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ELNE_HUMAN_30_247

Neutrophil elastase [Peptidase S1 family. Elastase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ELNE_HUMAN):D: Peptidase S1 (54, 55, 70, 71, 74, 109:115, 117, 158, 165, 180:182, 197:202, 216:223, 228)54, 55, 70, 71, 74, 109:115, 117, 158, 165, 180:182, 197:202, 216:223, 228

Full PDB list

1b0f, 1h1b, 1hne, 1ppf, 1ppg, 2rg3, 2z7f, 3q76, 3q77, 4nzl, 4wvp, 5a09, 5a0a, 5a0b, 5a0c, 5a8x, 5a8y, 5a8z, 5abw

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
5
4
C
5
5
H
7
0
C
7
1
Y
1
0
9
P
1
1
1
V
1
1
2
N
1
1
3
L
1
1
4
D
1
1
7
L
1
5
8
I
1
6
5
L
1
8
0
C
1
8
1
R
1
8
2
V
1
9
7
C
1
9
8
F
1
9
9
G
2
0
0
D
2
0
1
S
2
0
2
A
2
1
6
S
2
1
7
F
2
1
8
V
2
1
9
R
2
2
0
G
2
2
1
G
2
2
2
C
2
2
3
Y
2
2
8
[1]1b0f.a sei44 . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]1h1b.a 15129 . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]1hne.e msuAAPalv.0qe31 . . * . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]1ppf.e KPACTLE-NKC74 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ppg.e hmbAAPvai.0qe33 . . * . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]2z7f.e TYGQCLMLNP-MC91 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3q76.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3q77.a 2hy32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4nzl.a VDGITALH-R68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wvp.e btn.3v3.nlb.omt.oic.3v276 . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]5a09.a jjd33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a0a.e jjs29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a0b.a jjx40 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a0c.a jjv32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a8x.a iuy33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a8y.a mli,vbm42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a8z.a iul31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5abw.a wqq36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2rg3.a none . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .

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
F
5
4
C
5
5
H
7
0
C
7
1
N
7
4
Y
1
0
9
D
1
1
0
P
1
1
1
V
1
1
2
N
1
1
3
L
1
1
4
L
1
1
5
D
1
1
7
L
1
5
8
I
1
6
5
L
1
8
0
C
1
8
1
R
1
8
2
V
1
9
7
C
1
9
8
F
1
9
9
G
2
0
0
D
2
0
1
S
2
0
2
A
2
1
6
S
2
1
7
F
2
1
8
V
2
1
9
R
2
2
0
G
2
2
1
G
2
2
2
C
2
2
3
Y
2
2
8
[1]1b0f.a . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]1h1b.a . . * . . . . . . . * . . . . . . . . . * . . * . . . . . . . . .
[1]1hne.e . . * . . . . . . . * . . . . . . . . . * . . * . . . . . . . . .
[1]1ppf.e . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]1ppg.e . . * . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]2z7f.e . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]3q76.b . . * . . . . . . . * . . . . . . . . . . . . * . . . . * * . . .
[1]3q77.a . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]4nzl.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]4wvp.e . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]5a09.a . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]5a0a.e . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]5a0b.a . . * . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]5a0c.a . . * . . . . . . . * . . . . . . * . . * . . * . . . . . . . . .
[1]5a8x.a . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]5a8y.a . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]5a8z.a . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[1]5abw.a . . . . . . . . . . * . . . . . . . . . . . . * . . . . . . . . .
[2]2rg3.a . . * . . . . . . . * . . . . . . . . . . . . bg1 . . . . . . . . .

