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CKX1_MAIZE_14_534

Cytokinin dehydrogenase 1 [Oxygen-dependent FAD-linked oxidoreductase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CKX1_MAIZE):D: FAD-binding PCMH-type (99:107, 110, 111, 121, 146, 168:170, 173, 174, 176:178, 180, 181, 183, 184, 230, 233:235)
61, 253, 303, 304, 378, 381, 388, 390, 391, 397, 399, 427, 429, 456, 458, 491, 492, 527, 530
61, 99:107, 110, 111, 121, 146, 168:170, 173, 174, 176:178, 180, 181, 183, 184, 230, 233:235, 253, 303, 304, 378, 381, 388, 390, 391, 397, 399, 427, 429, 456, 458, 491, 492, 527, 530

Full PDB list

1w1o, 1w1q, 1w1r, 1w1s, 2qkn, 2qpm, 3bw7, 3c0p, 3dq0, 3kjm, 3s1c, 3s1d, 3s1e, 3s1f

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
6
1
F
1
0
0
R
1
0
1
G
1
0
2
R
1
0
3
G
1
0
4
H
1
0
5
S
1
0
6
L
1
0
7
Q
1
1
0
A
1
1
1
M
1
2
1
N
1
6
8
D
1
6
9
Y
1
7
0
L
1
7
3
T
1
7
4
G
1
7
6
G
1
7
7
T
1
7
8
S
1
8
0
N
1
8
1
G
1
8
3
I
1
8
4
G
2
3
0
G
2
3
3
V
2
3
4
I
2
3
5
R
2
5
3
T
3
0
4
V
3
7
8
E
3
8
1
L
3
8
8
W
3
9
1
W
3
9
7
N
3
9
9
P
4
2
7
I
4
2
9
S
4
5
6
L
4
5
8
Y
4
9
1
L
4
9
2
S
5
2
7
Q
5
3
0
[1]1w1o.a fad53 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1w1q.a fad,zip68 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1w1r.a fad,zea69 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1w1s.a emu,fad70 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qkn.a 245,245,fad87 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qpm.a 246,fad71 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . A . .
[1]3bw7.a fad.30168 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3c0p.a fad.ha867 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3dq0.a fad,mzo71 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kjm.a 245,fad70 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . A . .
[1]3s1c.a fad,zir77 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3s1d.a fad,zir77 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . S . . . . . . . . . . . .
[1]3s1e.a fad,zip68 . . . . . . * . . . . . T . . . . . . . . . . . . . . . . . . . . . . . Q . . . . . . .
[1]3s1f.a fad,zip68 . . . . . . * . . . . . T E . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
F
6
1
A
9
9
F
1
0
0
R
1
0
1
G
1
0
2
R
1
0
3
G
1
0
4
H
1
0
5
S
1
0
6
L
1
0
7
Q
1
1
0
A
1
1
1
M
1
2
1
G
1
4
6
N
1
6
8
D
1
6
9
Y
1
7
0
L
1
7
3
T
1
7
4
G
1
7
6
G
1
7
7
T
1
7
8
S
1
8
0
N
1
8
1
G
1
8
3
I
1
8
4
G
2
3
0
G
2
3
3
V
2
3
4
I
2
3
5
R
2
5
3
N
3
0
3
T
3
0
4
V
3
7
8
E
3
8
1
L
3
8
8
L
3
9
0
W
3
9
1
W
3
9
7
N
3
9
9
P
4
2
7
I
4
2
9
S
4
5
6
L
4
5
8
Y
4
9
1
L
4
9
2
S
5
2
7
Q
5
3
0
[1]1w1o.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]1w1q.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]1w1r.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]1w1s.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]2qkn.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]2qpm.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . A . .
[1]3bw7.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]3c0p.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]3dq0.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]3kjm.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A . .
[1]3s1c.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3s1d.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . S . . . . . . . . . . . . .
[1]3s1e.a . . . . . . . * . . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . Q . . . . . . .
[1]3s1f.a . . . . . . . * . . . . . . T E . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .

