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CLH1_HUMAN_1_362

Clathrin heavy chain 1 [Clathrin heavy chain family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CLH1_HUMAN):R: Globular terminal domain (50, 52, 62:68, 80, 82:84, 87, 89, 91:93, 96:98)
R: WD40-like repeat 1 (50, 52, 62:67)
R: WD40-like repeat 2 (68, 80, 82:84, 87, 89, 91:93, 96:98)
50, 52, 62:68, 80, 82:84, 87, 89, 91:93, 96:98

Full PDB list

1bpo, 1c9i, 1c9l, 1utc, 2xzg, 3gc3, 3gd1, 4g55, 5m5r, 5m5s, 5m5t, 5m5u, 5m5v, 5m61, 5ods (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
5
0
I
5
2
I
6
2
R
6
3
R
6
4
P
6
5
I
6
6
S
6
7
A
6
8
I
8
0
L
8
2
K
8
3
A
8
4
T
8
7
Q
8
9
F
9
1
I
9
3
K
9
6
K
9
8
[1]1c9i.a AVSLLDLDA64 . . . . . . . . . . . . . . . . . . .
[1]1c9i.b VSLLDLD53 . . . . . . . . . . . . . . . . . . .
[1]1c9l.a DTNLIEFE69 . . . . . . . . . . . . . . . . . . .
[1]2xzg.a vh127 . . . . . . . . . . . . . . . . . . .
[1]3gc3.b DTNLIELD56 . . . . . . . . . . . . . . . . . . .
[1]3gd1.i TNLIELDA61 . . . . . . . . . . . . . . . . . . .
[1]5m5r.a GDLLNLDL60 . . . . . . . . . . . . . . . . . . .
[1]5m5t.a ETLLDLD56 . . . . . . . . . . . . . . . . . . .
[1]5m5u.a SDILFPA53 . . . . . . . . . . . . . . . . . . .
[1]5m5v.a LPLLES43 . . . . . . . . . . . . . . . . . . .
[1]5m61.b ETLLDLDFD72 . . . . . . . . . . . . . . . . . . .
[2]1utc.b none . . . . . . . . . . . . . . . . . . .
[2]4g55.a vh228 . . . . . . . . . . . . . . . . . . .

