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KLKB1_HUMAN_388_632

Plasma kallikrein [Peptidase S1 family. Plasma kallikrein subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (KLKB1_HUMAN):D: Peptidase S1 (410, 412, 414:419, 434, 435, 437:439, 475, 477:480, 483, 524, 531, 555:557, 561, 572:576, 578, 596:602, 609)410, 412, 414:419, 434, 435, 437:439, 475, 477:480, 483, 524, 531, 555:557, 561, 572:576, 578, 596:602, 609

Full PDB list

2anw, 2any, 4ogx, 4ogy, 5f8t, 5f8x, 5f8z, 5tjx, 5tz9 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
4
1
0
L
4
1
2
A
4
1
4
Q
4
1
5
R
4
1
6
H
4
1
7
L
4
1
8
C
4
1
9
H
4
3
4
C
4
3
5
D
4
3
7
G
4
3
8
L
4
3
9
V
4
7
7
S
4
7
8
E
4
7
9
G
4
8
0
D
4
8
3
F
5
2
4
Y
5
5
5
I
5
5
7
M
5
6
1
D
5
7
2
A
5
7
3
C
5
7
4
K
5
7
5
G
5
7
6
S
5
7
8
T
5
9
6
S
5
9
7
W
5
9
8
G
5
9
9
E
6
0
0
G
6
0
1
C
6
0
2
G
6
0
9
[1]2anw.a bam9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ogx.a FTF-RIGVPRR,Y100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ogy.a V-FTFS-RIGVPRR,Y113 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ogy.b RIGVPRRD67 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5f8t.a CPKRFAALFC,mrz88 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5f8x.a CPARFAALWC,mrz87 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5f8z.a CPARFAALFC,mrz84 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5tjx.a gbt39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5tz9.e 7sd31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
V
4
1
0
L
4
1
2
A
4
1
4
Q
4
1
5
R
4
1
6
H
4
1
7
L
4
1
8
C
4
1
9
H
4
3
4
C
4
3
5
D
4
3
7
G
4
3
8
L
4
3
9
Y
4
7
5
V
4
7
7
S
4
7
8
E
4
7
9
G
4
8
0
D
4
8
3
F
5
2
4
I
5
3
1
Y
5
5
5
K
5
5
6
I
5
5
7
M
5
6
1
D
5
7
2
A
5
7
3
C
5
7
4
K
5
7
5
G
5
7
6
S
5
7
8
T
5
9
6
S
5
9
7
W
5
9
8
G
5
9
9
E
6
0
0
G
6
0
1
C
6
0
2
G
6
0
9
[1]2anw.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . * . . . . .
[1]4ogx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]4ogy.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]4ogy.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5f8t.a . . . . * . . . . . . . . . . . . . . . . . . . . . . . * . . . . * . . . . .
[1]5f8x.a . . . . * . . . . . . . . . . . . . . . . . . . . . . . * . . . . * . . . . .
[1]5f8z.a . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]5tjx.a . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . * . . . . .
[1]5tz9.e . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .

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
2anw.a:bam
4ogx.a:FTF-RIGVPRR,Y
4ogy.a:V-FTFS-RIGVPRR,Y
4ogy.b:RIGVPRRD
5f8t.a:CPKRFAALFC,mrz
5f8x.a:CPARFAALWC,mrz
5f8z.a:CPARFAALFC,mrz
5tjx.a:gbt
5tz9.e:7sd
[1] 2anw.a
0
1.7 2.4 1.8 1.6 1.7 1.7 2.6 2.5
[1] 4ogx.a 0.1
0.1
0.2 0.2 1.0 1.2 1.1 3.3 2.8
[1] 4ogy.a 0 0.1
0.1
0.1 1.6 1.5 1.5 2.8 2.6
[1] 4ogy.b 0 0.2 0.3
0
1.2 1.3 0.9 2.7 2.5
[1] 5f8t.a 0 3.6 4.1 1.5
0.1
0.9 0.1 2.1 1.9
[1] 5f8x.a 0 3.7 5.0 1.5 0
0
0 2.4 2.2
[1] 5f8z.a 0 3.0 4.5 1.2 0 0
0
1.8 1.8
[1] 5tjx.a 0.1 5.6 5.2 3.8 4.7 4.9 4.6
0
0
[1] 5tz9.e 0.1 5.2 4.5 4.5 3.2 3.8 3.3 0
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
2anw.a
4ogx.a
4ogy.a
4ogy.b
5f8t.a
5f8x.a
5f8z.a
5tjx.a
5tz9.e
[1] 2anw.a
0
.10 .08 .08 .15 .14 .15 .13 .12
[1] 4ogx.a .10
0
.04 .04 .18 .20 .18 .13 .08
[1] 4ogy.a .08 .04
0
.03 .15 .17 .16 .11 .09
[1] 4ogy.b .08 .04 .03
0
.16 .17 .16 .10 .10
[1] 5f8t.a .15 .18 .15 .16
0
.03 .03 .16 .14
[1] 5f8x.a .14 .20 .17 .17 .03
0
.02 .17 .16
[1] 5f8z.a .15 .18 .16 .16 .03 .02
0
.15 .14
[1] 5tjx.a .13 .13 .11 .10 .16 .17 .15
0
.07
[1] 5tz9.e .12 .08 .09 .10 .14 .16 .14 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 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
2anw.a
4ogx.a
4ogy.a
4ogy.b
5f8t.a
5f8x.a
5f8z.a
5tjx.a
5tz9.e
[1] 2anw.a
0
0.7 0.7 0.6 1.0 1.0 1.1 0.8 0.7
[1] 4ogx.a 0.7
0
0.3 0.5 1.1 1.1 1.1 1.0 0.9
[1] 4ogy.a 0.7 0.3
0
0.4 1.0 1.1 1.1 0.9 0.8
[1] 4ogy.b 0.6 0.5 0.4
0
0.9 0.9 0.9 0.8 0.7
[1] 5f8t.a 1.0 1.1 1.0 0.9
0
0.5 0.5 1.0 1.0
[1] 5f8x.a 1.0 1.1 1.1 0.9 0.5
0
0.1 1.0 1.1
[1] 5f8z.a 1.1 1.1 1.1 0.9 0.5 0.1
0
1.0 1.1
[1] 5tjx.a 0.8 1.0 0.9 0.8 1.0 1.0 1.0
0
0.4
[1] 5tz9.e 0.7 0.9 0.8 0.7 1.0 1.1 1.1 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
2anw.a
4ogx.a
4ogy.a
4ogy.b
5f8t.a
5f8x.a
5f8z.a
5tjx.a
5tz9.e
[1] 2anw.a
0
1.2 1.4 1.3 1.6 1.6 1.6 1.8 1.6
[1] 4ogx.a 1.2
0
0.7 0.7 1.8 1.6 1.6 1.6 1.6
[1] 4ogy.a 1.4 0.7
0
0.6 1.6 1.6 1.6 1.4 1.5
[1] 4ogy.b 1.3 0.7 0.6
0
1.5 1.2 1.3 1.4 1.5
[1] 5f8t.a 1.6 1.8 1.6 1.5
0
1.2 1.1 1.7 1.6
[1] 5f8x.a 1.6 1.6 1.6 1.2 1.2
0
0.5 1.8 1.8
[1] 5f8z.a 1.6 1.6 1.6 1.3 1.1 0.5
0
1.8 1.7
[1] 5tjx.a 1.8 1.6 1.4 1.4 1.7 1.8 1.8
0
0.8
[1] 5tz9.e 1.6 1.6 1.5 1.5 1.6 1.8 1.7 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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