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AROG_MYCTU_1_462

Phospho-2-dehydro-3-deoxyheptonate aldolase AroG [Class-II DAHP synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROG_MYCTU):R: Substrate binding (283, 284)
87, 126, 133:136, 248, 280, 282, 306, 337, 369, 380, 409, 411, 440, 441
87, 126, 133:136, 248, 280, 282:284, 306, 337, 369, 380, 409, 411, 440, 441
Metals (Me):Mn

Full PDB list

2b7o, 2w19, 2w1a, 2ypo, 2ypp, 2ypq, 3kgf, 3nud, 3nue, 3nv8, 3pfp, 3rzi, 5ckv, 5ckx, 5e2l, 5e40, 5e4n, 5e5g, 5e7z, 5ex4 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
C
8
7
R
1
2
6
K
1
3
3
P
1
3
4
R
1
3
5
S
1
3
6
E
2
4
8
W
2
8
0
G
2
8
2
E
2
8
3
R
2
8
4
K
3
0
6
R
3
3
7
H
3
6
9
K
3
8
0
E
4
1
1
C
4
4
0
D
4
4
1
[1]2b7o.b pep10 . . . . . . . . . . . . . . . . . . Mn
[1]2ypp.b none . . . . . . . . . . . . . . . . . . Mn
[1]3pfp.b 035,03638 . . . . . . . . . . . . . . . . . . Mn

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 Me
C
8
7
R
1
2
6
K
1
3
3
P
1
3
4
R
1
3
5
S
1
3
6
E
2
4
8
W
2
8
0
G
2
8
2
E
2
8
3
R
2
8
4
K
3
0
6
R
3
3
7
H
3
6
9
K
3
8
0
H
4
0
9
E
4
1
1
C
4
4
0
D
4
4
1
[1]2b7o.b . . . . . . . . . . . . . . . . . . . Mn
[1]2ypp.b . . . . . . . . . . . . . . . . . . . Mn
[1]3pfp.b . . . . . . . . . . . . . . . . . . . Mn

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
2b7o.b:pep
2ypp.b is apo
3pfp.b:035,036
[1] 2b7o.b
0.3
- 0.4
[1] 2ypp.b 0.2
-
0.3
[1] 3pfp.b 0.3 -
0.2
[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
2b7o.b
2ypp.b
3pfp.b
[1] 2b7o.b
0
.04 .03
[1] 2ypp.b .04
0
.04
[1] 3pfp.b .03 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
2b7o.b
2ypp.b
3pfp.b
[1] 2b7o.b
0
0.2 0.4
[1] 2ypp.b 0.2
0
0.4
[1] 3pfp.b 0.4 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
2b7o.b
2ypp.b
3pfp.b
[1] 2b7o.b
0
0.5 1.0
[1] 2ypp.b 0.5
0
1.0
[1] 3pfp.b 1.0 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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