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BEV1A_BETPN_2_160

Major pollen allergen Bet v 1-A [BetVI family]

Composition of the binding site

Protein chains monomer
A1 (BEV1A_BETPN):6:8, 10, 23, 24, 27, 28, 31, 39, 55, 57, 59, 68, 70, 72, 82, 84, 86, 99, 101, 103, 115, 117, 119, 121, 133, 134, 137, 138, 140:142, 1446:8, 10, 23, 24, 27, 28, 31, 39, 55, 57, 59, 68, 70, 72, 82, 84, 86, 99, 101, 103, 115, 117, 119, 121, 133, 134, 137, 138, 140:142, 144

Full PDB list

1bv1, 1fsk, 1llt, 1qmr, 4a80, 4a81, 4a83, 4a84, 4a85, 4a86, 4a87, 4a88, 4a8g, 4b9r, 4bk6, 4bk7, 4bkc, 4bkd, 4btz, 4mns, 4qip, 4z3l (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
6
T
8
T
1
0
F
2
3
I
2
4
G
2
7
D
2
8
F
3
1
I
3
9
K
5
5
I
5
7
F
5
9
V
6
8
D
7
0
V
7
2
Y
8
2
Y
8
4
V
8
6
I
9
9
N
1
0
1
I
1
0
3
I
1
1
7
N
1
1
9
Y
1
2
1
V
1
3
4
S
1
3
7
K
1
3
8
M
1
4
0
G
1
4
1
E
1
4
2
L
1
4
4
[1]4a80.a 2an21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a81.a 2an,dxc49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a83.a dxc28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a84.a dxc28 . . . . . . . V . . . . . . . . . . . . . . . . . . . . . . .
[1]4a85.a h3516 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a86.a 2an,h3537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a87.a na,nar21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a88.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a8g.a dmx17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4b9r.a none * . . . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]4bk6.b none C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bk7.a none F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bkc.b none * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bkd.a none * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4btz.a none * . . . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]4mns.a 2ax21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qip.a sds17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4z3l.b none . . . . . L . . . . . . . I . . . . . . . . . . . . . . . . .

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
Y
6
E
7
T
8
T
1
0
F
2
3
I
2
4
G
2
7
D
2
8
F
3
1
I
3
9
K
5
5
I
5
7
F
5
9
V
6
8
D
7
0
V
7
2
Y
8
2
Y
8
4
V
8
6
I
9
9
N
1
0
1
I
1
0
3
L
1
1
5
I
1
1
7
N
1
1
9
Y
1
2
1
Q
1
3
3
V
1
3
4
S
1
3
7
K
1
3
8
M
1
4
0
G
1
4
1
E
1
4
2
L
1
4
4
[1]4a80.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a81.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a83.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a84.a . . . . . . . . V . . . . . * . . . . . . . . . . . . . . . . . . .
[1]4a85.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a86.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a87.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a88.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4a8g.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4b9r.a * . . . . . . . * . . . . . . . . * . . . . . . . . . . . . * . . .
[1]4bk6.b C . . . . . . . * . . . . . . . . . . . . . . . . . . . . . * . . .
[1]4bk7.a F . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bkc.b * . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bkd.a * . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4btz.a * . . . . . . . * . . . . . . . . . . . . . . . . * . . . * . . . .
[1]4mns.a . . . . . . . . * . * . . . . . . . . . . . . . . . . . . . . . . .
[1]4qip.a . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4z3l.b . . . . . . L . * . . . . . I . . . . . . . . * . . . . . . . . . .

