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ATS4_HUMAN_213_440

A disintegrin and metalloproteinase with thrombospondin motifs 4

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ATS4_HUMAN):D: Peptidase M12B (248, 252, 326:332, 357, 358, 360:362, 365, 371, 389, 390, 392:396, 398:400, 403)248, 252, 326:332, 357, 358, 360:362, 365, 371, 389, 390, 392:396, 398:400, 403, 491
Metals (Me):Ca/Zn

Full PDB list

2rjp, 3b2z, 4wk7, 4wke, 4wki

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
A
2
5
2
T
3
2
9
L
3
3
0
G
3
3
1
M
3
3
2
F
3
5
7
T
3
5
8
A
3
6
0
H
3
6
1
E
3
6
2
H
3
6
5
H
3
7
1
V
3
9
0
A
3
9
2
P
3
9
3
V
3
9
4
M
3
9
5
V
3
9
8
[1]2rjp.d 88636 . . . . . . . . . Q . . . . . . . . Ca,Zn
[1]4wk7.a 3pq21 . . . . . . . . . . . . . . . . . . Ca,Zn
[1]4wke.a 3pu26 . . . . . . . . . . . . . . . . . . Ca,Zn
[1]4wki.a 3pw27 . . . . . . . . . . . . . . . . . . Ca,Zn
[2]3b2z.c none . . . . . . . . . Q . . . . . . . . Zn

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 Me
A
2
4
8
A
2
5
2
T
3
2
6
C
3
2
7
D
3
2
8
T
3
2
9
L
3
3
0
G
3
3
1
M
3
3
2
F
3
5
7
T
3
5
8
A
3
6
0
H
3
6
1
E
3
6
2
H
3
6
5
H
3
7
1
H
3
8
9
V
3
9
0
A
3
9
2
P
3
9
3
V
3
9
4
M
3
9
5
A
3
9
6
V
3
9
8
D
3
9
9
P
4
0
0
P
4
0
3
D
4
9
1
[1]2rjp.d . . . . . . . . . . . . . Q . . . . . . . . . . . . . . Ca,Zn
[1]4wk7.a . . . . . . . . . * . . . . . . . . . . . . . . . . . - Ca,Zn
[1]4wke.a . . . . . . . . . * . . . . . . . . . . . . . . . . . - Ca,Zn
[1]4wki.a . . . . . . . . . * . . . . . . . . . . . . . . . . . - Ca,Zn
[2]3b2z.c . . . * * * . . . * . . . Q . . . . . . . * . . . . . . Zn

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
2rjp.d:886
4wk7.a:3pq
4wke.a:3pu
4wki.a:3pw
3b2z.c is apo
[1] 2rjp.d
0
0.1 0.1 0.1 -
[1] 4wk7.a 1.7
0
0.2 0.1 -
[1] 4wke.a 1.9 0.1
0.1
0.1 -
[1] 4wki.a 1.7 0.1 0.1
0.1
-
[2] 3b2z.c 12 11 12 12
-
[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
2rjp.d
4wk7.a
4wke.a
4wki.a
3b2z.c
[1] 2rjp.d
0
.07 .07 .06 .49
[1] 4wk7.a .07
0
.01 .01 .45
[1] 4wke.a .07 .01
0
.01 .44
[1] 4wki.a .06 .01 .01
0
.45
[2] 3b2z.c .49 .45 .44 .45
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2rjp.d
4wk7.a
4wke.a
4wki.a
3b2z.c
[1] 2rjp.d
0
0.5 0.5 0.5 2.4
[1] 4wk7.a 0.5
0
0.1 0.2 2.4
[1] 4wke.a 0.5 0.1
0
0.1 2.3
[1] 4wki.a 0.5 0.2 0.1
0
2.3
[2] 3b2z.c 2.4 2.4 2.3 2.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
2rjp.d
4wk7.a
4wke.a
4wki.a
3b2z.c
[1] 2rjp.d
0
0.8 0.8 0.8 3.0
[1] 4wk7.a 0.8
0
0.4 0.5 2.9
[1] 4wke.a 0.8 0.4
0
0.3 2.9
[1] 4wki.a 0.8 0.5 0.3
0
2.9
[2] 3b2z.c 3.0 2.9 2.9 2.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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