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DGDA_BURCE_1_433

2,2-dialkylglycine decarboxylase [Class-III pyridoxal-phosphate-dependent aminotransferase family]

Composition of the binding site

Protein chains monomer
A1 (DGDA_BURCE):52, 53, 110:112, 115, 138:140, 210, 215, 243, 245, 246, 272, 40652, 53, 110:112, 115, 138:140, 210, 215, 243, 245, 246, 272, 406
Metals (Me):Cs/K

Full PDB list

1d7r, 1d7s, 1d7u, 1d7v, 1dgd, 1dge, 1dka, 1m0n, 1m0o, 1m0p, 1m0q, 1z3z, 1zc9, 1zob, 1zod, 2dkb (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
5
2
M
5
3
T
1
1
0
G
1
1
1
A
1
1
2
N
1
1
5
W
1
3
8
H
1
3
9
G
1
4
0
E
2
1
0
S
2
1
5
D
2
4
3
A
2
4
5
Q
2
4
6
K
2
7
2
R
4
0
6
[1]1d7r.a 5pa22 . . . . . . . . . . . . . . . . K
[1]1d7s.a dcs22 . . . . . . . . . . . . . . . . K
[1]1d7u.a lcs22 . . . . . . . . . . . . . . . . K
[1]1d7v.a nma22 . . . . . . . . . . . . . . . . K
[1]1m0n.a hcp25 . . . . . . . . . . . . . . . . K
[1]1m0o.a mpm24 . . . . . . . . . . . . . . . . K
[1]1m0p.a elp28 . . . . . . . . . . . . . . . . K
[1]1m0q.a epc22 . . . . . . . . . . . . . . . . K
[1]1z3z.a plp15 A . . . . . . . . . . . . . * . K
[1]1zc9.a pmp16 . . . . . . . . . . . . . . . . K
[1]1zod.a plp15 . . . . . . . . . . . . . . * . Cs

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 Me
Q
5
2
M
5
3
T
1
1
0
G
1
1
1
A
1
1
2
N
1
1
5
W
1
3
8
H
1
3
9
G
1
4
0
E
2
1
0
S
2
1
5
D
2
4
3
A
2
4
5
Q
2
4
6
K
2
7
2
R
4
0
6
[1]1d7r.a . . . . . . . . . . . . . . . . K
[1]1d7s.a . . . . . . . . . . . . . . . . K
[1]1d7u.a . . . . . . . . . . . . . . . . K
[1]1d7v.a . . . . . . * . . . . . . . . . K
[1]1m0n.a . . . . . . . . . . . . . . . . K
[1]1m0o.a . . . . . . . . . . . . . . . . K
[1]1m0p.a . . . . . . . . . . . . . . . . K
[1]1m0q.a . . . . . . * . . . . . . . . . K
[1]1z3z.a A . . . . . . . . . . . . . * . K
[1]1zc9.a . . . . . . . . . . . . . . . . K
[1]1zod.a . . . . . . . . . . . . . . * . Cs

