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1A1D_CYBSA_1_341

1-aminocyclopropane-1-carboxylate deaminase [ACC deaminase/D-cysteine desulfhydrase family]

Composition of the binding site

Protein chains monomer
A1 (1A1D_CYBSA):50, 51, 54, 74, 78:80, 102, 163, 164, 166, 199:205, 295, 296, 323:32550, 51, 54, 74, 78:80, 102, 163, 164, 166, 199:205, 295, 296, 323:325

Full PDB list

1f2d, 1j0c, 1j0d, 1j0e

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
N
5
0
K
5
1
K
5
4
G
7
4
S
7
8
N
7
9
Q
8
0
W
1
0
2
A
1
6
3
G
1
6
4
C
1
9
9
C
2
0
0
V
2
0
1
T
2
0
2
G
2
0
3
S
2
0
4
T
2
0
5
Y
2
9
5
E
2
9
6
L
3
2
3
G
3
2
4
G
3
2
5
[1]1f2d.a plp15 . * . . . . . . . . . . . . . . . . . . . .
[1]1j0c.a plp15 . T . . . . . . . . . . . . . . . . . . . .
[1]1j0d.a 5pa22 . T . . . . . . . . . . . . . . . . . . . .
[1]1j0e.a 1ac,plp22 . * . . . . . . . . . . . . . . . F . . . .

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
N
5
0
K
5
1
K
5
4
G
7
4
S
7
8
N
7
9
Q
8
0
W
1
0
2
A
1
6
3
G
1
6
4
S
1
6
6
C
1
9
9
C
2
0
0
V
2
0
1
T
2
0
2
G
2
0
3
S
2
0
4
T
2
0
5
Y
2
9
5
E
2
9
6
L
3
2
3
G
3
2
4
G
3
2
5
[1]1f2d.a . * . . . . . . . . . . . . . . . . . . . . .
[1]1j0c.a . T . . . . . . . . . . . . . . . . . . . . .
[1]1j0d.a . T . . . . . . . . . . . . . . . . . . . . .
[1]1j0e.a . * . . . . . . . . . . . . . . . . F . . . .

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
1f2d.a:plp
1j0c.a:plp
1j0d.a:5pa
1j0e.a:1ac,plp
[1] 1f2d.a
0.9
0.7 1.2 1.7
[1] 1j0c.a 0.4
0.2
1.2 1.6
[1] 1j0d.a 0.4 0.2
0.7
1.4
[1] 1j0e.a 1.0 0.6 1.0
1.5
[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
1f2d.a
1j0c.a
1j0d.a
1j0e.a
[1] 1f2d.a
0
.07 .07 .03
[1] 1j0c.a .07
0
.03 .06
[1] 1j0d.a .07 .03
0
.06
[1] 1j0e.a .03 .06 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1f2d.a
1j0c.a
1j0d.a
1j0e.a
[1] 1f2d.a
0
0.4 0.3 0.2
[1] 1j0c.a 0.4
0
0.3 0.4
[1] 1j0d.a 0.3 0.3
0
0.3
[1] 1j0e.a 0.2 0.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1f2d.a
1j0c.a
1j0d.a
1j0e.a
[1] 1f2d.a
0
0.5 0.5 0.3
[1] 1j0c.a 0.5
0
0.3 0.5
[1] 1j0d.a 0.5 0.3
0
0.5
[1] 1j0e.a 0.3 0.5 0.5
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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