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
1b0f.a:sei
1h1b.a:151
1hne.e:msuAAPalv.0qe
1ppf.e:KPACTLE-NKC
1ppg.e:hmbAAPvai.0qe
2z7f.e:TYGQCLMLNP-MC
3q76.b is apo
3q77.a:2hy
4nzl.a:VDGITALH-R
4wvp.e:btn.3v3.nlb.omt.oic.3v2
5a09.a:jjd
5a0a.e:jjs
5a0b.a:jjx
5a0c.a:jjv
5a8x.a:iuy
5a8y.a:mli,vbm
5a8z.a:iul
5abw.a:wqq
2rg3.a is apo
[1] 1b0f.a
0.7
1.4 1.3 0.4 1.5 0.5 - 1.7 0.4 1.9 2.3 2.5 1.7 2.2 1.6 1.6 2.2 0.3 -
[1] 1h1b.a 1.3
0.8
0.7 1.5 0.9 6.0 - 3.7 1.4 1.5 3.9 4.1 2.8 4.3 4.5 4.3 3.8 1.4 -
[1] 1hne.e 1.3 1.7
1.2
0.7 1.2 2.0 - 2.1 0.8 0.9 2.0 1.8 1.6 2.3 1.7 1.4 1.9 0.3 -
[1] 1ppf.e 0.6 1.3 1.0
0.1
1.1 1.0 - 0.7 0.4 0.6 0.9 1.2 0.6 1.2 0.7 0.7 1.0 0.1 -
[1] 1ppg.e 0.9 1.4 1.3 0.6
0.9
1.5 - 1.4 0.9 1.3 1.9 2.2 1.1 2.3 1.2 1.2 1.6 0.4 -
[1] 2z7f.e 0.6 0.8 1.4 0.5 1.2
0.1
- 2.8 0.1 1.6 2.7 2.9 2.6 3.1 2.7 2.8 2.9 0.3 -
[1] 3q76.b 2.3 1.1 1.6 0.8 2.0 2.4
-
3.1 1.0 3.6 3.3 3.2 3.1 3.8 2.9 3.1 3.3 1.3 -
[1] 3q77.a 1.3 1.9 1.4 0.8 1.5 2.6 -
0
1.0 1.3 0.1 0.1 0.1 0.1 0 0 0.1 0.3 -
[1] 4nzl.a 0.8 0.6 1.2 0.2 0.8 0.4 - 2.4
0
1.5 2.6 2.5 2.1 2.7 2.3 2.3 2.7 0.2 -
[1] 4wvp.e 0.7 1.7 1.1 0.2 1.3 1.7 - 0.7 0.8
0.6
1.2 1.3 1.2 1.5 1.0 0.9 1.2 0.4 -
[1] 5a09.a 1.3 1.9 1.4 0.6 1.5 2.5 - 0 1.0 1.4
0
0 0.2 0.1 0.1 0 0 0.4 -
[1] 5a0a.e 1.2 1.5 1.6 0.5 1.5 2.1 - 0.1 1.0 1.6 0
0
0.6 0.1 0.2 0.2 0 0.7 -
[1] 5a0b.a 1.4 1.9 1.6 0.8 1.5 2.5 - 0.1 1.1 1.2 0.1 0.4
0
0.2 0 0 0.1 0.3 -
[1] 5a0c.a 2.9 2.0 1.5 1.0 1.7 3.3 - 0 1.1 4.2 0 0 0.4
0
0.1 0 0.1 0.9 -
[1] 5a8x.a 1.3 2.4 1.5 0.7 1.5 2.3 - 0.1 1.0 1.1 0.1 0.4 0.1 0.3
0
0 0.1 0.1 -
[1] 5a8y.a 1.3 2.4 1.6 0.8 1.6 2.7 - 0 1.0 1.7 0.1 0.1 0.1 0.1 0
0
0.1 0.3 -
[1] 5a8z.a 1.2 1.3 1.6 0.5 1.5 1.8 - 0 1.0 1.6 0 0 0.2 0 0.1 0
0
0.6 -
[1] 5abw.a 1.1 2.0 1.7 0.7 1.6 2.6 - 0.5 0.7 2.1 0.7 1.0 0.3 0.8 0.4 0.4 0.8
0
-
[2] 2rg3.a 7.5 10 6.9 7.5 6.6 10 - 6.7 8.4 6.7 6.9 6.9 7.1 7.7 7.6 7.4 7.5 5.7