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
1d7r.a:5pa
1d7s.a:dcs
1d7u.a:lcs
1d7v.a:nma
1m0n.a:hcp
1m0o.a:mpm
1m0p.a:elp
1m0q.a:epc
1z3z.a:plp
1zc9.a:pmp
1zod.a:plp
[1] 1d7r.a
0.1
0 0 0.4 0.6 0.6 2.0 0.3 0.4 0.4 0.3
[1] 1d7s.a 0.1
0.1
0.1 0.3 0.4 0.3 1.7 0.2 0.5 0.6 0.6
[1] 1d7u.a 0.2 0.1
0
0.3 0.6 0.8 1.8 0.1 0.4 0.3 0.4
[1] 1d7v.a 0.2 0.2 0.2
0.2
0.4 0.4 2.2 0.2 0.6 0.5 0.6
[1] 1m0n.a 0.3 0 0.1 0.2
0.2
0.4 1.1 0.1 0.2 0.1 0.2
[1] 1m0o.a 0.1 0.1 0.1 0 0.3
0.1
1.1 0 0.5 0.3 0.5
[1] 1m0p.a 0.1 0.1 0.1 0.1 0.2 0.2
0.3
0.1 0.2 0.2 0.1
[1] 1m0q.a 0.3 0 0 0.4 0.8 1.0 3.2
0.2
0.3 0.2 0.3
[1] 1z3z.a 0.7 0.3 0.2 0.7 0.6 0.6 1.4 0.4
0.7
0.9 0.7
[1] 1zc9.a 0.1 0.1 0.1 0.2 0.5 0.4 1.6 0.1 0.2
0.2
0.2
[1] 1zod.a 0.6 0.6 0.2 0.7 0.7 0.5 1.5 0.4 0.7 0.7
0.7
[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
1d7r.a
1d7s.a
1d7u.a
1d7v.a
1m0n.a
1m0o.a
1m0p.a
1m0q.a
1z3z.a
1zc9.a
1zod.a
[1] 1d7r.a
0
.04 .02 .04 .11 .07 .14 .09 .09 .04 .07
[1] 1d7s.a .04
0
.03 .04 .12 .06 .13 .11 .08 .04 .04
[1] 1d7u.a .02 .03
0
.05 .09 .05 .12 .08 .09 .04 .07
[1] 1d7v.a .04 .04 .05
0
.13 .08 .13 .08 .11 .05 .08
[1] 1m0n.a .11 .12 .09 .13
0
.07 .06 .14 .06 .09 .09
[1] 1m0o.a .07 .06 .05 .08 .07
0
.07 .13 .08 .04 .04
[1] 1m0p.a .14 .13 .12 .13 .06 .07
0
.19 .11 .09 .09
[1] 1m0q.a .09 .11 .08 .08 .14 .13 .19
0
.17 .09 .14
[1] 1z3z.a .09 .08 .09 .11 .06 .08 .11 .17
0
.10 .05
[1] 1zc9.a .04 .04 .04 .05 .09 .04 .09 .09 .10
0
.05
[1] 1zod.a .07 .04 .07 .08 .09 .04 .09 .14 .05 .05
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
1d7r.a
1d7s.a
1d7u.a
1d7v.a
1m0n.a
1m0o.a
1m0p.a
1m0q.a
1z3z.a
1zc9.a
1zod.a
[1] 1d7r.a
0
0.1 0.1 0.2 0.3 0.2 0.2 0.2 0.2 0.2 0.3
[1] 1d7s.a 0.1
0
0.1 0.2 0.3 0.1 0.2 0.2 0.2 0.2 0.2
[1] 1d7u.a 0.1 0.1
0
0.2 0.3 0.2 0.3 0.3 0.3 0.2 0.3
[1] 1d7v.a 0.2 0.2 0.2
0
0.3 0.2 0.3 0.3 0.3 0.3 0.3
[1] 1m0n.a 0.3 0.3 0.3 0.3
0
0.2 0.2 0.2 0.3 0.3 0.2
[1] 1m0o.a 0.2 0.1 0.2 0.2 0.2
0
0.2 0.2 0.3 0.2 0.3
[1] 1m0p.a 0.2 0.2 0.3 0.3 0.2 0.2
0
0.2 0.2 0.3 0.2
[1] 1m0q.a 0.2 0.2 0.3 0.3 0.2 0.2 0.2
0
0.3 0.3 0.2
[1] 1z3z.a 0.2 0.2 0.3 0.3 0.3 0.3 0.2 0.3
0
0.3 0.2
[1] 1zc9.a 0.2 0.2 0.2 0.3 0.3 0.2 0.3 0.3 0.3
0
0.3
[1] 1zod.a 0.3 0.2 0.3 0.3 0.2 0.3 0.2 0.2 0.2 0.3
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
1d7r.a
1d7s.a
1d7u.a
1d7v.a
1m0n.a
1m0o.a
1m0p.a
1m0q.a
1z3z.a
1zc9.a
1zod.a
[1] 1d7r.a
0
0.3 0.3 0.3 0.5 0.5 0.6 0.5 0.5 0.4 0.5
[1] 1d7s.a 0.3
0
0.2 0.4 0.6 0.5 0.6 0.6 0.5 0.5 0.6
[1] 1d7u.a 0.3 0.2
0
0.4 0.6 0.6 0.6 0.6 0.5 0.5 0.6
[1] 1d7v.a 0.3 0.4 0.4
0
0.5 0.5 0.6 0.5 0.5 0.5 0.6
[1] 1m0n.a 0.5 0.6 0.6 0.5
0
0.4 0.4 0.4 0.4 0.5 0.4
[1] 1m0o.a 0.5 0.5 0.6 0.5 0.4
0
0.3 0.4 0.4 0.4 0.4
[1] 1m0p.a 0.6 0.6 0.6 0.6 0.4 0.3
0
0.5 0.4 0.5 0.4
[1] 1m0q.a 0.5 0.6 0.6 0.5 0.4 0.4 0.5
0
0.5 0.4 0.5
[1] 1z3z.a 0.5 0.5 0.5 0.5 0.4 0.4 0.4 0.5
0
0.5 0.3
[1] 1zc9.a 0.4 0.5 0.5 0.5 0.5 0.4 0.5 0.4 0.5
0
0.5
[1] 1zod.a 0.5 0.6 0.6 0.6 0.4 0.4 0.4 0.5 0.3 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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