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AGAA_GEOSE_1_729

Alpha-galactosidase AgaA [Glycosyl hydrolase 36 family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (AGAA_GEOSE):R: Substrate binding (366, 367)
R: Substrate binding (476, 478, 480)
199, 336, 411, 443, 526, 528, 529, 545, 548
199, 336, 366, 367, 411, 443, 476, 478, 480, 526, 528, 529, 545, 548
A3 (AGAA_GEOSE):53, 55, 56, 6553, 55, 56, 65

Full PDB list

4fnp, 4fnq, 4fnr, 4fns, 4fnt (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A3
W
3
3
6
D
3
6
6
D
3
6
7
W
4
1
1
R
4
4
3
K
4
7
6
D
4
7
8
N
4
8
0
C
5
2
6
G
5
2
8
G
5
2
9
W
5
4
5
D
5
4
8
D
5
3
R
6
5
[1]4fnp.d none . . . . . . . . . . . . . . .
[1]4fns.a dgj11 . . . . . . . . . . . . . . .
[1]4fnt.a none . . . . . . . . . . . . N . .
[1]4fnt.c raf34 . . . . . . . . . . . . N . .

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 A3
W
1
9
9
W
3
3
6
D
3
6
6
D
3
6
7
W
4
1
1
R
4
4
3
K
4
7
6
D
4
7
8
N
4
8
0
C
5
2
6
G
5
2
8
G
5
2
9
W
5
4
5
D
5
4
8
D
5
3
A
5
5
F
5
6
R
6
5
[1]4fnp.d . . . . . . . . . . . . . . . . . .
[1]4fns.a . . . . . . . . . . . . . . . . . .
[1]4fnt.a . . . . . . . . . . . . . N . . . .
[1]4fnt.c . . . . . . . . . . . . . N . . . .

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
4fnp.d is apo
4fns.a:dgj
4fnt.a is apo
4fnt.c:raf
[1] 4fnp.d
-
0.2 - 0.1
[1] 4fns.a -
0.2
- 0
[1] 4fnt.a - 0.1
-
0.2
[1] 4fnt.c - 0.2 -
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
4fnp.d
4fns.a
4fnt.a
4fnt.c
[1] 4fnp.d
0
.01 .02 .01
[1] 4fns.a .01
0
.02 0
[1] 4fnt.a .02 .02
0
.02
[1] 4fnt.c .01 0 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
4fnp.d
4fns.a
4fnt.a
4fnt.c
[1] 4fnp.d
0
0.4 0.5 0.3
[1] 4fns.a 0.4
0
0.7 0.3
[1] 4fnt.a 0.5 0.7
0
0.7
[1] 4fnt.c 0.3 0.3 0.7
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
4fnp.d
4fns.a
4fnt.a
4fnt.c
[1] 4fnp.d
0
0.7 0.8 0.5
[1] 4fns.a 0.7
0
0.9 0.5
[1] 4fnt.a 0.8 0.9
0
1.0
[1] 4fnt.c 0.5 0.5 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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