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CD1D_HUMAN_20_296

Antigen-presenting glycoprotein CD1d

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CD1D_HUMAN):R: Glycolipid binding (169, 171, 172)
D: Ig-like (187)
28, 30:32, 44, 46:48, 56, 58, 65, 81, 84, 86:88, 90, 91, 94, 95, 97:99, 102, 103, 106, 108, 112, 114, 116, 118, 132, 134, 136, 141, 142, 149, 158, 166, 175, 176, 179, 180, 183, 184
28, 30:32, 44, 46:48, 56, 58, 65, 81, 84, 86:88, 90, 91, 94, 95, 97:99, 102, 103, 106, 108, 112, 114, 116, 118, 132, 134, 136, 141, 142, 149, 158, 166, 169, 171, 172, 175, 176, 179, 180, 183, 184, 187

Full PDB list

1zt4, 2po6, 3huj, 3sdx, 3tzv, 3u0p, 3vwj, 3vwk, 4en3, 4lhu, 4wo4, 4ww2, 4wwk (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
2
8
C
3
0
L
3
1
Q
3
2
G
4
6
L
4
7
A
4
8
H
5
6
W
5
8
V
6
5
W
8
1
L
8
4
H
8
6
I
8
7
F
8
8
V
9
0
Y
9
1
S
9
4
F
9
5
R
9
7
D
9
8
V
9
9
F
1
0
2
L
1
0
8
L
1
1
2
L
1
1
4
V
1
1
6
A
1
1
8
F
1
3
2
V
1
3
4
F
1
3
6
L
1
4
2
W
1
4
9
W
1
5
8
L
1
6
6
D
1
6
9
W
1
7
1
T
1
7
2
T
1
7
5
V
1
7
6
L
1
7
9
C
1
8
4
F
1
8
7
[1]3huj.c agh60 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3sdx.a gcy45 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3tzv.c d12,hex,lsc53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3u0p.a hex,lsc,und52 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3u0p.c lsc35 . . . . . . . . . . . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3u0p.e none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3vwj.a db354 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3vwk.a 4gh58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4lhu.a jls,N66 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ww2.c jls58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
8
C
3
0
L
3
1
Q
3
2
T
4
4
G
4
6
L
4
7
A
4
8
H
5
6
W
5
8
V
6
5
W
8
1
L
8
4
H
8
6
I
8
7
F
8
8
V
9
0
Y
9
1
S
9
4
F
9
5
R
9
7
D
9
8
V
9
9
F
1
0
2
A
1
0
3
L
1
0
6
L
1
0
8
L
1
1
2
L
1
1
4
V
1
1
6
A
1
1
8
F
1
3
2
V
1
3
4
F
1
3
6
I
1
4
1
L
1
4
2
W
1
4
9
W
1
5
8
L
1
6
6
D
1
6
9
W
1
7
1
T
1
7
2
T
1
7
5
V
1
7
6
L
1
7
9
L
1
8
0
T
1
8
3
C
1
8
4
F
1
8
7
[1]3huj.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3sdx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3tzv.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3u0p.a . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3u0p.c . . . . . . . . . * . . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3u0p.e . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . .
[1]3vwj.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3vwk.a . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4lhu.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ww2.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
3huj.c:agh
3sdx.a:gcy
3tzv.c:d12,hex,lsc
3u0p.a:hex,lsc,und
3u0p.c:lsc
3u0p.e is apo
3vwj.a:db3
3vwk.a:4gh
4lhu.a:N,jls
4ww2.c:jls
[1] 3huj.c
0.2
0.2 1.4 0.2 0.4 - 0.6 0.5 0.3 0.6
[1] 3sdx.a 0
0
0.3 0 0 - 0.1 0.2 0 0.2
[1] 3tzv.c 0.1 0.2
0.2
0.3 0.2 - 0.2 0 0.2 0.2
[1] 3u0p.a 0.3 0.2 1.2
0
0 - 0.2 0.1 0 0
[1] 3u0p.c 0.5 0.3 1.5 0.3
0
- 0.2 0.2 0.1 0.3
[1] 3u0p.e 0.5 0.5 1.5 0.9 0
-
0.4 1.0 0.2 0.2
[1] 3vwj.a 0 0.3 0.6 0 0.1 -
0.2
0.3 0.2 0.4
[1] 3vwk.a 0 0.2 1.0 0 0.2 - 0.1
0.2
0 0.1
[1] 4lhu.a 0.3 0.3 1.3 0.2 0.2 - 0.3 0.5
0
0.2
[1] 4ww2.c 0.4 0.7 3.0 0.5 0.4 - 0.5 0.5 0.1
0.1
[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
3huj.c
3sdx.a
3tzv.c
3u0p.a
3u0p.c
3u0p.e
3vwj.a
3vwk.a
4lhu.a
4ww2.c
[1] 3huj.c
0
.04 .05 .05 .04 .06 .03 .04 .04 .06
[1] 3sdx.a .04
0
.02 .04 .04 .03 .02 .02 .03 .07
[1] 3tzv.c .05 .02
0
.04 .04 .04 .03 .03 .04 .06
[1] 3u0p.a .05 .04 .04
0
.02 .06 .03 .02 .03 .04
[1] 3u0p.c .04 .04 .04 .02
0
.04 .03 .03 .02 .05
[1] 3u0p.e .06 .03 .04 .06 .04
0
.05 .05 .05 .08
[1] 3vwj.a .03 .02 .03 .03 .03 .05
0
.02 .03 .07
[1] 3vwk.a .04 .02 .03 .02 .03 .05 .02
0
.03 .05
[1] 4lhu.a .04 .03 .04 .03 .02 .05 .03 .03
0
.05
[1] 4ww2.c .06 .07 .06 .04 .05 .08 .07 .05 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
3huj.c
3sdx.a
3tzv.c
3u0p.a
3u0p.c
3u0p.e
3vwj.a
3vwk.a
4lhu.a
4ww2.c
[1] 3huj.c
0
0.4 0.5 0.7 0.5 0.6 0.5 0.4 0.4 0.3
[1] 3sdx.a 0.4
0
0.4 0.7 0.5 0.6 0.4 0.3 0.5 0.4
[1] 3tzv.c 0.5 0.4
0
0.7 0.6 0.8 0.5 0.4 0.6 0.6
[1] 3u0p.a 0.7 0.7 0.7
0
0.5 0.7 0.7 0.7 0.8 0.8
[1] 3u0p.c 0.5 0.5 0.6 0.5
0
0.4 0.6 0.6 0.6 0.5
[1] 3u0p.e 0.6 0.6 0.8 0.7 0.4
0
0.7 0.7 0.6 0.6
[1] 3vwj.a 0.5 0.4 0.5 0.7 0.6 0.7
0
0.4 0.5 0.5
[1] 3vwk.a 0.4 0.3 0.4 0.7 0.6 0.7 0.4
0
0.5 0.5
[1] 4lhu.a 0.4 0.5 0.6 0.8 0.6 0.6 0.5 0.5
0
0.3
[1] 4ww2.c 0.3 0.4 0.6 0.8 0.5 0.6 0.5 0.5 0.3
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

