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APOA_HUMAN_4123_4201

Apolipoprotein(a) [Peptidase S1 family. Plasminogen subfamily]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (APOA_HUMAN):D: Kringle 37 (4156:4158, 4163, 4177, 4179, 4183, 4185, 4192, 4193)4156:4158, 4163, 4177, 4179, 4183, 4185, 4192, 4193
A2 (APOA_HUMAN):D: Kringle 37 (4152)4152

Full PDB list

1kiv, 3kiv, 4bv5, 4bv7, 4bvc, 4bvd, 4kiv

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
4
1
5
6
Q
4
1
5
7
R
4
1
5
8
Y
4
1
6
3
D
4
1
7
7
D
4
1
7
9
W
4
1
8
3
F
4
1
8
5
R
4
1
9
2
W
4
1
9
3
[1]1kiv.a none . . . . . . . . . .
[1]3kiv.a aca9 . . . . . . . . . .
[1]4bv5.a 5c320 . . . . . . . . . .
[1]4bv7.a bv711 . . . . . . . . . .
[1]4bvc.a bv525 . . . . . . . . . .
[1]4bvd.a bu623 . . . . . . . . . .
[1]4kiv.a none . . . . . . . . . R

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 A2
H
4
1
5
6
Q
4
1
5
7
R
4
1
5
8
Y
4
1
6
3
D
4
1
7
7
D
4
1
7
9
W
4
1
8
3
F
4
1
8
5
R
4
1
9
2
W
4
1
9
3
T
4
1
5
2
[1]1kiv.a . . . . . . . . . . .
[1]3kiv.a . . . . . . . . . . .
[1]4bv5.a . . . . . . . . . . .
[1]4bv7.a . . . . . . . . . . .
[1]4bvc.a . . . . . . . . . . .
[1]4bvd.a . . . . . . . . . . .
[1]4kiv.a . . . . . . . . . R .

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
1kiv.a is apo
3kiv.a:aca
4bv5.a:5c3
4bv7.a:bv7
4bvc.a:bv5
4bvd.a:bu6
4kiv.a is apo
[1] 1kiv.a
-
0.3 0.3 0.3 0.5 0.4 -
[1] 3kiv.a -
0.2
0.3 0.2 0.9 0.8 -
[1] 4bv5.a - 0
0
0.2 1.1 0.4 -
[1] 4bv7.a - 0 0
0
0.1 0 -
[1] 4bvc.a - 0.4 0 0.1
0
0 -
[1] 4bvd.a - 0 0 0.1 0.1
0
-
[1] 4kiv.a - 1.5 0.9 1.4 1.1 1.3
-
[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
1kiv.a
3kiv.a
4bv5.a
4bv7.a
4bvc.a
4bvd.a
4kiv.a
[1] 1kiv.a
0
.10 .12 .04 .07 .04 .15
[1] 3kiv.a .10
0
.02 .08 .12 .08 .25
[1] 4bv5.a .12 .02
0
.10 .14 .10 .26
[1] 4bv7.a .04 .08 .10
0
.04 0 .16
[1] 4bvc.a .07 .12 .14 .04
0
.04 .13
[1] 4bvd.a .04 .08 .10 0 .04
0
.16
[1] 4kiv.a .15 .25 .26 .16 .13 .16
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
1kiv.a
3kiv.a
4bv5.a
4bv7.a
4bvc.a
4bvd.a
4kiv.a
[1] 1kiv.a
0
0.4 0.4 0.4 0.3 0.4 0.5
[1] 3kiv.a 0.4
0
0.3 0.3 0.3 0.4 0.4
[1] 4bv5.a 0.4 0.3
0
0.3 0.3 0.3 0.5
[1] 4bv7.a 0.4 0.3 0.3
0
0.3 0.2 0.6
[1] 4bvc.a 0.3 0.3 0.3 0.3
0
0.3 0.6
[1] 4bvd.a 0.4 0.4 0.3 0.2 0.3
0
0.6
[1] 4kiv.a 0.5 0.4 0.5 0.6 0.6 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1kiv.a
3kiv.a
4bv5.a
4bv7.a
4bvc.a
4bvd.a
4kiv.a
[1] 1kiv.a
0
1.1 1.3 0.8 1.1 0.8 0.7
[1] 3kiv.a 1.1
0
1.0 1.0 1.3 1.1 1.1
[1] 4bv5.a 1.3 1.0
0
1.1 1.0 1.0 1.3
[1] 4bv7.a 0.8 1.0 1.1
0
0.7 0.4 1.0
[1] 4bvc.a 1.1 1.3 1.0 0.7
0
0.7 1.2
[1] 4bvd.a 0.8 1.1 1.0 0.4 0.7
0
1.0
[1] 4kiv.a 0.7 1.1 1.3 1.0 1.2 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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