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FA9_HUMAN_131_461

Coagulation factor IX [Peptidase S1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (FA9_HUMAN):D: Peptidase S1 (252, 267, 268, 310:312, 358, 361, 362, 387, 388, 405:411, 429:435, 442)252, 267, 268, 310:312, 358, 361, 362, 387, 388, 405:411, 429:435, 442

Full PDB list

1rfn, 2wph, 2wpi, 2wpj, 2wpk, 2wpl, 2wpm, 3kcg, 3lc3, 3lc5, 4yzu, 4z0k, 4zae, 5egm, 5jb8, 5jb9, 5jba, 5jbb, 5jbc, 5tno, 5tnt (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
2
6
7
N
3
1
0
K
3
1
1
Y
3
1
2
R
3
5
8
H
3
6
1
F
3
8
8
D
4
0
5
S
4
0
6
C
4
0
7
Q
4
0
8
G
4
0
9
D
4
1
0
S
4
1
1
I
4
2
9
S
4
3
0
W
4
3
1
G
4
3
2
E
4
3
3
E
4
3
4
C
4
3
5
G
4
4
2
[1]1rfn.b pbz10 . . . . . . . . . . . . . . . . . . . . . .
[1]2wpk.e dpnPR30 . . T . . . . . . . . . . . . . . . . . . .
[1]2wpm.e EGR22 . . T . . . . . . . . . . . . . . . . . . .
[1]3kcg.l VIAGR35 . . . . . . . . . . . . . A . . . . . . . .
[1]3lc3.b iyx,iyx44 . . . . . . . . . . . . . . . . . . . . . .
[1]3lc5.b izx31 . . . . . . . . . . . . . . . . . . . . . .
[1]4yzu.b 4k627 . . . . . . . . . . . . . . . . . . . . . .
[1]4z0k.b 4ln30 . . . . . . . . . . . . . . . . . . . . . .
[1]4zae.b 4m135 . . . . . . . . . . . . . . . . . . . . . .
[1]5egm.b 5ny40 . . . . . . . . . . . . . . . . . . . . . .
[1]5jb8.e 0gj25 * . T . . . . . . . . . . * . . . . . . . .
[1]5jb9.e 0g630 * . T . . . . . . . . . . * . . . . . . . .
[1]5jbb.e 0gj25 * . T . . . . . . . . . . * V . . . . . . .
[1]5jbc.e 0g630 * . T . . . . . . . . . . * V . . . . . . .
[1]5tno.b unl30 . . . . . . . . . . . . . . . . . . . . . .
[1]5tnt.b 7gq34 . . . . . . . . . . . . . . . . . . . . . .

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
C
2
5
2
H
2
6
7
C
2
6
8
N
3
1
0
K
3
1
1
Y
3
1
2
R
3
5
8
H
3
6
1
K
3
6
2
K
3
8
7
F
3
8
8
D
4
0
5
S
4
0
6
C
4
0
7
Q
4
0
8
G
4
0
9
D
4
1
0
S
4
1
1
I
4
2
9
S
4
3
0
W
4
3
1
G
4
3
2
E
4
3
3
E
4
3
4
C
4
3
5
G
4
4
2
[1]1rfn.b . . . . . * . . . . . . . . * . . * . . . . . . . .
[1]2wpk.e . * . . T * * . . . . . . . * . . * . . . . . . . .
[1]2wpm.e . * . . T * . . . . . . . . * . . * . . . . . * . .
[1]3kcg.l . . . . . * . . . . . . . . * . . A . . . . . * . .
[1]3lc3.b . . . . . * . . . . . . . . . . . * . . . . . . . .
[1]3lc5.b . . . . . * . . - . . . . . . . . * . . . . . . . .
[1]4yzu.b . . . . . * . . . . . . . . . . . * . . . . . . . .
[1]4z0k.b . . . . . * . . . . . . . . . . . * . . . . . . . .
[1]4zae.b . . . . . * . . . . . . . . . . . * . . . . . . . .
[1]5egm.b . . . . . * . . . . . . . . . . . * . . . . . . . .
[1]5jb8.e . * . . T * . . . . . . . . * . . * . . . . . * . .
[1]5jb9.e . * . . T * . . . . * . . . . . . * . . . . . . . .