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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1w1o.a:fad
1w1q.a:fad,zip
1w1r.a:fad,zea
1w1s.a:emu,fad
2qkn.a:245,fad
2qpm.a:246,fad
3bw7.a:fad.301
3c0p.a:fad.ha8
3dq0.a:fad,mzo
3kjm.a:245,fad
3s1c.a:fad,zir
3s1d.a:fad,zir
3s1e.a:fad,zip
3s1f.a:fad,zip
[1] 1w1o.a
0.9
0.8 1.0 0.7 1.2 1.0 0.8 0.6 0.8 0.9 2.3 2.3 0.6 0.7
[1] 1w1q.a 1.2
0.9
0.9 1.0 1.3 1.1 1.3 1.2 1.4 1.1 2.4 1.6 0.9 0.8
[1] 1w1r.a 1.2 1.0
1.0
1.0 1.2 1.0 1.3 1.2 1.4 0.9 2.6 2.4 0.8 0.8
[1] 1w1s.a 1.6 1.2 1.5
1.2
1.7 1.6 1.5 1.3 1.9 1.3 3.3 2.6 1.3 1.0
[1] 2qkn.a 1.2 0.7 1.0 0.9
1.2
1.0 1.0 0.8 1.0 0.8 1.1 1.2 0.7 0.6
[1] 2qpm.a 1.6 1.3 1.6 1.3 1.4
1.2
1.7 1.3 1.6 1.2 2.5 2.7 1.0 0.9
[1] 3bw7.a 1.2 1.0 1.4 0.9 1.5 1.0
1.0
0.7 1.1 1.2 1.7 1.4 1.0 0.5
[1] 3c0p.a 1.3 1.3 1.4 1.0 1.7 1.0 1.0
0.8
1.4 1.1 2.4 2.2 0.9 0.7
[1] 3dq0.a 1.2 1.0 1.0 0.9 1.4 1.4 1.1 1.0
1.1
0.9 1.5 0.9 0.7 0.6
[1] 3kjm.a 1.4 1.1 1.1 1.0 1.2 0.9 1.3 1.1 1.3
1.0
1.0 1.0 1.0 0.7
[1] 3s1c.a 1.2 0.9 0.9 1.0 1.4 1.5 1.0 0.9 0.9 0.8
0.7
0.5 0.7 0.5
[1] 3s1d.a 1.2 1.0 1.0 0.9 1.2 1.2 1.1 1.0 1.1 1.1 1.1
0.8
1.0 0.6
[1] 3s1e.a 1.0 1.0 0.9 0.9 1.8 1.7 1.2 1.1 1.1 1.1 1.5 1.3
0.8
0.8
[1] 3s1f.a 1.4 1.2 1.3 1.4 1.7 1.5 1.2 1.1 1.3 1.5 2.9 2.4 1.1
1.0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1w1o.a
1w1q.a
1w1r.a
1w1s.a
2qkn.a
2qpm.a
3bw7.a
3c0p.a
3dq0.a
3kjm.a
3s1c.a
3s1d.a
3s1e.a
3s1f.a
[1] 1w1o.a
0
.02 .02 .02 .04 .03 .03 .02 .03 .06 .06 .05 .04 .03
[1] 1w1q.a .02
0
.01 .02 .03 .02 .02 .02 .02 .04 .05 .04 .04 .04
[1] 1w1r.a .02 .01
0
.01 .03 .02 .03 .01 .03 .05 .06 .04 .05 .03
[1] 1w1s.a .02 .02 .01
0
.04 .03 .04 .02 .04 .06 .06 .05 .05 .03
[1] 2qkn.a .04 .03 .03 .04
0
.04 .02 .03 .01 .03 .03 .02 .03 .05
[1] 2qpm.a .03 .02 .02 .03 .04
0
.04 .03 .04 .05 .06 .06 .05 .05
[1] 3bw7.a .03 .02 .03 .04 .02 .04
0
.02 .01 .04 .03 .03 .03 .04
[1] 3c0p.a .02 .02 .01 .02 .03 .03 .02
0
.03 .05 .05 .05 .05 .02
[1] 3dq0.a .03 .02 .03 .04 .01 .04 .01 .03
0
.04 .02 .02 .02 .04
[1] 3kjm.a .06 .04 .05 .06 .03 .05 .04 .05 .04
0
.03 .02 .04 .07
[1] 3s1c.a .06 .05 .06 .06 .03 .06 .03 .05 .02 .03
0
.01 .04 .05
[1] 3s1d.a .05 .04 .04 .05 .02 .06 .03 .05 .02 .02 .01
0
.03 .05
[1] 3s1e.a .04 .04 .05 .05 .03 .05 .03 .05 .02 .04 .04 .03
0
.06
[1] 3s1f.a .03 .04 .03 .03 .05 .05 .04 .02 .04 .07 .05 .05 .06
