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AVR4_CHICK_25_149

Avidin-related protein 4/5 [Avidin/streptavidin family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AVR4_CHICK):D: Avidin-like (36, 38, 40, 57, 59, 61:63, 92, 94, 95, 97, 99, 101, 119, 121, 123, 136, 140)36, 38, 40, 57, 59, 61:63, 92, 94, 95, 97, 99, 101, 119, 121, 123, 136, 140

Full PDB list

1y52, 1y53, 1y55, 2fhl, 2fhn, 2of8, 2of9, 2ofa, 2ofb (redundant Pocketome entry); 4bcs (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
N
3
6
L
3
8
S
4
0
Y
5
7
T
5
9
V
6
1
A
6
2
D
6
3
W
9
2
F
9
4
S
9
5
S
9
7
T
9
9
F
1
0
1
W
1
1
9
L
1
2
1
S
1
2
3
R
1
3
6
N
1
4
0
[1]1y53.x none . . . . . . . . . . . . . . . . . . .
[1]1y55.x btn16 . . . . . . . . . . . . . . . . . . .
[1]2fhl.a bni25 . . . . . . . . . . . . . . . . . . .
[1]2of8.a bni25 . . . . . . . A . . . . . . . . . . .
[1]2of9.a none . . . . . . . A . . . . . . . . . . .
[1]2ofa.a none . . . . . . . . . . . . . . . . . L .
[1]2ofb.a bni25 . . . . . . . . . . . . . . . . . L .

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
3
6
L
3
8
S
4
0
Y
5
7
T
5
9
V
6
1
A
6
2
D
6
3
W
9
2
F
9
4
S
9
5
S
9
7
T
9
9
F
1
0
1
W
1
1
9
L
1
2
1
S
1
2
3
R
1
3
6
N
1
4
0
[1]1y53.x . . . . . . . * . . . . . . . . . * .
[1]1y55.x . . . . . . . * . . . . . . . . . * .
[1]2fhl.a . . . . . . . . . . . . . . . . . . .
[1]2of8.a . . . . . . . A . . . . . . . . . . .
[1]2of9.a . . . . . . . A . . . . . . . . . * .
[1]2ofa.a . . . . . . . . . . . . . . . . . L .
[1]2ofb.a . . . . . . . . . . . . . . . . . L .

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
1y53.x is apo
1y55.x:btn
2fhl.a:bni
2of8.a:bni
2of9.a is apo
2ofa.a is apo
2ofb.a:bni
[1] 1y53.x
-
0 1.9 2.1 - - 2.3
[1] 1y55.x -
0
1.8 2.0 - - 1.6
[1] 2fhl.a - 0
0.2
0.9 - - 0.9
[1] 2of8.a - 0 0.1
0
- - 0.2
[1] 2of9.a - 0.1 0.3 0.6
-
- 1.6
[1] 2ofa.a - 0.1 0.3 0.2 -
-
0.1
[1] 2ofb.a - 0 0.2 0 - -
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
1y53.x
1y55.x
2fhl.a
2of8.a
2of9.a
2ofa.a
2ofb.a
[1] 1y53.x
0
.01 .10 .14 .11 .15 .14
[1] 1y55.x .01
0
.09 .13 .11 .15 .14
[1] 2fhl.a .10 .09
0
.04 .04 .06 .05
[1] 2of8.a .14 .13 .04
0
.08 .03 .02
[1] 2of9.a .11 .11 .04 .08
0
.09 .09
[1] 2ofa.a .15 .15 .06 .03 .09
0
.01
[1] 2ofb.a .14 .14 .05 .02 .09 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1y53.x
1y55.x
2fhl.a
2of8.a
2of9.a
2ofa.a
2ofb.a
[1] 1y53.x
0
0.2 0.2 0.2 0.2 0.4 0.3
[1] 1y55.x 0.2
0
0.1 0.1 0.1 0.3 0.1
[1] 2fhl.a 0.2 0.1
0
0.1 0.2 0.3 0.1
[1] 2of8.a 0.2 0.1 0.1
0
0.2 0.2 0.1
[1] 2of9.a 0.2 0.1 0.2 0.2
0
0.3 0.2
[1] 2ofa.a 0.4 0.3 0.3 0.2 0.3
0
0.3
[1] 2ofb.a 0.3 0.1 0.1 0.1 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

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
1y53.x
1y55.x
2fhl.a
2of8.a
2of9.a
2ofa.a
2ofb.a
[1] 1y53.x
0
0.2 0.5 0.6 0.4 0.5 0.5
[1] 1y55.x 0.2
0
0.4 0.6 0.4 0.4 0.4
[1] 2fhl.a 0.5 0.4
0
0.5 0.5 0.3 0.1
[1] 2of8.a 0.6 0.6 0.5
0
0.3 0.3 0.1
[1] 2of9.a 0.4 0.4 0.5 0.3
0
0.3 0.3
[1] 2ofa.a 0.5 0.4 0.3 0.3 0.3
0
0.3
[1] 2ofb.a 0.5 0.4 0.1 0.1 0.3 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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