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
1b0f.a
1h1b.a
1hne.e
1ppf.e
1ppg.e
2z7f.e
3q76.b
3q77.a
4nzl.a
4wvp.e
5a09.a
5a0a.e
5a0b.a
5a0c.a
5a8x.a
5a8y.a
5a8z.a
5abw.a
2rg3.a
[1] 1b0f.a
0
.23 .11 .10 .10 .07 .14 .07 .09 .10 .06 .09 .08 .16 .07 .08 .11 .10 .37
[1] 1h1b.a .23
0
.23 .24 .23 .20 .22 .21 .22 .26 .23 .24 .23 .28 .22 .21 .25 .24 .47
[1] 1hne.e .11 .23
0
.08 .08 .13 .19 .06 .11 .09 .09 .09 .08 .16 .06 .07 .09 .08 .34
[1] 1ppf.e .10 .24 .08
0
.10 .09 .19 .07 .10 .05 .08 .08 .07 .15 .07 .08 .07 .10 .33
[1] 1ppg.e .10 .23 .08 .10
0
.11 .15 .08 .08 .11 .08 .08 .08 .18 .08 .08 .10 .10 .34
[1] 2z7f.e .07 .20 .13 .09 .11
0
.14 .09 .07 .12 .08 .09 .08 .19 .10 .09 .11 .11 .36
[1] 3q76.b .14 .22 .19 .19 .15 .14
0
.16 .16 .20 .17 .18 .17 .25 .17 .16 .19 .18 .45
[1] 3q77.a .07 .21 .06 .07 .08 .09 .16
0
.10 .08 .04 .05 .03 .12 .01 .02 .05 .04 .32
[1] 4nzl.a .09 .22 .11 .10 .08 .07 .16 .10
0
.12 .10 .11 .10 .21 .11 .10 .13 .08 .39
[1] 4wvp.e .10 .26 .09 .05 .11 .12 .20 .08 .12
0
.09 .08 .08 .14 .07 .09 .08 .09 .30
[1] 5a09.a .06 .23 .09 .08 .08 .08 .17 .04 .10 .09
0
.04 .03 .14 .05 .03 .05 .06 .32
[1] 5a0a.e .09 .24 .09 .08 .08 .09 .18 .05 .11 .08 .04
0
.04 .13 .05 .04 .05 .06 .30
[1] 5a0b.a .08 .23 .08 .07 .08 .08 .17 .03 .10 .08 .03 .04
0
.14 .03 .03 .05 .05 .31
[1] 5a0c.a .16 .28 .16 .15 .18 .19 .25 .12 .21 .14 .14 .13 .14
0
.11 .12 .12 .14 .38
[1] 5a8x.a .07 .22 .06 .07 .08 .10 .17 .01 .11 .07 .05 .05 .03 .11
0
.02 .05 .04 .32
[1] 5a8y.a .08 .21 .07 .08 .08 .09 .16 .02 .10 .09 .03 .04 .03 .12 .02
0
.05 .04 .32
[1] 5a8z.a .11 .25 .09 .07 .10 .11 .19 .05 .13 .08 .05 .05 .05 .12 .05 .05
0
.07 .31
[1] 5abw.a .10 .24 .08 .10 .10 .11 .18 .04 .08 .09 .06 .06 .05 .14 .04 .04 .07
0
.32
[2] 2rg3.a .37 .47 .34 .33 .34 .36 .45 .32 .39 .30 .32 .30 .31 .38 .32 .32 .31 .32
