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DAPB_ECOLI_1_273

4-hydroxy-tetrahydrodipicolinate reductase [DapB family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DAPB_ECOLI):R: Substrate binding (169, 170)
104, 127, 159, 160, 163, 168, 243
104, 127, 159, 160, 163, 168:170, 243

Full PDB list

1arz, 1dih, 1dru, 1drv, 1drw (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
T
1
0
4
A
1
2
7
H
1
6
0
K
1
6
3
S
1
6
8
G
1
6
9
T
1
7
0
F
2
4
3
[1]1arz.c pdc12 . . . . . . . .
[1]1drv.a none . . . . . . . .

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
1
0
4
A
1
2
7
H
1
5
9
H
1
6
0
K
1
6
3
S
1
6
8
G
1
6
9
T
1
7
0
F
2
4
3
[1]1arz.c . . . . . . . . .
[1]1drv.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
1arz.c:pdc
1drv.a is apo
[1] 1arz.c
0.2
-
[1] 1drv.a 0.6
-
[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
1arz.c
1drv.a
[1] 1arz.c
0
.04
[1] 1drv.a .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1arz.c
1drv.a
[1] 1arz.c
0
2.7
[1] 1drv.a 2.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 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
1arz.c
1drv.a
[1] 1arz.c
0
2.4
[1] 1drv.a 2.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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