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BZNB_PSEFL_1_563

Benzaldehyde lyase [TPP enzyme family]

Composition of the binding site

Protein chains homodimer
A1 (BZNB_PSEFL):393:397, 419:421, 447:450, 453, 475, 477:481393:397, 419:421, 447:450, 453, 475, 477:481
A2 (BZNB_PSEFL):25:29, 50, 73, 76, 77, 80, 112, 11325:29, 50, 73, 76, 77, 80, 112, 113
Metals (Me):Ca/Mg

Full PDB list

2ag0, 2ag1, 2uz1, 3d7k, 3iae, 3iaf, 4qpz, 4qq8 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
G
3
9
3
A
3
9
4
L
3
9
5
T
3
9
6
Y
3
9
7
G
4
1
9
S
4
2
0
M
4
2
1
G
4
4
7
D
4
4
8
G
4
4
9
S
4
5
0
Y
4
5
3
N
4
7
5
S
4
7
7
W
4
7
8
G
4
7
9
A
4
8
0
T
4
8
1
L
2
5
H
2
6
G
2
7
A
2
8
E
5
0
G
7
3
G
7
6
I
7
7
C
8
0
L
1
1
2
Q
1
1
3
[1]2ag1.a tpp26 . . . . . . . * . . . . . . . . . . . . . . . . T . G N . . Mg
[1]2uz1.a tpp26 . . . . . . . . . . . . . . . . . . . . . . . . T . G N . .
[1]3d7k.a d7k39 . . . . . . . . . . . . . . . . . . . . . . . . T . G N . . Ca
[1]3iae.a d7k39 . . . . . . . . . . . . . . . . . . . . . . S . T . G N . . Ca
[1]3iaf.a tpp26 . . . . . . . . . . . . . . . . . . . . . . * . T . G N . . Mg
[1]4qpz.c tpp26 . G . . . N . . . . . . . . . . . W . . . . I . T . G N . . Mg

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 A2 Me
G
3
9
3
A
3
9
4
L
3
9
5
T
3
9
6
Y
3
9
7
G
4
1
9
S
4
2
0
M
4
2
1
G
4
4
7
D
4
4
8
G
4
4
9
S
4
5
0
Y
4
5
3
N
4
7
5
S
4
7
7
W
4
7
8
G
4
7
9
A
4
8
0
T
4
8
1
L
2
5
H
2
6
G
2
7
A
2
8
H
2
9
E
5
0
G
7
3
G
7
6
I
7
7
C
8
0
L
1
1
2
Q
1
1
3
[1]2ag1.a . . . . . . . * . . . . . . . . . . . . . . . . . T . G N . . Mg
[1]2uz1.a . . . . . . . . . . . . . . . . . . . . . . . . . T . G N . .
[1]3d7k.a . . . . . . . . . . . . . . . . . . . . . . . . . T . G N . . Ca
[1]3iae.a . . . . . . . . . . . . . . . . . . . . . . S . . T . G N . . Ca
[1]3iaf.a . . . . . . . . . . . . . . . . . . . . . . sep . . T . G N . . Mg
[1]4qpz.c . G . . . N . . . . . . . . . . . W . . . . I . . T . G N . . Mg

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
2ag1.a:tpp
2uz1.a:tpp
3d7k.a:d7k
3iae.a:d7k
3iaf.a:tpp
4qpz.c:tpp
[1] 2ag1.a
0.1
0.1 0.3 0.4 0 0.1
[1] 2uz1.a 0.1
0
0.1 0.3 0.1 0.1
[1] 3d7k.a 0.2 0.3
0.4
0.6 0.1 0.2
[1] 3iae.a 0.1 0.1 0.1
0.4
0 0.1
[1] 3iaf.a 0.3 0.3 2.6 2.9
0
0.3
[1] 4qpz.c 0.4 0.3 5.2 5.5 0.6
0.3
[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
2ag1.a
2uz1.a
3d7k.a
3iae.a
3iaf.a
4qpz.c
[1] 2ag1.a
0
.01 .01 .01 .10 .19
[1] 2uz1.a .01
0
.02 .01 .09 .19
[1] 3d7k.a .01 .02
0
.01 .10 .19
[1] 3iae.a .01 .01 .01
0
.09 .19
[1] 3iaf.a .10 .09 .10 .09
0
.22
[1] 4qpz.c .19 .19 .19 .19 .22
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
2ag1.a
2uz1.a
3d7k.a
3iae.a
3iaf.a
4qpz.c
[1] 2ag1.a
0
0.4 0.3 0.3 0.5 0.4
[1] 2uz1.a 0.4
0
0.4 0.2 0.5 0.4
[1] 3d7k.a 0.3 0.4
0
0.4 0.5 0.5
[1] 3iae.a 0.3 0.2 0.4
0
0.4 0.3
[1] 3iaf.a 0.5 0.5 0.5 0.4
0
0.5
[1] 4qpz.c 0.4 0.4 0.5 0.3 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
2ag1.a
2uz1.a
3d7k.a
3iae.a
3iaf.a
4qpz.c
[1] 2ag1.a
0
0.5 0.4 0.5 0.7 0.8
[1] 2uz1.a 0.5
0
0.4 0.4 0.7 0.7
[1] 3d7k.a 0.4 0.4
0
0.3 0.7 0.8
[1] 3iae.a 0.5 0.4 0.3
0
0.6 0.7
[1] 3iaf.a 0.7 0.7 0.7 0.6
0
0.8
[1] 4qpz.c 0.8 0.7 0.8 0.7 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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