[1]5jbb.e . * . . T * * . . . . . . . * . . * V . . . . . . .
[1]5jbc.e . * . . T . . . . . . . . . * . . * V . . . . . . .
[1]5tno.b . . . . . * . . . . . . . . . . . * . . . . . . . .
[1]5tnt.b . . . . . * . . . . . . . . . . . * . . . . * . . .

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
1rfn.b:pbz
2wpk.e:dpnPR
2wpm.e:EGR
3kcg.l:VIAGR
3lc3.b:iyx
3lc5.b:izx
4yzu.b:4k6
4z0k.b:4ln
4zae.b:4m1
5egm.b:5ny
5jb8.e:0gj
5jb9.e:0g6
5jbb.e:0gj
5jbc.e:0g6
5tno.b:unl
5tnt.b:7gq
[1] 1rfn.b
0
2.6 1.8 1.6 1.8 2.0 0.4 1.0 1.8 0.6 1.8 2.7 1.8 2.5 1.1 1.0
[1] 2wpk.e 0.1
1.1
1.5 0.8 2.8 2.0 1.2 1.7 2.8 1.8 1.3 1.4 1.3 1.1 2.4 1.8
[1] 2wpm.e 0.2 1.9
1.3
0.9 2.5 2.0 1.1 1.8 1.7 1.4 0.9 2.1 0.9 2.0 1.6 1.5
[1] 3kcg.l 0.2 1.9 0.9
0
1.9 1.9 0.9 1.5 1.5 1.2 1.0 2.1 1.1 2.0 1.6 1.7
[1] 3lc3.b 0 2.5 1.5 1.8
0
1.3 0.1 0.1 0.2 0.1 1.4 2.8 1.4 2.5 0.1 0.2
[1] 3lc5.b 0.1 2.5 2.0 0.8 1.1
0
0.1 0.6 0.7 0.3 2.1 3.0 2.1 2.7 0.8 0.7
[1] 4yzu.b 0 2.6 1.5 2.1 1.7 1.7
0
0.2 0.3 0.1 1.6 3.3 1.6 2.6 0.1 0.1
[1] 4z0k.b 0 3.2 1.7 2.1 1.7 1.4 0
0
0.2 0.4 1.9 3.4 1.9 3.3 0.4 0.1
[1] 4zae.b 0 3.0 1.4 2.0 1.0 1.2 0 0.2
0
0 1.6 3.2 1.6 3.2 0.1 0.1
[1] 5egm.b 0.4 2.8 1.6 2.5 1.0 1.6 0.2 0.3 0.4
0
1.9 3.8 2.0 3.6 0.3 0.3
[1] 5jb8.e 0.2 1.9 1.5 0.7 2.3 2.0 1.5 1.8 2.0 1.6
1.5
2.4 1.3 1.8 1.9 1.9
[1] 5jb9.e 0.1 1.3 1.5 2.2 3.4 1.3 1.8 2.1 2.3 2.0 1.4
1.5
1.4 1.3 2.4 2.0
[1] 5jbb.e 0.2 1.9 1.5 0.7 2.1 2.1 1.3 1.4 2.3 1.5 1.5 2.4
1.5
2.0 1.8 1.9
[1] 5jbc.e 0 1.4 1.5 0.7 2.5 2.0 1.5 1.9 2.0 1.4 1.6 1.5 1.5
1.5
1.9 2.0
[1] 5tno.b 0.1 3.3 1.7 1.9 1.3 1.9 0.1 0.2 0.2 0.1 1.8 3.4 1.8 3.5
0
0
[1] 5tnt.b 0.2 2.6 1.6 2.3 1.7 2.0 0.1 0.1 0.2 0.3 1.9 3.5 1.9 3.0 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
1rfn.b
2wpk.e
2wpm.e
3kcg.l
3lc3.b
3lc5.b
4yzu.b
4z0k.b
4zae.b
5egm.b
5jb8.e
5jb9.e
5jbb.e
5jbc.e
5tno.b
5tnt.b
[1] 1rfn.b
0
.10 .07 .10 .12 .12 .15 .15 .13 .16 .09 .17 .10 .10 .15 .15
[1] 2wpk.e .10
0
