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ALBU_HORSE_25_607

Serum albumin [ALB/AFP/VDB family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ALBU_HORSE):D: Albumin 2 (229, 232, 233, 235, 236, 239, 251, 255, 259, 346:348, 350, 351, 354, 370, 373, 374, 377)
D: Albumin 3 (503:505)
229, 232, 233, 235, 236, 239, 251, 255, 259, 346:348, 350, 351, 354, 370, 373, 374, 377, 503:505

Full PDB list

3v08, 4f5t, 4f5u, 4j2v, 4ot2, 4zbq, 4zbr, 5dby, 5dqf, 5hoz, 5id9, 5iih, 5iiu, 5iix, 5ij5, 5ije, 5v0v (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
2
9
R
2
3
2
A
2
3
3
K
2
3
5
A
2
3
6
V
2
3
9
F
2
5
1
S
2
5
5
T
2
5
9
D
3
4
7
L
3
5
0
G
3
5
1
L
3
5
4
L
3
7
0
A
3
7
3
K
3
7
4
E
3
7
7
S
5
0
3
L
5
0
4
A
5
0
5
[1]4f5u.a none . . . . . . . . . . . . . . . . . . . .
[1]4j2v.a mli7 . . . . . . . . . . . . . . . . . . . .
[1]4ot2.a nps17 . . . . . . . . . . . . . . . . . . . .
[1]4zbr.a mli,nps24 . . . . . . . . . . . . . . . . . . . .
[1]5dqf.a cze27 . . . . . . . . . . . . . . . . . . . .
[1]5id9.a 6a424 . . . . . . . . . . . . . . . . . . . .
[1]5v0v.a 8qp,8qs42 . . . . . . . . . . . . . . . . . . . .

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
2
2
9
R
2
3
2
A
2
3
3
K
2
3
5
A
2
3
6
V
2
3
9
F
2
5
1
S
2
5
5
T
2
5
9
K
3
4
6
D
3
4
7
V
3
4
8
L
3
5
0
G
3
5
1
L
3
5
4
L
3
7
0
A
3
7
3
K
3
7
4
E
3
7
7
S
5
0
3
L
5
0
4
A
5
0
5
[1]4f5u.a . . . . . . . . . . . . . . . . . * . . . .
[1]4j2v.a . . . . . . . . . . . . . . . . . * . * . .
[1]4ot2.a . * . . . . . . . . . . . . . . . . . . . .
[1]4zbr.a . * . . . . . . . . . . . . . . . . . . . .
[1]5dqf.a . . . . . . . . . . . . . . . . . . . . . .
[1]5id9.a . * . . . . . . . . . . . . . . . . . . . .
[1]5v0v.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
4f5u.a is apo
4j2v.a:mli
4ot2.a:nps
4zbr.a:mli,nps
5dqf.a:cze
5id9.a:6a4
5v0v.a:8qp,8qs
[1] 4f5u.a
-
0 0 0 0.6 0.6 1.3
[1] 4j2v.a -
0
0.3 0.7 0.2 0.7 2.7
[1] 4ot2.a - 0
0.1
0 0.7 0.1 1.7
[1] 4zbr.a - 0 0.2
0
1.0 0.1 1.1
[1] 5dqf.a - 0 0 0.4
0
0.3 1.8
[1] 5id9.a - 0 0.2 0 1.2
0
1.6
[1] 5v0v.a - 0 0 0 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
4f5u.a
4j2v.a
4ot2.a
4zbr.a
5dqf.a
5id9.a
5v0v.a
[1] 4f5u.a
0
.06 .10 .11 .08 .14 .10
[1] 4j2v.a .06
0
.15 .15 .13 .17 .16
[1] 4ot2.a .10 .15
0
.01 .02 .04 .08
[1] 4zbr.a .11 .15 .01
0
.03 .05 .07
[1] 5dqf.a .08 .13 .02 .03
0
.05 .09
[1] 5id9.a .14 .17 .04 .05 .05
0
.10
[1] 5v0v.a .10 .16 .08 .07 .09 .10
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

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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
4f5u.a
4j2v.a
4ot2.a
4zbr.a
5dqf.a
5id9.a
5v0v.a
[1] 4f5u.a
0
0.3 0.5 0.5 0.5 0.7 0.6
[1] 4j2v.a 0.3
0
0.6 0.5 0.6 0.7 0.7
[1] 4ot2.a 0.5 0.6
0
0.2 0.3 0.5 0.3
[1] 4zbr.a 0.5 0.5 0.2
0
0.2 0.5 0.3
[1] 5dqf.a 0.5 0.6 0.3 0.2
0
0.6 0.3
[1] 5id9.a 0.7 0.7 0.5 0.5 0.6
0
0.6
[1] 5v0v.a 0.6 0.7 0.3 0.3 0.3 0.6
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
4f5u.a
4j2v.a
4ot2.a
4zbr.a
5dqf.a
5id9.a
5v0v.a
[1] 4f5u.a
0
1.4 1.7 1.6 1.5 1.8 1.5
[1] 4j2v.a 1.4
0
1.2 1.2 1.3 1.3 1.0
[1] 4ot2.a 1.7 1.2
0
0.5 0.7 0.7 0.8
[1] 4zbr.a 1.6 1.2 0.5
0
0.7 0.8 0.9
[1] 5dqf.a 1.5 1.3 0.7 0.7
0
1.0 1.0
[1] 5id9.a 1.8 1.3 0.7 0.8 1.0
0
1.0
[1] 5v0v.a 1.5 1.0 0.8 0.9 1.0 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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