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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1w1o.a
1w1q.a
1w1r.a
1w1s.a
2qkn.a
2qpm.a
3bw7.a
3c0p.a
3dq0.a
3kjm.a
3s1c.a
3s1d.a
3s1e.a
3s1f.a
[1] 1w1o.a
0
0.1 0.1 0.2 0.4 0.3 0.4 0.3 0.4 1.7 0.4 0.4 0.3 0.3
[1] 1w1q.a 0.1
0
0.1 0.1 0.4 0.3 0.4 0.3 0.4 1.7 0.4 0.4 0.3 0.4
[1] 1w1r.a 0.1 0.1
0
0.1 0.4 0.3 0.4 0.3 0.4 1.7 0.4 0.4 0.3 0.4
[1] 1w1s.a 0.2 0.1 0.1
0
0.4 0.3 0.5 0.3 0.4 1.7 0.4 0.4 0.3 0.4
[1] 2qkn.a 0.4 0.4 0.4 0.4
0
0.2 0.2 0.2 0.2 1.6 0.2 0.2 0.2 0.2
[1] 2qpm.a 0.3 0.3 0.3 0.3 0.2
0
0.4 0.2 0.3 1.6 0.3 0.3 0.2 0.3
[1] 3bw7.a 0.4 0.4 0.4 0.5 0.2 0.4
0
0.3 0.2 1.6 0.3 0.3 0.3 0.2
[1] 3c0p.a 0.3 0.3 0.3 0.3 0.2 0.2 0.3
0
0.3 1.7 0.2 0.2 0.2 0.2
[1] 3dq0.a 0.4 0.4 0.4 0.4 0.2 0.3 0.2 0.3
0
1.6 0.2 0.2 0.2 0.1
[1] 3kjm.a 1.7 1.7 1.7 1.7 1.6 1.6 1.6 1.7 1.6
0
1.6 1.6 1.6 1.6
[1] 3s1c.a 0.4 0.4 0.4 0.4 0.2 0.3 0.3 0.2 0.2 1.6
0
0.2 0.2 0.2
[1] 3s1d.a 0.4 0.4 0.4 0.4 0.2 0.3 0.3 0.2 0.2 1.6 0.2
0
0.2 0.2
[1] 3s1e.a 0.3 0.3 0.3 0.3 0.2 0.2 0.3 0.2 0.2 1.6 0.2 0.2
0
0.2
[1] 3s1f.a 0.3 0.4 0.4 0.4 0.2 0.3 0.2 0.2 0.1 1.6 0.2 0.2 0.2
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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1w1o.a
1w1q.a
1w1r.a
1w1s.a
2qkn.a
2qpm.a
3bw7.a
3c0p.a
3dq0.a
3kjm.a
3s1c.a
3s1d.a
3s1e.a
3s1f.a
[1] 1w1o.a
0
0.3 0.1 0.2 0.6 0.4 0.6 0.4 0.5 2.4 0.8 0.6 0.5 0.5
[1] 1w1q.a 0.3
0
0.3 0.3 0.5 0.5 0.5 0.4 0.5 2.4 0.7 0.6 0.4 0.5
[1] 1w1r.a 0.1 0.3
0
0.2 0.6 0.4 0.6 0.3 0.5 2.4 0.8 0.6 0.5 0.5
[1] 1w1s.a 0.2 0.3 0.2
0
0.6 0.4 0.6 0.4 0.6 2.4 0.8 0.6 0.5 0.5
[1] 2qkn.a 0.6 0.5 0.6 0.6
0
0.4 0.3 0.4 0.3 2.2 0.6 0.5 0.4 0.4
[1] 2qpm.a 0.4 0.5 0.4 0.4 0.4
0
0.5 0.3 0.4 2.3 0.7 0.5 0.5 0.4
[1] 3bw7.a 0.6 0.5 0.6 0.6 0.3 0.5
0
0.4 0.3 2.3 0.6 0.5 0.4 0.3
[1] 3c0p.a 0.4 0.4 0.3 0.4 0.4 0.3 0.4
0
0.4 2.3 0.7 0.5 0.4 0.3
[1] 3dq0.a 0.5 0.5 0.5 0.6 0.3 0.4 0.3 0.4
0
2.2 0.6 0.5 0.3 0.3
[1] 3kjm.a 2.4 2.4 2.4 2.4 2.2 2.3 2.3 2.3 2.2
0
2.2 2.2 2.3 2.3
[1] 3s1c.a 0.8 0.7 0.8 0.8 0.6 0.7 0.6 0.7 0.6 2.2
0
0.3 0.6 0.6
[1] 3s1d.a 0.6 0.6 0.6 0.6 0.5 0.5 0.5 0.5 0.5 2.2 0.3
0
0.5 0.4
[1] 3s1e.a 0.5 0.4 0.5 0.5 0.4 0.5 0.4 0.4 0.3 2.3 0.6 0.5
0
0.4
[1] 3s1f.a 0.5 0.5 0.5 0.5 0.4 0.4 0.3 0.3 0.3 2.3 0.6 0.4 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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