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1b0f.a
1h1b.a
1hne.e
1ppf.e
1ppg.e
2z7f.e
3q76.b
3q77.a
4nzl.a
4wvp.e
5a09.a
5a0a.e
5a0b.a
5a0c.a
5a8x.a
5a8y.a
5a8z.a
5abw.a
2rg3.a
[1] 1b0f.a
0
0.5 0.6 0.5 0.5 0.4 0.8 0.6 0.5 0.7 0.7 0.7 0.5 0.8 0.6 0.6 0.7 0.5 0.4
[1] 1h1b.a 0.5
0
0.7 0.7 0.6 0.5 0.7 0.8 0.6 0.9 0.9 0.9 0.7 1.0 0.8 0.8 0.9 0.7 0.6
[1] 1hne.e 0.6 0.7
0
0.6 0.5 0.7 0.8 0.6 0.7 0.7 0.7 0.7 0.6 0.9 0.6 0.6 0.7 0.5 0.5
[1] 1ppf.e 0.5 0.7 0.6
0
0.4 0.6 0.8 0.4 0.5 0.4 0.5 0.5 0.4 0.7 0.4 0.5 0.5 0.4 0.4
[1] 1ppg.e 0.5 0.6 0.5 0.4
0
0.6 0.8 0.4 0.5 0.5 0.5 0.6 0.4 0.8 0.5 0.5 0.6 0.4 0.4
[1] 2z7f.e 0.4 0.5 0.7 0.6 0.6
0
0.7 0.7 0.5 0.8 0.7 0.8 0.6 0.9 0.7 0.7 0.8 0.6 0.6
[1] 3q76.b 0.8 0.7 0.8 0.8 0.8 0.7
0
1.0 0.8 0.9 1.0 1.1 0.9 1.1 0.9 1.0 1.0 0.9 0.8
[1] 3q77.a 0.6 0.8 0.6 0.4 0.4 0.7 1.0
0
0.7 0.5 0.3 0.2 0.3 0.5 0.3 0.2 0.3 0.3 0.4
[1] 4nzl.a 0.5 0.6 0.7 0.5 0.5 0.5 0.8 0.7
0
0.6 0.7 0.8 0.6 1.0 0.7 0.7 0.8 0.5 0.6
[1] 4wvp.e 0.7 0.9 0.7 0.4 0.5 0.8 0.9 0.5 0.6
0
0.5 0.6 0.5 0.7 0.4 0.5 0.6 0.5 0.6
[1] 5a09.a 0.7 0.9 0.7 0.5 0.5 0.7 1.0 0.3 0.7 0.5
0
0.4 0.3 0.4 0.3 0.3 0.2 0.4 0.5
[1] 5a0a.e 0.7 0.9 0.7 0.5 0.6 0.8 1.1 0.2 0.8 0.6 0.4
0
0.4 0.6 0.4 0.3 0.3 0.4 0.6
[1] 5a0b.a 0.5 0.7 0.6 0.4 0.4 0.6 0.9 0.3 0.6 0.5 0.3 0.4
0
0.5 0.3 0.3 0.3 0.4 0.5
[1] 5a0c.a 0.8 1.0 0.9 0.7 0.8 0.9 1.1 0.5 1.0 0.7 0.4 0.6 0.5
0
0.5 0.5 0.4 0.7 0.8
[1] 5a8x.a 0.6 0.8 0.6 0.4 0.5 0.7 0.9 0.3 0.7 0.4 0.3 0.4 0.3 0.5
0
0.3 0.3 0.4 0.5
[1] 5a8y.a 0.6 0.8 0.6 0.5 0.5 0.7 1.0 0.2 0.7 0.5 0.3 0.3 0.3 0.5 0.3
0
0.3 0.3 0.5
[1] 5a8z.a 0.7 0.9 0.7 0.5 0.6 0.8 1.0 0.3 0.8 0.6 0.2 0.3 0.3 0.4 0.3 0.3
0
0.5 0.6
[1] 5abw.a 0.5 0.7 0.5 0.4 0.4 0.6 0.9 0.3 0.5 0.5 0.4 0.4 0.4 0.7 0.4 0.3 0.5
0
0.4
[2] 2rg3.a 0.4 0.6 0.5 0.4 0.4 0.6 0.8 0.4 0.6 0.6 0.5 0.6 0.5 0.8 0.5 0.5 0.6 0.4
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
