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PLMN_HUMAN_183_266

Plasminogen [Peptidase S1 family. Plasminogen subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PLMN_HUMAN):D: Kringle 2 (219, 238, 240, 244, 246, 253, 254)219, 238, 240, 244, 246, 253, 254, 725:728, 730, 731

Full PDB list

1i5k, 1ki0, 2doh, 2doi, 4a5t, 4dur (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
Y
2
1
9
D
2
3
8
E
2
4
0
W
2
4
4
F
2
4
6
R
2
5
3
W
2
5
4
[1]1i5k.a R11 . . D . . . .
[1]1ki0.a bcn11 . . . . . . .
[1]2doh.x R11 . . . . . . .
[2]4dur.a none . . . . . . .

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
Y
2
1
9
D
2
3
8
E
2
4
0
W
2
4
4
F
2
4
6
R
2
5
3
W
2
5
4
E
7
2
5
N
7
2
6
K
7
2
7
V
7
2
8
N
7
3
0
R
7
3
1
[1]1i5k.a . . D . . . . - - - - - -
[1]1ki0.a . . . . . . . - - - - - -
[1]2doh.x . . . . . . . - - - - - -
[2]4dur.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
1i5k.a:R
1ki0.a:bcn
2doh.x:R
4dur.a is apo
[1] 1i5k.a
0
0.3 0 -
[1] 1ki0.a 0.1
0.1
0.2 -
[1] 2doh.x 0 0
0
-
[2] 4dur.a 5.9 6.6 6.1
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1i5k.a
1ki0.a
2doh.x
4dur.a
[1] 1i5k.a
0
.03 .02 .58
[1] 1ki0.a .03
0
.02 .60
[1] 2doh.x .02 .02
0
.61
[2] 4dur.a .58 .60 .61
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
1i5k.a
1ki0.a
2doh.x
4dur.a
[1] 1i5k.a
0
0.6 0.4 0.6
[1] 1ki0.a 0.6
0
0.4 0.6
[1] 2doh.x 0.4 0.4
0
0.5
[2] 4dur.a 0.6 0.6 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1i5k.a
1ki0.a
2doh.x
4dur.a
[1] 1i5k.a
0
1.2 0.8 0.7
[1] 1ki0.a 1.2
0
1.4 1.4
[1] 2doh.x 0.8 1.4
0
1.0
[2] 4dur.a 0.7 1.4 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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