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
4a80.a:2an
4a81.a:2an,dxc
4a83.a:dxc
4a84.a:dxc
4a85.a:h35
4a86.a:2an,h35
4a87.a:na,nar
4a88.a is apo
4a8g.a:dmx
4b9r.a is apo
4bk6.b is apo
4bk7.a is apo
4bkc.b is apo
4bkd.a is apo
4btz.a is apo
4mns.a:2ax
4qip.a:sds
4z3l.b is apo
[1] 4a80.a
0.1
0.9 0.5 2.1 0.1 0.4 0.1 - 0 - - - - - - 0.3 0 -
[1] 4a81.a 0.1
0.3
0.1 1.6 0.2 0.9 0.3 - 0.1 - - - - - - 0.5 0.2 -
[1] 4a83.a 0.7 0.8
0
1.4 0.2 1.6 0.6 - 0.1 - - - - - - 0.3 0.3 -
[1] 4a84.a 0.6 1.1 0.7
0
0.2 0.9 0.4 - 0.1 - - - - - - 0.6 0.3 -
[1] 4a85.a 0.2 1.3 0.4 1.7
0
0.6 0.2 - 0 - - - - - - 0.1 0.1 -
[1] 4a86.a 0.2 0.5 0.5 1.8 0
0.2
0.2 - 0 - - - - - - 0.2 0.1 -
[1] 4a87.a 0.6 1.2 0.5 1.9 0.1 0.7
0.2
- 0 - - - - - - 0.1 0 -
[1] 4a88.a 0.7 1.1 0.5 1.9 0.1 1.0 0.5
-
0 - - - - - - 0.3 0.4 -
[1] 4a8g.a 0.4 1.2 0.7 1.8 0.1 0.9 0.5 -
0
- - - - - - 0.2 0.5 -
[1] 4b9r.a 0.5 1.8 1.1 2.0 0.1 0.5 0.4 - 0.3
-
- - - - - 0.3 0 -
[1] 4bk6.b 0.4 2.4 2.0 2.0 0.1 1.2 0.2 - 0.6 -
-
- - - - 0.4 0.5 -
[1] 4bk7.a 0.4 1.1 0.5 1.8 0 0.5 0.2 - 0 - -
-
- - - 0.3 0.1 -
[1] 4bkc.b 0.9 1.6 1.1 1.4 0.1 1.6 0.6 - 0.6 - - -
-
- - 0.5 1.1 -
[1] 4bkd.a 1.3 2.4 0.7 1.9 0.3 1.8 1.0 - 0.2 - - - -
-
- 0.4 0.8 -
[1] 4btz.a 1.7 2.0 0.7 1.9 0.2 1.6 1.0 - 0.4 - - - - -
-
0.2 1.1 -
[1] 4mns.a 0.6 1.9 1.1 1.6 0.2 1.6 0.4 - 0.6 - - - - - -
0.2
0.8 -
[1] 4qip.a 0.3 0.6 0.4 1.8 0 0.3 0.1 - 0 - - - - - - 0.2
0
-
[1] 4z3l.b 1.1 3.3 2.0 3.7 0.8 3.0 0.7 - 2.0 - - - - - - 0.6 1.4
-
[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
4a80.a
4a81.a
4a83.a
4a84.a
4a85.a
4a86.a
4a87.a
4a88.a
4a8g.a
4b9r.a
4bk6.b
4bk7.a
4bkc.b
4bkd.a
4btz.a
4mns.a
4qip.a
4z3l.b
[1] 4a80.a
0
.05 .06 .09 .04 .02 .04 .05 .05 .08 .10 .02 .10 .12 .09 .09 .03 .15
[1] 4a81.a .05
0
.03 .08 .05 .04 .06 .06 .07 .07 .10 .04 .09 .09 .09 .09 .05 .19
[1] 4a83.a .06 .03
0
.07 .04 .06 .05 .06 .07 .08 .11 .05 .09 .08 .10 .09 .06 .18
[1] 4a84.a .09 .08 .07
0
.08 .07 .10 .10 .11 .12 .14 .08 .12 .14 .12 .13 .09 .23
[1] 4a85.a .04 .05 .04 .08
0
.04 .02 .05 .05 .06 .09 .03 .09 .09 .09 .06 .04 .16
[1] 4a86.a .02 .04 .06 .07 .04
0
.04 .04 .05 .07 .10 .01 .10 .11 .07 .08 .02 .17
[1] 4a87.a .04 .06 .05 .10 .02 .04
0