.07 .12 .18 .16 .22 .22 .21 .24 .06 .16 .05 .05 .22 .22
[1] 2wpm.e .07 .07
0
.10 .13 .14 .18 .18 .17 .20 .06 .16 .07 .08 .19 .19
[1] 3kcg.l .10 .12 .10
0
.18 .13 .22 .22 .20 .24 .10 .21 .12 .12 .22 .22
[1] 3lc3.b .12 .18 .13 .18
0
.11 .09 .07 .07 .08 .16 .13 .17 .17 .08 .08
[1] 3lc5.b .12 .16 .14 .13 .11
0
.14 .13 .12 .13 .17 .13 .17 .16 .12 .14
[1] 4yzu.b .15 .22 .18 .22 .09 .14
0
.05 .04 .07 .22 .15 .22 .23 .07 .05
[1] 4z0k.b .15 .22 .18 .22 .07 .13 .05
0
.04 .04 .21 .11 .22 .22 .04 .03
[1] 4zae.b .13 .21 .17 .20 .07 .12 .04 .04
0
.05 .20 .12 .21 .21 .08 .05
[1] 5egm.b .16 .24 .20 .24 .08 .13 .07 .04 .05
0
.24 .14 .25 .25 .05 .05
[1] 5jb8.e .09 .06 .06 .10 .16 .17 .22 .21 .20 .24
0
.15 .03 .03 .22 .22
[1] 5jb9.e .17 .16 .16 .21 .13 .13 .15 .11 .12 .14 .15
0
.16 .16 .15 .13
[1] 5jbb.e .10 .05 .07 .12 .17 .17 .22 .22 .21 .25 .03 .16
0
.03 .22 .22
[1] 5jbc.e .10 .05 .08 .12 .17 .16 .23 .22 .21 .25 .03 .16 .03
0
.23 .23
[1] 5tno.b .15 .22 .19 .22 .08 .12 .07 .04 .08 .05 .22 .15 .22 .23
0
.04
[1] 5tnt.b .15 .22 .19 .22 .08 .14 .05 .03 .05 .05 .22 .13 .22 .23 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1rfn.b
2wpk.e
2wpm.e
3kcg.l
3lc3.b
3lc5.b
4yzu.b
4z0k.b
4zae.b
5egm.b
5jb8.e
5jb9.e
5jbb.e
5jbc.e
5tno.b
5tnt.b
[1] 1rfn.b
0
1.3 1.4 0.5 1.3 0.7 0.7 0.6 0.7 0.8 1.3 1.3 1.3 1.3 0.6 0.6
[1] 2wpk.e 1.3
0
0.8 1.1 0.6 1.1 1.4 1.3 1.5 1.5 0.2 0.3 0.2 0.2 1.4 1.4
[1] 2wpm.e 1.4 0.8
0
1.2 0.9 1.3 1.6 1.5 1.6 1.6 0.8 0.8 0.8 0.7 1.5 1.5
[1] 3kcg.l 0.5 1.1 1.2
0
1.2 0.5 0.8 0.6 0.8 0.9 1.2 1.2 1.1 1.1 0.7 0.8
[1] 3lc3.b 1.3 0.6 0.9 1.2
0
1.2 1.2 1.2 1.2 1.3 0.6 0.6 0.6 0.6 1.3 1.3
[1] 3lc5.b 0.7 1.1 1.3 0.5 1.2
0
1.0 0.8 1.0 1.0 1.1 1.2 1.1 1.1 0.9 0.9
[1] 4yzu.b 0.7 1.4 1.6 0.8 1.2 1.0
0
0.4 0.2 0.2 1.5 1.5 1.4 1.4 0.3 0.3
[1] 4z0k.b 0.6 1.3 1.5 0.6 1.2 0.8 0.4
0
0.5 0.5 1.4 1.4 1.3 1.3 0.3 0.3
[1] 4zae.b 0.7 1.5 1.6 0.8 1.2 1.0 0.2 0.5
0
0.2 1.5 1.5 1.5 1.5 0.3 0.3
[1] 5egm.b 0.8 1.5 1.6 0.9 1.3 1.0 0.2 0.5 0.2
