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CRY2_MOUSE_6_512

Cryptochrome-2 [DNA photolyase class-1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CRY2_MOUSE):R: Required for inhibition of CLOCK-ARNTL- mediated transcription (399, 403, 405:407, 410, 411, 414, 415, 417, 418, 428, 429, 431)
269, 270, 273, 283, 307, 308, 310, 311, 314, 370, 373, 376, 377, 380
269, 270, 273, 283, 307, 308, 310, 311, 314, 370, 373, 376, 377, 380, 399, 403, 405:407, 410, 411, 414, 415, 417, 418, 428, 429, 431

Full PDB list

4i6e, 4i6g, 4i6j, 4mlp, 4u8h (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
S
2
7
0
L
2
7
3
F
2
8
3
Q
3
0
7
W
3
1
0
R
3
1
1
F
3
1
4
W
3
7
0
H
3
7
3
R
3
7
6
H
3
7
7
A
3
8
0
F
3
9
9
L
4
0
3
D
4
0
5
A
4
0
6
D
4
0
7
V
4
1
0
N
4
1
1
S
4
1
4
W
4
1
5
W
4
1
7
L
4
1
8
Y
4
3
1
[1]4i6e.a none . . . . . . . . . . . . . . . . . . . . . . . .
[1]4i6g.a fad53 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4i6j.a MPTW37 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4mlp.c 2cx28 . . . . . . . . . . . . . . . . . . . . . . . .

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
L
2
6
9
S
2
7
0
L
2
7
3
F
2
8
3
Q
3
0
7
L
3
0
8
W
3
1
0
R
3
1
1
F
3
1
4
W
3
7
0
H
3
7
3
R
3
7
6
H
3
7
7
A
3
8
0
F
3
9
9
L
4
0
3
D
4
0
5
A
4
0
6
D
4
0
7
V
4
1
0
N
4
1
1
S
4
1
4
W
4
1
5
W
4
1
7
L
4
1
8
F
4
2
8
H
4
2
9
Y
4
3
1
[1]4i6e.a . . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]4i6g.a . . . . . . . . . . . . . . . . . . . . . . . . . * . .
[1]4i6j.a . . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]4mlp.c . . . . . . . . . . * . . . . . . . . . . . . . . . . .

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
4i6e.a is apo
4i6g.a:fad
4i6j.a:MPTW
4mlp.c:2cx
[1] 4i6e.a
-
4.5 1.1 0.3
[1] 4i6g.a -
0
3.5 0.6
[1] 4i6j.a - 4.3
0
0.2
[1] 4mlp.c - 3.5 3.5
0
[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
4i6e.a
4i6g.a
4i6j.a
4mlp.c
[1] 4i6e.a
0
.24 .06 .17
[1] 4i6g.a .24
0
.26 .18
[1] 4i6j.a .06 .26
0
.18
[1] 4mlp.c .17 .18 .18
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
4i6e.a
4i6g.a
4i6j.a
4mlp.c
[1] 4i6e.a
0
1.1 1.0 0.8
[1] 4i6g.a 1.1
0
1.3 1.0
[1] 4i6j.a 1.0 1.3
0
1.0
[1] 4mlp.c 0.8 1.0 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
4i6e.a
4i6g.a
4i6j.a
4mlp.c
[1] 4i6e.a
0
2.2 1.7 1.4
[1] 4i6g.a 2.2
0
2.3 2.2
[1] 4i6j.a 1.7 2.3
0
2.1
[1] 4mlp.c 1.4 2.2 2.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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