.a 1.0 0.3
0
0.3 0.4 0.3 0.5 0.3 1.8 0.4 0.6 0.5 0.3 0.4 0.3 0.4 1.0 0.6 0.3 0.2
[1] 1brb.e 1.0 0.4 0.3
0
0.3 0.5 0.5 0.4 1.8 0.4 0.5 0.5 0.4 0.3 0.3 0.3 1.1 0.6 0.5 0.4
[1] 1brc.e 0.9 0.5 0.4 0.3
0
0.6 0.5 0.5 1.8 0.5 0.4 0.4 0.5 0.4 0.4 0.4 1.1 0.6 0.5 0.4
[1] 1dpo.a 1.1 0.2 0.3 0.5 0.6
0
0.5 0.2 1.8 0.3 0.7 0.6 0.3 0.4 0.3 0.4 1.0 0.5 0.3 0.3
[1] 1ezs.c 1.1 0.5 0.5 0.5 0.5 0.5
0
0.5 1.9 0.5 0.4 0.3 0.5 0.5 0.5 0.5 1.1 0.6 0.5 0.4
[1] 1j14.a 1.0 0.2 0.3 0.4 0.5 0.2 0.5
0
1.8 0.3 0.6 0.6 0.3 0.3 0.3 0.3 1.0 0.5 0.3 0.3
[1] 1j16.a 2.0 1.8 1.8 1.8 1.8 1.8 1.9 1.8
0
1.8 1.9 1.9 1.8 1.7 1.7 1.8 1.2 1.9 1.9 1.8
[1] 1k9o.e 1.1 0.3 0.4 0.4 0.5 0.3 0.5 0.3 1.8
0
0.6 0.6 0.4 0.3 0.3 0.3 1.1 0.5 0.4 0.4
[1] 1slu.b 1.0 0.6 0.6 0.5 0.4 0.7 0.4 0.6 1.9 0.6
0
0.3 0.6 0.5 0.5 0.5 1.1 0.7 0.5 0.5
[1] 1slw.b 1.0 0.6 0.5 0.5 0.4 0.6 0.3 0.6 1.9 0.6 0.3
0
0.5 0.5 0.5 0.5 1.1 0.7 0.5 0.5
[1] 1trm.a 1.0 0.3 0.3 0.4 0.5 0.3 0.5 0.3 1.8 0.4 0.6 0.5
0
0.4 0.4 0.4 1.1 0.5 0.3 0.3
[1] 3fp6.e 1.0 0.4 0.4 0.3 0.4 0.4 0.5 0.3 1.7 0.3 0.5 0.5 0.4
0
0.1 0.2 1.0 0.5 0.4 0.3
[1] 3fp7.e 1.0 0.3 0.3 0.3 0.4 0.3 0.5 0.3 1.7 0.3 0.5 0.5 0.4 0.1
0
0.2 1.0 0.5 0.4 0.3
[1] 3tgk.e 1.0 0.4 0.4 0.3 0.4 0.4 0.5 0.3 1.8 0.3 0.5 0.5 0.4 0.2 0.2
0
1.0 0.5 0.4 0.3
[2] 1j17.t 1.4 1.0 1.0 1.1 1.1 1.0 1.1 1.0 1.2 1.1 1.1 1.1 1.1 1.0 1.0 1.0
0
1.1 1.1 1.0
[2] 1ql9.a 1.1 0.5 0.6 0.6 0.6 0.5 0.6 0.5 1.9 0.5 0.7 0.7 0.5 0.5 0.5 0.5 1.1
0
0.6 0.5
[3] 1anb.a 1.0 0.3 0.3 0.5 0.5 0.3 0.5 0.3 1.9 0.4 0.5 0.5 0.3 0.4 0.4 0.4 1.1 0.6
0
0.2
[3] 1anc.a 1.0 0.3 0.2 0.4 0.4 0.3 0.4 0.3 1.8 0.4 0.5 0.5 0.3 0.3 0.3 0.3 1.0 0.5 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
1amh.b
1and.a
1bra.a
1brb.e
1brc.e
1dpo.a
1ezs.c
1j14.a
1j16.a
1k9o.e
1slu.b
1slw.b
1trm.a
3fp6.e
3fp7.e
3tgk.e
1j17.t
1ql9.a
1anb.a
1anc.a
[1] 1amh.b
0