.03 .05 .05 .11 .02 .10 .09 .07 .06 .03 .16
[1] 4a88.a .05 .06 .06 .10 .05 .04 .03
0
.07 .06 .12 .04 .11 .08 .06 .09 .04 .17
[1] 4a8g.a .05 .07 .07 .11 .05 .05 .05 .07
0
.08 .09 .04 .11 .09 .11 .07 .06 .17
[1] 4b9r.a .08 .07 .08 .12 .06 .07 .05 .06 .08
0
.10 .06 .11 .08 .09 .09 .06 .18
[1] 4bk6.b .10 .10 .11 .14 .09 .10 .11 .12 .09 .10
0
.10 .07 .13 .15 .08 .10 .19
[1] 4bk7.a .02 .04 .05 .08 .03 .01 .02 .04 .04 .06 .10
0
.10 .11 .08 .07 .03 .16
[1] 4bkc.b .10 .09 .09 .12 .09 .10 .10 .11 .11 .11 .07 .10
0
.10 .13 .08 .10 .16
[1] 4bkd.a .12 .09 .08 .14 .09 .11 .09 .08 .09 .08 .13 .11 .10
0
.10 .11 .11 .19
[1] 4btz.a .09 .09 .10 .12 .09 .07 .07 .06 .11 .09 .15 .08 .13 .10
0
.13 .08 .21
[1] 4mns.a .09 .09 .09 .13 .06 .08 .06 .09 .07 .09 .08 .07 .08 .11 .13
0
.07 .13
[1] 4qip.a .03 .05 .06 .09 .04 .02 .03 .04 .06 .06 .10 .03 .10 .11 .08 .07
0
.16
[1] 4z3l.b .15 .19 .18 .23 .16 .17 .16 .17 .17 .18 .19 .16 .16 .19 .21 .13 .16
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
4a80.a
4a81.a
4a83.a
4a84.a
4a85.a
4a86.a
4a87.a
4a88.a
4a8g.a
4b9r.a
4bk6.b
4bk7.a
4bkc.b
4bkd.a
4btz.a
4mns.a
4qip.a
4z3l.b
[1] 4a80.a
0
0.3 0.6 0.6 0.1 0.1 0.2 0.2 0.2 0.3 0.4 0.2 0.5 0.5 0.3 0.6 0.2 0.7
[1] 4a81.a 0.3
0
0.5 0.6 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.4 0.5 0.4 0.6 0.3 0.6
[1] 4a83.a 0.6 0.5
0
0.3 0.6 0.6 0.6 0.6 0.6 0.6 0.7 0.6 0.8 0.7 0.7 0.8 0.6 0.8
[1] 4a84.a 0.6 0.6 0.3
0
0.6 0.6 0.6 0.6 0.6 0.6 0.8 0.6 0.8 0.8 0.6 0.8 0.6 0.8
[1] 4a85.a 0.1 0.3 0.6 0.6
0
0.2 0.1 0.1 0.2 0.3 0.4 0.2 0.4 0.5 0.3 0.6 0.3 0.7
[1] 4a86.a 0.1 0.3 0.6 0.6 0.2
0
0.2 0.2 0.2 0.3 0.5 0.2 0.5 0.6 0.3 0.6 0.2 0.7
[1] 4a87.a 0.2 0.3 0.6 0.6 0.1 0.2
0
0.1 0.2 0.3 0.4 0.2 0.5 0.5 0.3 0.6 0.2 0.7
[1] 4a88.a 0.2 0.3 0.6 0.6 0.1 0.2 0.1
0
0.1 0.3 0.4 0.2 0.5 0.5 0.3 0.6 0.3 0.7
[1] 4a8g.a 0.2 0.3 0.6 0.6 0.2 0.2 0.2 0.1
0
0.3 0.4 0.2 0.5 0.5 0.3 0.6 0.3 0.7
[1] 4b9r.a 0.3 0.3 0.6 0.6 0.3 0.3 0.3 0.3 0.3
0
0.5 0.3 0.4 0.6 0.2 0.6 0.3 0.6
[1] 4bk6.b 0.4 0.4 0.7 0.8 0.4 0.5 0.4 0.4 0.4 0.5
0
0.5 0.2 0.5 0.4 0.6 0.5 0.7
[1] 4bk7.a 0.2 0.3 0.6 0.6 0.2 0.2 0.2 0.2 0.2 0.3 0.5
0
0.5 0.6 0.4 0.6 0.2 0.8
[1] 4bkc.b 0.5 0.4 0.8 0.8 0.4 0.5 0.5 0.5 0.5 0.4 0.2 0.5
0