1b0f.a
1h1b.a
1hne.e
1ppf.e
1ppg.e
2z7f.e
3q76.b
3q77.a
4nzl.a
4wvp.e
5a09.a
5a0a.e
5a0b.a
5a0c.a
5a8x.a
5a8y.a
5a8z.a
5abw.a
2rg3.a
[1] 1b0f.a
0
1.5 1.1 1.0 0.8 1.0 1.2 1.2 1.1 1.1 1.1 1.1 1.0 1.2 1.1 1.1 1.1 1.0 1.0
[1] 1h1b.a 1.5
0
1.5 1.6 1.4 1.4 1.4 1.5 1.6 1.6 1.6 1.6 1.5 1.8 1.6 1.5 1.6 1.5 1.4
[1] 1hne.e 1.1 1.5
0
0.9 0.8 0.8 1.1 0.8 1.1 0.9 1.0 1.0 1.0 1.4 1.0 0.9 1.0 0.9 0.9
[1] 1ppf.e 1.0 1.6 0.9
0
0.7 1.0 1.2 1.0 0.8 0.8 0.8 0.9 1.0 1.3 0.7 0.8 0.8 0.7 0.9
[1] 1ppg.e 0.8 1.4 0.8 0.7
0
0.9 1.1 0.9 0.9 0.7 0.8 0.8 0.8 1.3 0.8 0.7 0.8 0.7 0.7
[1] 2z7f.e 1.0 1.4 0.8 1.0 0.9
0
0.9 1.0 1.0 1.1 1.1 1.2 1.1 1.4 1.1 1.1 1.1 1.0 1.1
[1] 3q76.b 1.2 1.4 1.1 1.2 1.1 0.9
0
1.2 1.3 1.3 1.3 1.4 1.2 1.6 1.3 1.4 1.4 1.2 1.2
[1] 3q77.a 1.2 1.5 0.8 1.0 0.9 1.0 1.2
0
1.2 0.9 0.7 0.6 0.7 1.1 0.7 0.7 0.7 0.8 1.0
[1] 4nzl.a 1.1 1.6 1.1 0.8 0.9 1.0 1.3 1.2
0
0.9 1.1 1.1 1.2 1.6 1.0 1.1 1.1 0.8 1.1
[1] 4wvp.e 1.1 1.6 0.9 0.8 0.7 1.1 1.3 0.9 0.9
0
0.8 0.8 0.9 1.3 0.7 0.8 0.8 0.8 0.9
[1] 5a09.a 1.1 1.6 1.0 0.8 0.8 1.1 1.3 0.7 1.1 0.8
0
0.4 0.7 1.0 0.5 0.5 0.3 0.6 0.9
[1] 5a0a.e 1.1 1.6 1.0 0.9 0.8 1.2 1.4 0.6 1.1 0.8 0.4
0
0.8 1.1 0.6 0.5 0.5 0.7 0.9
[1] 5a0b.a 1.0 1.5 1.0 1.0 0.8 1.1 1.2 0.7 1.2 0.9 0.7 0.8
0
1.2 0.7 0.6 0.7 0.8 1.0
[1] 5a0c.a 1.2 1.8 1.4 1.3 1.3 1.4 1.6 1.1 1.6 1.3 1.0 1.1 1.2
0
1.1 1.1 1.0 1.3 1.4
[1] 5a8x.a 1.1 1.6 1.0 0.7 0.8 1.1 1.3 0.7 1.0 0.7 0.5 0.6 0.7 1.1
0
0.5 0.5 0.5 0.9
[1] 5a8y.a 1.1 1.5 0.9 0.8 0.7 1.1 1.4 0.7 1.1 0.8 0.5 0.5 0.6 1.1 0.5
0
0.4 0.6 0.9
[1] 5a8z.a 1.1 1.6 1.0 0.8 0.8 1.1 1.4 0.7 1.1 0.8 0.3 0.5 0.7 1.0 0.5 0.4
0
0.7 1.0
[1] 5abw.a 1.0 1.5 0.9 0.7 0.7 1.0 1.2 0.8 0.8 0.8 0.6 0.7 0.8 1.3 0.5 0.6 0.7
0
0.8
[2] 2rg3.a 1.0 1.4 0.9 0.9 0.7 1.1 1.2 1.0 1.1 0.9 0.9 0.9 1.0 1.4 0.9 0.9 1.0 0.8
0
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