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
3huj.c
3sdx.a
3tzv.c
3u0p.a
3u0p.c
3u0p.e
3vwj.a
3vwk.a
4lhu.a
4ww2.c
[1] 3huj.c
0
0.5 1.0 1.0 0.8 1.0 0.6 0.5 0.8 0.7
[1] 3sdx.a 0.5
0
0.9 1.0 0.8 1.0 0.5 0.5 0.9 0.8
[1] 3tzv.c 1.0 0.9
0
1.1 1.1 1.3 0.9 0.9 1.1 1.1
[1] 3u0p.a 1.0 1.0 1.1
0
0.6 1.0 1.0 1.0 1.1 1.0
[1] 3u0p.c 0.8 0.8 1.1 0.6
0
0.7 0.9 0.9 0.9 0.8
[1] 3u0p.e 1.0 1.0 1.3 1.0 0.7
0
1.1 1.0 0.9 1.0
[1] 3vwj.a 0.6 0.5 0.9 1.0 0.9 1.1
0
0.5 0.9 0.9
[1] 3vwk.a 0.5 0.5 0.9 1.0 0.9 1.0 0.5
0
0.9 0.8
[1] 4lhu.a 0.8 0.9 1.1 1.1 0.9 0.9 0.9 0.9
0
0.7
[1] 4ww2.c 0.7 0.8 1.1 1.0 0.8 1.0 0.9 0.8 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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