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PLMN_HUMAN_266_341

Plasminogen [Peptidase S1 family. Plasminogen subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PLMN_HUMAN):D: Kringle 3 (307, 309, 330, 334, 336, 343, 344)307, 309, 330, 334, 336, 343, 344
Metals (Me):K

Full PDB list

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

Pocket contact map

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PDB.ch
   
ligand
A1 Me
R
3
0
9
K
3
3
0
W
3
3
4
H
3
3
6
R
3
4
3
W
3
4
4
[1]1ki0.a bcn11 . . . . . .
[1]4dur.a none . . . . . . K

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 Me
H
3
0
7
R
3
0
9
K
3
3
0
W
3
3
4
H
3
3
6
R
3
4
3
W
3
4
4
[1]1ki0.a . . . . . . .
[1]4dur.a . . . . . . . K

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
1ki0.a:bcn
4dur.a is apo
[1] 1ki0.a
0.2
-
[1] 4dur.a 0.1
-
[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
1ki0.a
4dur.a
[1] 1ki0.a
0
.03
[1] 4dur.a .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1ki0.a
4dur.a
[1] 1ki0.a
0
0.3
[1] 4dur.a 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1ki0.a
4dur.a
[1] 1ki0.a
0
0.7
[1] 4dur.a 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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