1.7 1.9 1.5 1.4 1.8 1.8 1.7 1.9 1.9 1.7 1.7 1.9 1.7 1.9 1.6 1.6 1.6 2.4 2.3
[1] 1and.a 1.7
0
0.9 1.4 1.4 1.2 1.0 0.9 1.7 1.1 1.3 1.3 0.9 1.5 1.5 1.5 1.4 1.7 1.7 1.5
[1] 1bra.a 1.9 0.9
0
1.5 1.2 1.2 1.0 0.5 1.6 1.2 1.2 1.3 1.0 1.5 1.6 1.7 1.6 1.8 1.5 1.5
[1] 1brb.e 1.5 1.4 1.5
0
0.6 1.6 1.6 1.5 1.9 1.6 1.6 1.6 1.6 1.1 1.2 0.7 1.6 1.0 2.1 2.0
[1] 1brc.e 1.4 1.4 1.2 0.6
0
1.4 1.4 1.3 1.9 1.3 1.3 1.3 1.4 0.8 0.8 0.7 1.6 1.0 1.9 1.9
[1] 1dpo.a 1.8 1.2 1.2 1.6 1.4
0
1.4 0.9 1.6 1.0 1.2 1.3 1.3 1.8 1.9 1.7 1.6 1.9 1.8 1.7
[1] 1ezs.c 1.8 1.0 1.0 1.6 1.4 1.4
0
0.9 1.7 1.3 1.0 0.9 1.2 1.5 1.5 1.6 1.5 1.9 1.7 1.5
[1] 1j14.a 1.7 0.9 0.5 1.5 1.3 0.9 0.9
0
1.5 1.0 1.0 1.0 1.0 1.5 1.5 1.6 1.4 1.7 1.6 1.5
[1] 1j16.a 1.9 1.7 1.6 1.9 1.9 1.6 1.7 1.5
0
1.6 1.7 1.7 1.7 1.9 1.9 1.9 1.9 2.1 2.2 2.1
[1] 1k9o.e 1.9 1.1 1.2 1.6 1.3 1.0 1.3 1.0 1.6
0
1.5 1.5 1.4 1.7 1.9 1.7 1.6 1.8 1.8 1.7
[1] 1slu.b 1.7 1.3 1.2 1.6 1.3 1.2 1.0 1.0 1.7 1.5
0
0.6 1.3 1.5 1.6 1.6 1.5 1.9 1.8 1.7
[1] 1slw.b 1.7 1.3 1.3 1.6 1.3 1.3 0.9 1.0 1.7 1.5 0.6
0
1.3 1.4 1.5 1.7 1.5 1.8 1.9 1.7
[1] 1trm.a 1.9 0.9 1.0 1.6 1.4 1.3 1.2 1.0 1.7 1.4 1.3 1.3
0
1.6 1.7 1.8 1.6 1.8 1.8 1.6
[1] 3fp6.e 1.7 1.5 1.5 1.1 0.8 1.8 1.5 1.5 1.9 1.7 1.5 1.4 1.6
0
0.2 0.9 1.8 1.3 2.1 2.0
[1] 3fp7.e 1.9 1.5 1.6 1.2 0.8 1.9 1.5 1.5 1.9 1.9 1.6 1.5 1.7 0.2
0
1.0 1.8 1.4 2.1 2.0
[1] 3tgk.e 1.6 1.5 1.7 0.7 0.7 1.7 1.6 1.6 1.9 1.7 1.6 1.7 1.8 0.9 1.0
0
1.6 1.1 2.2 2.1
[2] 1j17.t 1.6 1.4 1.6 1.6 1.6 1.6 1.5 1.4 1.9 1.6 1.5 1.5 1.6 1.8 1.8 1.6
0
1.5 2.2 2.1
[2] 1ql9.a 1.6 1.7 1.8 1.0 1.0 1.9 1.9 1.7 2.1 1.8 1.9 1.8 1.8 1.3 1.4 1.1 1.5
0
2.3 2.2
[3] 1anb.a 2.4 1.7 1.5 2.1 1.9 1.8 1.7 1.6 2.2 1.8 1.8 1.9 1.8 2.1 2.1 2.2 2.2 2.3
0
0.6
[3] 1anc.a 2.3 1.5 1.5 2.0 1.9 1.7 1.5 1.5 2.1 1.7 1.7 1.7 1.6 2.0 2.0 2.1 2.1 2.2 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...