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BRPF1_HUMAN_1076_1205

Peregrin

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BRPF1_HUMAN):D: PWWP (1093:1096, 1099, 1111, 1114, 1117:1121, 1124, 1126, 1127, 1130, 1146, 1147, 1149, 1151:1155)
1180
1093:1096, 1099, 1111, 1114, 1117:1121, 1124, 1126, 1127, 1130, 1146, 1147, 1149, 1151:1155, 1180

Full PDB list

2x35, 2x4w, 2x4x, 2x4y, 3l42, 3mo8, 5c6s (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
1
0
9
4
G
1
0
9
5
Y
1
0
9
6
Y
1
0
9
9
F
1
1
1
4
G
1
1
1
7
P
1
1
1
9
I
1
1
2
0
P
1
1
2
1
P
1
1
2
4
V
1
1
2
7
L
1
1
3
0
L
1
1
4
6
F
1
1
4
7
D
1
1
4
9
K
1
1
5
1
R
1
1
5
2
T
1
1
5
3
W
1
1
5
4
Q
1
1
5
5
[1]2x35.a none . . . . . . . . . . . . . . . . . . . .
[1]2x4w.a SAPATGGVm3lKPHR94 . . . . . . . . . . . . . . . . . . . .
[1]2x4x.c SAPATGGVm3lKPH83 . . . . . . . . . . . . . . . . . . . .
[1]2x4y.a KSAPATGGVm3lKPHR103 . . . . . . . . . . . . . . . . . . . .
[1]2x4y.c KSAPATGGVm3lKPH92 . . . . . . . . . . . . . . . . . . . .
[1]2x4y.g SAPATGGVm3lKP73 . . . . . . . . . . . . . . . . . . . .
[1]3mo8.a PATGGVm3lKPHRY96 . . . . . . . . . . . . . . . . . . . .
[1]5c6s.a 4k811 . . . . . . . . . . . . . . . . . . . .

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
C
1
0
9
3
R
1
0
9
4
G
1
0
9
5
Y
1
0
9
6
Y
1
0
9
9
E
1
1
1
1
F
1
1
1
4
G
1
1
1
7
V
1
1
1
8
P
1
1
1
9
I
1
1
2
0
P
1
1
2
1
P
1
1
2
4
E
1
1
2
6
V
1
1
2
7
L
1
1
3
0
L
1
1
4
6
F
1
1
4
7
D
1
1
4
9
K
1
1
5
1
R
1
1
5
2
T
1
1
5
3
W
1
1
5
4
Q
1
1
5
5
R
1
1
8
0
[1]2x35.a . . . . . . . . . . . . . . . . . . . . . * . . .
[1]2x4w.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x4x.c . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x4y.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x4y.c . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x4y.g . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3mo8.a . . . . . . . . . . . . . . . . . . . . * . . . .
[1]5c6s.a . . . . . . . . . . . . . . . . . . . . . * . . .

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
2x35.a is apo
2x4w.a:SAPATGGVm3lKPHR
2x4x.c:SAPATGGVm3lKPH
2x4y.a:KSAPATGGVm3lKPHR
2x4y.c:KSAPATGGVm3lKPH
2x4y.g:SAPATGGVm3lKP
3mo8.a:PATGGVm3lKPHRY
5c6s.a:4k8
[1] 2x35.a
-
0.7 1.7 0.5 2.0 0.6 0.4 0
[1] 2x4w.a -
0
0.8 0.1 0.9 0 0 0
[1] 2x4x.c - 0.1
0
0 0 0 0.2 0
[1] 2x4y.a - 0 0.1
0
0.4 0 0.1 0
[1] 2x4y.c - 0.1 0 0
0
0 0.1 0
[1] 2x4y.g - 0.1 0.2 0 0.1
0
0.1 0
[1] 3mo8.a - 1.2 1.2 0.7 1.3 0.7
0
0
[1] 5c6s.a - 1.0 1.4 0.8 1.4 0.7 0.5
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
2x35.a
2x4w.a
2x4x.c
2x4y.a
2x4y.c
2x4y.g
3mo8.a
5c6s.a
[1] 2x35.a
0
.13 .12 .10 .11 .11 .13 .07
[1] 2x4w.a .13
0
.06 .06 .06 .06 .10 .07
[1] 2x4x.c .12 .06
0
.03 .01 .02 .09 .09
[1] 2x4y.a .10 .06 .03
0
.02 .03 .10 .08
[1] 2x4y.c .11 .06 .01 .02
0
.01 .09 .08
[1] 2x4y.g .11 .06 .02 .03 .01
0
.09 .08
[1] 3mo8.a .13 .10 .09 .10 .09 .09
0
.13
[1] 5c6s.a .07 .07 .09 .08 .08 .08 .13
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
2x35.a
2x4w.a
2x4x.c
2x4y.a
2x4y.c
2x4y.g
3mo8.a
5c6s.a
[1] 2x35.a
0
1.1 1.0 0.9 0.9 0.8 1.0 0.7
[1] 2x4w.a 1.1
0
0.7 0.9 0.6 0.6 0.4 0.7
[1] 2x4x.c 1.0 0.7
0
0.4 0.3 0.4 0.9 0.7
[1] 2x4y.a 0.9 0.9 0.4
0
0.4 0.4 0.9 0.7
[1] 2x4y.c 0.9 0.6 0.3 0.4
0
0.3 0.7 0.6
[1] 2x4y.g 0.8 0.6 0.4 0.4 0.3
0
0.7 0.5
[1] 3mo8.a 1.0 0.4 0.9 0.9 0.7 0.7
0
0.7
[1] 5c6s.a 0.7 0.7 0.7 0.7 0.6 0.5 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
2x35.a
2x4w.a
2x4x.c
2x4y.a
2x4y.c
2x4y.g
3mo8.a
5c6s.a
[1] 2x35.a
0
2.0 1.9 2.1 1.9 1.8 2.0 1.7
[1] 2x4w.a 2.0
0
1.3 1.6 1.4 1.6 1.1 1.3
[1] 2x4x.c 1.9 1.3
0
1.3 1.1 1.1 1.5 1.3
[1] 2x4y.a 2.1 1.6 1.3
0
1.0 1.2 1.8 1.7
[1] 2x4y.c 1.9 1.4 1.1 1.0
0
1.1 1.5 1.4
[1] 2x4y.g 1.8 1.6 1.1 1.2 1.1
0
1.8 1.3
[1] 3mo8.a 2.0 1.1 1.5 1.8 1.5 1.8
0
1.6
[1] 5c6s.a 1.7 1.3 1.3 1.7 1.4 1.3 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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