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
V
5
0
I
5
2
I
6
2
R
6
3
R
6
4
P
6
5
I
6
6
S
6
7
A
6
8
I
8
0
L
8
2
K
8
3
A
8
4
T
8
7
Q
8
9
F
9
1
N
9
2
I
9
3
K
9
6
S
9
7
K
9
8
[1]1c9i.a . . . . * . . . . . . . . . . . . . * . .
[1]1c9i.b . . . . * . . . . . . . . . . . . . * . .
[1]1c9l.a . . . . * . . . . . . . . . . . . . . . .
[1]2xzg.a . . . . * . * . . . . . . . . . . . . . .
[1]3gc3.b . . * . . . . . . . . . . . . . . . . . .
[1]3gd1.i . . . . . . . . . . . . . . . . . . . . .
[1]5m5r.a . . . . * . . . . . . . . . . . . . . . .
[1]5m5t.a . . . . . . . . . . . . . . . . . . . . .
[1]5m5u.a . . . . * . . . . . . . . . . . . . . . .
[1]5m5v.a . . . . * . . . . . . . . . . . . . . . .
[1]5m61.b . . . . * . . . . . . . . . . . . . . . .
[2]1utc.b * . . . * . . . . . . . . . . * . . * . .
[2]4g55.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
1c9i.a:AVSLLDLDA
1c9i.b:VSLLDLD
1c9l.a:DTNLIEFE
2xzg.a:vh1
3gc3.b:DTNLIELD
3gd1.i:TNLIELDA
5m5r.a:GDLLNLDL
5m5t.a:ETLLDLD
5m5u.a:SDILFPA
5m5v.a:LPLLES
5m61.b:ETLLDLDFD
1utc.b is apo
4g55.a:vh2
[1] 1c9i.a
0.2
0.5 0.8 0.8 0.8 0.5 1.1 0.1 0.8 0.1 0.2 - 0.9
[1] 1c9i.b 0.2
0.3
0.2 1.7 0.6 1.0 1.0 0.1 0 0.1 0.1 - 2.2
[1] 1c9l.a 0.2 0.2
0.1
0.9 0.3 0.4 1.1 0.2 0.9 0.1 0.4 - 1.3
[1] 2xzg.a 3.6 4.0 3.5
0
4.3 5.2 3.9 4.6 3.2 3.7 4.5 - 2.6
[1] 3gc3.b 0.1 0.3 0.2 1.0
0
0.5 0.1 0.1 0.1 0 0 - 1.6
[1] 3gd1.i 0.6 0.5 0.3 0.8 0.4
0
0.8 0.4 0.2 0.1 0.4 - 1.2
[1] 5m5r.a 0.2 0.1 0.4 0.4 0.2 0.9
0
0.1 2.6 0 1.6 - 2.0
[1] 5m5t.a 0.1 0.1 0.6 0.7 0.5 0.7 0.5
0
0.5 0 0 - 1.2
[1] 5m5u.a 0.2 0.7 0.2 1.2 0.1 0.9 0.1 0.1
0
0 0.1 - 2.4
[1] 5m5v.a 0.2 0.9 0.2 1.2 0.5 0.7 0.6 0.1 0.1
0
0 - 2.6
[1] 5m61.b 0 0.3 0.6 2.1 0.5 0.8 0.1 0 0.4 0
0
- 2.7
[2] 1utc.b 2.1 1.6 3.2 2.9 2.8 2.9 2.5 2.2 0.8 1.5 2.1
-
1.9
[2] 4g55.a 2.4 0.8 3.5 1.9 3.3 3.0 2.1 1.9 4.1 1.0 4.7 -
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1c9i.a
1c9i.b
1c9l.a
2xzg.a
3gc3.b
3gd1.i
5m5r.a
5m5t.a
5m5u.a
5m5v.a
5m61.b
1utc.b
4g55.a
[1] 1c9i.a
0
.16 .05 .31 .17 .15 .16 .12 .19 .15 .18 .23 .29
[1] 1c9i.b .16
0
.12 .20 .17 .18 .13 .19 .13 .10 .15 .24 .22
[1] 1c9l.a .05 .12
0
.30 .14 .12 .14 .11 .16 .12 .16 .24 .30
[1] 2xzg.a .31 .20 .30
0
.24 .28 .18 .28 .20 .20 .18 .38 .26
[1] 3gc3.b .17 .17 .14 .24
0
.11 .13 .10 .09 .13 .13 .27 .34
[1] 3gd1.i .15 .18 .12 .28 .11
0
.16 .10 .16 .16 .20 .31 .35
[1] 5m5r.a .16 .13 .14 .18 .13 .16
0
.11 .07 .04 .05 .28 .23
[1] 5m5t.a .12 .19 .11 .28 .10 .10 .11
0
.10 .12 .10 .26 .32
[1] 5m5u.a .19 .13 .16 .20 .09 .16 .07 .10
0
.07 .05 .26 .28
[1] 5m5v.a .15 .10 .12 .20 .13 .16 .04 .12 .07
0
.06 .25 .24
[1] 5m61.b .18 .15 .16 .18 .13 .20 .05 .10 .05 .06
0
.28 .24
[2] 1utc.b .23 .24 .24 .38 .27 .31 .28 .26 .26 .25 .28
0
.24
[2] 4g55.a .29 .22 .30 .26 .34 .35 .23 .32 .28 .24 .24 .24
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