0
1.5 1.6 1.5 1.5 0.4 0.4
[1] 5jb8.e 1.3 0.2 0.8 1.2 0.6 1.1 1.5 1.4 1.5 1.5
0
0.2 0.1 0.2 1.4 1.4
[1] 5jb9.e 1.3 0.3 0.8 1.2 0.6 1.2 1.5 1.4 1.5 1.6 0.2
0
0.2 0.2 1.5 1.5
[1] 5jbb.e 1.3 0.2 0.8 1.1 0.6 1.1 1.4 1.3 1.5 1.5 0.1 0.2
0
0.2 1.4 1.4
[1] 5jbc.e 1.3 0.2 0.7 1.1 0.6 1.1 1.4 1.3 1.5 1.5 0.2 0.2 0.2
0
1.4 1.4
[1] 5tno.b 0.6 1.4 1.5 0.7 1.3 0.9 0.3 0.3 0.3 0.4 1.4 1.5 1.4 1.4
0
0.2
[1] 5tnt.b 0.6 1.4 1.5 0.8 1.3 0.9 0.3 0.3 0.3 0.4 1.4 1.5 1.4 1.4 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1rfn.b
2wpk.e
2wpm.e
3kcg.l
3lc3.b
3lc5.b
4yzu.b
4z0k.b
4zae.b
5egm.b
5jb8.e
5jb9.e
5jbb.e
5jbc.e
5tno.b
5tnt.b
[1] 1rfn.b
0
1.6 1.8 0.8 2.2 1.1 1.0 0.9 1.0 1.1 1.6 1.7 1.6 1.6 1.0 1.0
[1] 2wpk.e 1.6
0
1.1 1.5 0.9 1.7 1.7 1.7 1.8 1.8 0.5 0.8 0.5 0.5 1.7 1.8
[1] 2wpm.e 1.8 1.1
0
1.8 1.4 1.9 2.0 1.9 2.0 2.1 1.2 1.4 1.3 1.2 2.0 2.0
[1] 3kcg.l 0.8 1.5 1.8
0
2.1 1.0 1.1 1.1 1.2 1.2 1.5 1.7 1.5 1.5 1.1 1.1
[1] 3lc3.b 2.2 0.9 1.4 2.1
0
1.7 2.2 2.3 2.2 2.2 0.9 1.1 1.0 1.0 2.3 2.3
[1] 3lc5.b 1.1 1.7 1.9 1.0 1.7
0
1.3 1.1 1.3 1.3 1.7 1.7 1.7 1.7 1.3 1.2
[1] 4yzu.b 1.0 1.7 2.0 1.1 2.2 1.3
0
0.9 0.3 0.5 1.8 1.8 1.7 1.8 0.7 0.7
[1] 4z0k.b 0.9 1.7 1.9 1.1 2.3 1.1 0.9
0
0.9 0.9 1.7 1.8 1.7 1.7 0.6 0.6
[1] 4zae.b 1.0 1.8 2.0 1.2 2.2 1.3 0.3 0.9
0
0.5 1.8 1.8 1.8 1.8 0.7 0.6
[1] 5egm.b 1.1 1.8 2.1 1.2 2.2 1.3 0.5 0.9 0.5
0
1.8 1.8 1.8 1.8 0.7 0.7
[1] 5jb8.e 1.6 0.5 1.2 1.5 0.9 1.7 1.8 1.7 1.8 1.8
0
0.8 0.4 0.6 1.7 1.7
[1] 5jb9.e 1.7 0.8 1.4 1.7 1.1 1.7 1.8 1.8 1.8 1.8 0.8
0
0.9 0.9 1.8 1.8
[1] 5jbb.e 1.6 0.5 1.3 1.5 1.0 1.7 1.7 1.7 1.8 1.8 0.4 0.9
0
0.6 1.7 1.7
[1] 5jbc.e 1.6 0.5 1.2 1.5 1.0 1.7 1.8 1.7 1.8 1.8 0.6 0.9 0.6
0
1.8 1.8
[1] 5tno.b 1.0 1.7 2.0 1.1 2.3 1.3 0.7 0.6 0.7 0.7 1.7 1.8 1.7 1.8
0
0.3
[1] 5tnt.b 1.0 1.8 2.0 1.1 2.3 1.2 0.7 0.6 0.6 0.7 1.7 1.8 1.7 1.8 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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