0.6 0.5 0.6 0.5 0.7
[1] 4bkd.a 0.5 0.5 0.7 0.8 0.5 0.6 0.5 0.5 0.5 0.6 0.5 0.6 0.6
0
0.5 0.8 0.6 0.8
[1] 4btz.a 0.3 0.4 0.7 0.6 0.3 0.3 0.3 0.3 0.3 0.2 0.4 0.4 0.5 0.5
0
0.6 0.4 0.7
[1] 4mns.a 0.6 0.6 0.8 0.8 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.8 0.6
0
0.6 0.6
[1] 4qip.a 0.2 0.3 0.6 0.6 0.3 0.2 0.2 0.3 0.3 0.3 0.5 0.2 0.5 0.6 0.4 0.6
0
0.7
[1] 4z3l.b 0.7 0.6 0.8 0.8 0.7 0.7 0.7 0.7 0.7 0.6 0.7 0.8 0.7 0.8 0.7 0.6 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
4a80.a
4a81.a
4a83.a
4a84.a
4a85.a
4a86.a
4a87.a
4a88.a
4a8g.a
4b9r.a
4bk6.b
4bk7.a
4bkc.b
4bkd.a
4btz.a
4mns.a
4qip.a
4z3l.b
[1] 4a80.a
0
0.8 1.2 1.1 0.7 0.6 0.4 0.7 0.7 0.6 0.9 0.5 0.9 0.8 0.9 1.0 0.8 1.0
[1] 4a81.a 0.8
0
1.1 1.0 0.9 1.0 0.8 0.7 1.0 0.8 1.0 0.8 1.2 1.0 0.9 1.3 1.0 1.1
[1] 4a83.a 1.2 1.1
0
0.9 1.4 1.3 1.2 1.3 1.3 1.3 1.5 1.2 1.6 1.3 1.4 1.6 1.4 1.3
[1] 4a84.a 1.1 1.0 0.9
0
1.1 1.2 1.0 0.9 1.2 1.1 1.4 0.9 1.5 1.3 1.1 1.6 1.1 1.3
[1] 4a85.a 0.7 0.9 1.4 1.1
0
0.9 0.5 0.7 0.6 0.8 1.1 0.6 1.1 1.0 0.9 1.1 0.6 1.1
[1] 4a86.a 0.6 1.0 1.3 1.2 0.9
0
0.7 0.8 0.8 0.7 0.9 0.6 1.1 0.9 1.0 1.0 0.9 1.0
[1] 4a87.a 0.4 0.8 1.2 1.0 0.5 0.7
0
0.4 0.7 0.7 0.9 0.4 1.0 0.8 0.8 1.1 0.7 1.0
[1] 4a88.a 0.7 0.7 1.3 0.9 0.7 0.8 0.4
0
0.9 0.7 0.9 0.4 1.1 0.9 0.6 1.2 0.8 1.1
[1] 4a8g.a 0.7 1.0 1.3 1.2 0.6 0.8 0.7 0.9
0
0.8 1.0 0.7 1.1 0.9 1.1 1.1 0.8 1.0
[1] 4b9r.a 0.6 0.8 1.3 1.1 0.8 0.7 0.7 0.7 0.8
0
0.9 0.6 1.1 0.9 0.8 1.0 0.9 1.0
[1] 4bk6.b 0.9 1.0 1.5 1.4 1.1 0.9 0.9 0.9 1.0 0.9
0
1.0 0.4 0.8 1.1 0.8 1.2 1.1
[1] 4bk7.a 0.5 0.8 1.2 0.9 0.6 0.6 0.4 0.4 0.7 0.6 1.0
0
1.0 0.9 0.8 1.1 0.8 1.0
[1] 4bkc.b 0.9 1.2 1.6 1.5 1.1 1.1 1.0 1.1 1.1 1.1 0.4 1.0
0
0.8 1.2 0.8 1.2 1.1
[1] 4bkd.a 0.8 1.0 1.3 1.3 1.0 0.9 0.8 0.9 0.9 0.9 0.8 0.9 0.8
0
1.1 1.1 1.1 1.1
[1] 4btz.a 0.9 0.9 1.4 1.1 0.9 1.0 0.8 0.6 1.1 0.8 1.1 0.8 1.2 1.1
0
1.3 1.0 1.2
[1] 4mns.a 1.0 1.3 1.6 1.6 1.1 1.0 1.1 1.2 1.1 1.0 0.8 1.1 0.8 1.1 1.3
0
1.2 1.0
[1] 4qip.a 0.8 1.0 1.4 1.1 0.6 0.9 0.7 0.8 0.8 0.9 1.2 0.8 1.2 1.1 1.0 1.2
0
1.1
[1] 4z3l.b 1.0 1.1 1.3 1.3 1.1 1.0 1.0 1.1 1.0 1.0 1.1 1.0 1.1 1.1 1.2 1.0 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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