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PLMN_HUMAN_101_183

Plasminogen [Peptidase S1 family. Plasminogen subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PLMN_HUMAN):D: Kringle 1 (136, 137, 156, 158, 163, 165, 172, 173)136, 137, 156, 158, 163, 165, 172, 173

Full PDB list

1cea, 1ceb, 1ki0, 1pkr, 2doh, 2doi, 4a5t, 4cik, 4dur (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
R
1
3
6
F
1
3
7
D
1
5
6
D
1
5
8
W
1
6
3
Y
1
6
5
R
1
7
2
Y
1
7
3
[1]1cea.a aca9 . . . . . . . .
[1]1ceb.a amh11 . . . . . . . .
[1]1ki0.a bcn11 . . . . . . . .
[1]2doh.x none . . . . . . . .
[1]4cik.a xo319 . . . . . . . .

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

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PDB.ch
A1
R
1
3
6
F
1
3
7
D
1
5
6
D
1
5
8
W
1
6
3
Y
1
6
5
R
1
7
2
Y
1
7
3
[1]1cea.a . . . . . . . .
[1]1ceb.a . . . . . . . .
[1]1ki0.a . . . . . . . .
[1]2doh.x . . . . . . . .
[1]4cik.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
1cea.a:aca
1ceb.a:amh
1ki0.a:bcn
2doh.x is apo
4cik.a:xo3
[1] 1cea.a
0.1
0.2 0 - 0.2
[1] 1ceb.a 0.2
0.2
0.1 - 0.2
[1] 1ki0.a 0.5 0.5
0.1
- 0.5
[1] 2doh.x 0.2 0.2 0.1
-
0.3
[1] 4cik.a 0.3 0.7 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
1cea.a
1ceb.a
1ki0.a
2doh.x
4cik.a
[1] 1cea.a
0
.04 .11 .06 .10
[1] 1ceb.a .04
0
.10 .05 .09
[1] 1ki0.a .11 .10
0
.08 .09
[1] 2doh.x .06 .05 .08
0
.09
[1] 4cik.a .10 .09 .09 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1cea.a
1ceb.a
1ki0.a
2doh.x
4cik.a
[1] 1cea.a
0
0.3 0.5 0.5 0.6
[1] 1ceb.a 0.3
0
0.7 0.6 0.7
[1] 1ki0.a 0.5 0.7
0
0.2 0.3
[1] 2doh.x 0.5 0.6 0.2
0
0.3
[1] 4cik.a 0.6 0.7 0.3 0.3
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
1cea.a
1ceb.a
1ki0.a
2doh.x
4cik.a
[1] 1cea.a
0
0.9 0.6 0.9 0.7
[1] 1ceb.a 0.9
0
1.3 1.2 1.4
[1] 1ki0.a 0.6 1.3
0
1.3 0.6
[1] 2doh.x 0.9 1.2 1.3
0
1.4
[1] 4cik.a 0.7 1.4 0.6 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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