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DAPB_MYCTU_1_245

4-hydroxy-tetrahydrodipicolinate reductase [DapB family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DAPB_MYCTU):R: Substrate binding (142, 143)
77, 103, 104, 132, 133, 136, 138, 141, 192, 217
77, 103, 104, 132, 133, 136, 138, 141:143, 192, 217

Full PDB list

1c3v, 1p9l, 1yl5, 1yl6, 1yl7, 5tek, 5tjy (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
T
7
7
P
1
0
3
N
1
0
4
H
1
3
2
H
1
3
3
K
1
3
6
S
1
4
1
G
1
4
2
T
1
4
3
A
1
9
2
F
2
1
7
[1]5tek.a none . . . . . . . . . . .
[1]5tjy.a pdc12 . . . . . . . . . . .

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
T
7
7
P
1
0
3
N
1
0
4
H
1
3
2
H
1
3
3
K
1
3
6
D
1
3
8
S
1
4
1
G
1
4
2
T
1
4
3
A
1
9
2
F
2
1
7
[1]5tek.a . . . . . . . . . . . .
[1]5tjy.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
5tek.a is apo
5tjy.a:pdc
[1] 5tek.a
-
0
[1] 5tjy.a -
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
5tek.a
5tjy.a
[1] 5tek.a
0
0
[1] 5tjy.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
5tek.a
5tjy.a
[1] 5tek.a
0
3.1
[1] 5tjy.a 3.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.6 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
5tek.a
5tjy.a
[1] 5tek.a
0
3.4
[1] 5tjy.a 3.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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