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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
1c9i.a
1c9i.b
1c9l.a
2xzg.a
3gc3.b
3gd1.i
5m5r.a
5m5t.a
5m5u.a
5m5v.a
5m61.b
1utc.b
4g55.a
[1] 1c9i.a
0
0.2 0.2 0.5 0.5 0.7 0.4 0.3 0.3 0.3 0.3 0.6 0.8
[1] 1c9i.b 0.2
0
0.3 0.5 0.5 0.7 0.5 0.4 0.4 0.4 0.4 0.6 0.7
[1] 1c9l.a 0.2 0.3
0
0.6 0.5 0.7 0.5 0.3 0.4 0.4 0.3 0.6 0.8
[1] 2xzg.a 0.5 0.5 0.6
0
0.6 0.7 0.6 0.5 0.5 0.6 0.5 0.6 0.5
[1] 3gc3.b 0.5 0.5 0.5 0.6
0
0.7 0.4 0.4 0.4 0.4 0.4 0.7 0.8
[1] 3gd1.i 0.7 0.7 0.7 0.7 0.7
0
0.7 0.7 0.7 0.7 0.6 0.9 0.9
[1] 5m5r.a 0.4 0.5 0.5 0.6 0.4 0.7
0
0.3 0.4 0.5 0.3 0.7 0.8
[1] 5m5t.a 0.3 0.4 0.3 0.5 0.4 0.7 0.3
0
0.3 0.3 0.1 0.5 0.8
[1] 5m5u.a 0.3 0.4 0.4 0.5 0.4 0.7 0.4 0.3
0
0.3 0.3 0.6 0.8
[1] 5m5v.a 0.3 0.4 0.4 0.6 0.4 0.7 0.5 0.3 0.3
0
0.3 0.6 0.9
[1] 5m61.b 0.3 0.4 0.3 0.5 0.4 0.6 0.3 0.1 0.3 0.3
0
0.5 0.8
[2] 1utc.b 0.6 0.6 0.6 0.6 0.7 0.9 0.7 0.5 0.6 0.6 0.5
0
0.8
[2] 4g55.a 0.8 0.7 0.8 0.5 0.8 0.9 0.8 0.8 0.8 0.9 0.8 0.8
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
1c9i.a
1c9i.b
1c9l.a
2xzg.a
3gc3.b
3gd1.i
5m5r.a
5m5t.a
5m5u.a
5m5v.a
5m61.b
1utc.b
4g55.a
[1] 1c9i.a
0
0.7 0.4 1.5 0.9 1.1 1.0 0.7 0.9 1.0 0.9 1.2 1.7
[1] 1c9i.b 0.7
0
0.7 1.5 0.9 1.1 1.2 0.8 0.8 0.9 0.8 1.2 1.9
[1] 1c9l.a 0.4 0.7
0
1.5 0.9 1.0 1.0 0.7 0.8 0.9 0.9 1.2 1.7
[1] 2xzg.a 1.5 1.5 1.5
0
1.5 1.7 1.3 1.6 1.4 1.6 1.4 1.7 1.6
[1] 3gc3.b 0.9 0.9 0.9 1.5
0
0.9 1.0 0.7 0.7 0.9 0.9 1.4 1.9
[1] 3gd1.i 1.1 1.1 1.0 1.7 0.9
0
1.2 1.0 1.0 1.0 1.1 1.4 2.0
[1] 5m5r.a 1.0 1.2 1.0 1.3 1.0 1.2
0
0.9 1.0 1.1 1.1 1.5 1.5
[1] 5m5t.a 0.7 0.8 0.7 1.6 0.7 1.0 0.9
0
0.7 0.9 0.7 1.2 1.8
[1] 5m5u.a 0.9 0.8 0.8 1.4 0.7 1.0 1.0 0.7
0
0.5 0.7 1.3 1.9
[1] 5m5v.a 1.0 0.9 0.9 1.6 0.9 1.0 1.1 0.9 0.5
0
0.9 1.3 2.0
[1] 5m61.b 0.9 0.8 0.9 1.4 0.9 1.1 1.1 0.7 0.7 0.9
0
1.2 1.9
[2] 1utc.b 1.2 1.2 1.2 1.7 1.4 1.4 1.5 1.2 1.3 1.3 1.2
0
1.7
[2] 4g55.a 1.7 1.9 1.7 1.6 1.9 2.0 1.5 1.8 1.9 2.0 1.9 1.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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