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ALBU_BOVIN_25_607

Serum albumin [ALB/AFP/VDB family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ALBU_BOVIN):D: Albumin 1 (173)
D: Albumin 2 (218, 221, 222, 225, 233, 234, 237, 238, 241, 242, 245, 246, 261, 265, 280, 283, 284, 287, 310, 313, 314, 367, 370)
D: Albumin 3 (474, 477, 478, 504)
173, 218, 221, 222, 225, 233, 234, 237, 238, 241, 242, 245, 246, 261, 265, 280, 283, 284, 287, 310, 313, 314, 367, 370, 474, 477, 478, 504

Full PDB list

3v03, 4f5s, 4jk4, 4luf, 4luh, 4or0 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
1
7
3
R
2
1
8
L
2
2
1
R
2
2
2
S
2
2
5
L
2
3
4
W
2
3
7
S
2
3
8
R
2
4
1
L
2
4
2
L
2
6
1
H
2
6
5
R
2
8
0
L
2
8
3
A
2
8
4
I
2
8
7
S
3
1
0
I
3
1
3
A
3
1
4
S
3
6
7
L
3
7
0
D
4
7
4
S
4
7
7
L
4
7
8
L
5
0
4
[1]4f5s.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4luf.a 2q517 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4luh.a diu,diu24 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4or0.a nps17 . . . . . . . . . . . . . . . . . . . . . . . . .

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
Y
1
7
3
R
2
1
8
L
2
2
1
R
2
2
2
S
2
2
5
A
2
3
3
L
2
3
4
W
2
3
7
S
2
3
8
R
2
4
1
L
2
4
2
K
2
4
5
F
2
4
6
L
2
6
1
H
2
6
5
R
2
8
0
L
2
8
3
A
2
8
4
I
2
8
7
S
3
1
0
I
3
1
3
A
3
1
4
S
3
6
7
L
3
7
0
D
4
7
4
S
4
7
7
L
4
7
8
L
5
0
4
[1]4f5s.a . . . . . . . * . * . . . . . . . . . . . . . . . . . .
[1]4luf.a . . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]4luh.a . . . . . . . . . * . . . . . . . . . . . . . . . . . .
[1]4or0.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
4f5s.a is apo
4luf.a:2q5
4luh.a:diu
4or0.a:nps
[1] 4f5s.a
-
4.6 2.8 0.3
[1] 4luf.a -
0.1
0.4 2.5
[1] 4luh.a - 1.9
0.3
2.0
[1] 4or0.a - 3.9 3.3
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
4f5s.a
4luf.a
4luh.a
4or0.a
[1] 4f5s.a
0
.11 .09 .06
[1] 4luf.a .11
0
.09 .08
[1] 4luh.a .09 .09
0
.14
[1] 4or0.a .06 .08 .14
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
4f5s.a
4luf.a
4luh.a
4or0.a
[1] 4f5s.a
0
0.8 0.8 0.4
[1] 4luf.a 0.8
0
0.1 1.1
[1] 4luh.a 0.8 0.1
0
1.1
[1] 4or0.a 0.4 1.1 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
4f5s.a
4luf.a
4luh.a
4or0.a
[1] 4f5s.a
0
1.6 1.6 0.8
[1] 4luf.a 1.6
0
0.7 1.8
[1] 4luh.a 1.6 0.7
0
1.9
[1] 4or0.a 0.8 1.8 1.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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