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DCOR_TRYBB_1_423

Ornithine decarboxylase [Orn/Lys/Arg decarboxylase class-II family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DCOR_TRYBB):R: Pyridoxal phosphate binding (272:275)
R: Substrate binding (329, 330)
65, 67, 86, 152, 164, 195, 197, 198, 234, 235, 387
65, 67, 86, 152, 164, 195, 197, 198, 234, 235, 272:275, 329, 330, 387
A2 (DCOR_TRYBB):321, 358, 359, 395321, 358, 359, 395

Full PDB list

1f3t, 1njj, 1qu4, 1szr, 2tod (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
A
6
5
K
6
7
R
1
5
2
H
1
9
5
S
1
9
8
G
2
3
4
G
2
3
5
E
2
7
2
G
2
7
4
R
2
7
5
Y
3
2
9
D
3
3
0
Y
3
8
7
C
3
5
8
D
3
5
9
F
3
9
5
[1]1f3t.b plp.put21 . . . . . . . . . . . . . . . .
[1]1qu4.b plp15 . * . . . . . . . . . . . . . .
[1]1szr.a plg20 . * . . . . . . . . . . . . . .
[1]1szr.b orx24 . * . . . . . . . . . . . . . .
[1]1szr.c pxp16 . * . . . . . . . . . . . . . .
[1]2tod.a dmo.plp22 . A . . . . . . . . . . . * . .

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
A
6
5
K
6
7
D
8
6
R
1
5
2
L
1
6
4
H
1
9
5
G
1
9
7
S
1
9
8
G
2
3
4
G
2
3
5
E
2
7
2
P
2
7
3
G
2
7
4
R
2
7
5
Y
3
2
9
D
3
3
0
Y
3
8
7
Y
3
2
1
C
3
5
8
D
3
5
9
F
3
9
5
[1]1f3t.b . . . . . . . . . . . . . . . . . . * . .
[1]1qu4.b . * . . . . . * . . . . . . . . . . . . .
[1]1szr.a . * . . - . . . . . . . . . . . . . * . .
[1]1szr.b . * . . - . . . . . . . . . . . . . . . .
[1]1szr.c . * . . - . . . . . . . . . . . . . . . .
[1]2tod.a . 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
1f3t.b:plp.put
1qu4.b:plp
1szr.a:plg
1szr.b:orx
1szr.c:pxp
2tod.a:dmo.plp
[1] 1f3t.b
0
0 0.1 0.1 0.1 0.7
[1] 1qu4.b 0.4
0.6
1.6 1.2 0.6 0.8
[1] 1szr.a 0.6 0.6
0.7
1.1 0.7 1.5
[1] 1szr.b 0.4 0.6 0.6
0.8
0.7 1.1
[1] 1szr.c 0.5 0.6 0.8 0.8
0.7
1.2
[1] 2tod.a 0 0.1 0.6 0.7 0.1
0.5
[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
1f3t.b
1qu4.b
1szr.a
1szr.b
1szr.c
2tod.a
[1] 1f3t.b
0
.13 .07 .09 .10 .04
[1] 1qu4.b .13
0
.09 .07 .06 .09
[1] 1szr.a .07 .09
0
.05 .06 .10
[1] 1szr.b .09 .07 .05
0
0 .11
[1] 1szr.c .10 .06 .06 0
0
.10
[1] 2tod.a .04 .09 .10 .11 .10
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
1f3t.b
1qu4.b
1szr.a
1szr.b
1szr.c
2tod.a
[1] 1f3t.b
0
0.9 0.4 0.3 0.4 0.9
[1] 1qu4.b 0.9
0
0.5 0.5 0.5 0.3
[1] 1szr.a 0.4 0.5
0
0.2 0.4 0.5
[1] 1szr.b 0.3 0.5 0.2
0
0.2 0.5
[1] 1szr.c 0.4 0.5 0.4 0.2
0
0.5
[1] 2tod.a 0.9 0.3 0.5 0.5 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
1f3t.b
1qu4.b
1szr.a
1szr.b
1szr.c
2tod.a
[1] 1f3t.b
0
1.2 0.6 0.7 0.7 1.0
[1] 1qu4.b 1.2
0
0.7 0.6 0.5 0.5
[1] 1szr.a 0.6 0.7
0
0.5 0.5 0.6
[1] 1szr.b 0.7 0.6 0.5
0
0.3 0.7
[1] 1szr.c 0.7 0.5 0.5 0.3
0
0.6
[1] 2tod.a 1.0 0.5 0.6 0.7 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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