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TPA_HUMAN_302_562

Tissue-type plasminogen activator [Peptidase S1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (TPA_HUMAN):D: Peptidase S1 (357, 358, 401:403, 454, 484, 507:513, 531:537, 544)357, 358, 401:403, 454, 484, 507:513, 531:537, 544

Full PDB list

1a5h, 1bda, 1rtf, 5brr

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
3
5
7
C
3
5
8
D
4
0
1
T
4
0
2
Y
4
0
3
R
4
8
4
D
5
0
7
A
5
0
8
C
5
0
9
Q
5
1
0
G
5
1
1
D
5
1
2
S
5
1
3
I
5
3
1
S
5
3
2
W
5
3
3
G
5
3
4
L
5
3
5
G
5
3
6
C
5
3
7
G
5
4
4
[1]1a5h.a bba28 . . . . . . . . . . . . . . . . . . . . .
[1]1bda.a 2z041 * . . . . . . . . . . . * . . . . . . . .
[1]1rtf.b ben9 . . . . . . . . . . . . . . . . . . . . .
[1]5brr.e VSAR29 . . . . . . . . . . . . A . . . . . . . .

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
H
3
5
7
C
3
5
8
D
4
0
1
T
4
0
2
Y
4
0
3
A
4
5
4
R
4
8
4
D
5
0
7
A
5
0
8
C
5
0
9
Q
5
1
0
G
5
1
1
D
5
1
2
S
5
1
3
I
5
3
1
S
5
3
2
W
5
3
3
G
5
3
4
L
5
3
5
G
5
3
6
C
5
3
7
G
5
4
4
[1]1a5h.a . . . . . . . . . . * . . * . . . . . . . .
[1]1bda.a * . . . * . * . . . * . . * . . . . . . . .
[1]1rtf.b * . . . . . * . . . * . . * . . . . . . . .
[1]5brr.e . . . . . . . . . . . . . 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
1a5h.a:bba
1bda.a:2z0
1rtf.b:ben
5brr.e:VSAR
[1] 1a5h.a
0
1.9 0.1 2.4
[1] 1bda.a 2.8
1.5
0.2 1.7
[1] 1rtf.b 2.7 1.6
0
1.8
[1] 5brr.e 0.8 1.4 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
1a5h.a
1bda.a
1rtf.b
5brr.e
[1] 1a5h.a
0
.13 .16 .13
[1] 1bda.a .13
0
.09 .17
[1] 1rtf.b .16 .09
0
.20
[1] 5brr.e .13 .17 .20
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
1a5h.a
1bda.a
1rtf.b
5brr.e
[1] 1a5h.a
0
0.4 0.3 0.6
[1] 1bda.a 0.4
0
0.4 0.6
[1] 1rtf.b 0.3 0.4
0
0.6
[1] 5brr.e 0.6 0.6 0.6
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

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
1a5h.a
1bda.a
1rtf.b
5brr.e
[1] 1a5h.a
0
1.1 1.2 0.9
[1] 1bda.a 1.1
0
0.8 1.3
[1] 1rtf.b 1.2 0.8
0
1.3
[1] 5brr.e 0.9 1.3 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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