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CD1A_HUMAN_18_295

T-cell surface glycoprotein CD1a

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CD1A_HUMAN):R: Glycolipid binding (90, 91, 93, 94)
D: Ig-like (186)
27, 29, 31, 45:47, 55:57, 64, 80, 83, 86, 87, 89, 97, 98, 101, 115, 117, 118, 131, 133, 148, 161, 164, 165, 167, 168, 171, 175, 178, 179, 182, 183
27, 29, 31, 45:47, 55:57, 64, 80, 83, 86, 87, 89:91, 93, 94, 97, 98, 101, 115, 117, 118, 131, 133, 148, 161, 164, 165, 167, 168, 171, 175, 178, 179, 182, 183, 186

Full PDB list

1onq, 1xz0, 4x6c, 4x6d, 4x6e, 4x6f, 5j1a (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
7
V
2
9
W
3
1
V
4
5
S
4
6
H
5
5
T
5
6
W
5
7
I
6
4
W
8
0
L
8
3
F
8
7
I
8
9
R
9
0
T
9
1
R
9
3
S
9
4
G
9
7
I
9
8
Y
1
0
1
V
1
1
5
G
1
1
7
L
1
3
1
L
1
3
3
W
1
4
8
F
1
6
1
V
1
6
4
L
1
6
5
Q
1
6
7
N
1
6
8
E
1
7
1
T
1
7
5
L
1
7
9
T
1
8
2
C
1
8
3
F
1
8
6
[1]1onq.a slf55 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1xz0.a jh058 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x6d.a ola20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x6d.c pam18 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x6e.a 42h35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x6f.a 3xu56 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5j1a.a 6f823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
F
2
7
V
2
9
W
3
1
V
4
5
S
4
6
G
4
7
H
5
5
T
5
6
W
5
7
I
6
4
W
8
0
L
8
3
L
8
6
F
8
7
I
8
9
R
9
0
T
9
1
R
9
3
S
9
4
G
9
7
I
9
8
Y
1
0
1
V
1
1
5
G
1
1
7
G
1
1
8
L
1
3
1
L
1
3
3
W
1
4
8
F
1
6
1
V
1
6
4
L
1
6
5
Q
1
6
7
N
1
6
8
E
1
7
1
T
1
7
5
L
1
7
8
L
1
7
9
T
1
8
2
C
1
8
3
F
1
8
6
[1]1onq.a . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1xz0.a . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x6d.a . . * . . . . . . . . . . * . * . * . . . . . . . . . . . . . . . . . . . . . .
[1]4x6d.c . . * . . . . . . . . . . * . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]4x6e.a . . . . . . . . . . . . . * . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]4x6f.a . . . . . . . . . . . . . * . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]5j1a.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
1onq.a:slf
1xz0.a:jh0
4x6d.a:ola
4x6d.c:pam
4x6e.a:42h
4x6f.a:3xu
5j1a.a:6f8
[1] 1onq.a
0.5
0.2 0 0 0 0.2 3.1
[1] 1xz0.a 1.2
0
0 0 0 0.2 2.9
[1] 4x6d.a 4.9 5.8
0
0 3.3 3.3 5.3
[1] 4x6d.c 3.7 4.5 0
0
3.4 3.1 6.0
[1] 4x6e.a 2.2 1.9 0.1 0
0
1.4 2.8
[1] 4x6f.a 3.1 2.0 0 0 0
0.1
2.9
[1] 5j1a.a 5.6 2.0 0 0 0.1 0.8
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
1onq.a
1xz0.a
4x6d.a
4x6d.c
4x6e.a
4x6f.a
5j1a.a
[1] 1onq.a
0
.04 .19 .17 .08 .08 .20
[1] 1xz0.a .04
0
.17 .17 .09 .09 .17
[1] 4x6d.a .19 .17
0
.07 .17 .17 .27
[1] 4x6d.c .17 .17 .07
0
.16 .15 .25
[1] 4x6e.a .08 .09 .17 .16
0
.03 .14
[1] 4x6f.a .08 .09 .17 .15 .03
0
.13
[1] 5j1a.a .20 .17 .27 .25 .14 .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
1onq.a
1xz0.a
4x6d.a
4x6d.c
4x6e.a
4x6f.a
5j1a.a
[1] 1onq.a
0
0.4 0.8 0.8 0.6 0.5 0.8
[1] 1xz0.a 0.4
0
0.7 0.8 0.8 0.6 0.8
[1] 4x6d.a 0.8 0.7
0
0.6 0.9 0.7 0.8
[1] 4x6d.c 0.8 0.8 0.6
0
0.7 0.7 0.9
[1] 4x6e.a 0.6 0.8 0.9 0.7
0
0.4 1.0
[1] 4x6f.a 0.5 0.6 0.7 0.7 0.4
0
0.7
[1] 5j1a.a 0.8 0.8 0.8 0.9 1.0 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
1onq.a
1xz0.a
4x6d.a
4x6d.c
4x6e.a
4x6f.a
5j1a.a
[1] 1onq.a
0
0.6 1.5 1.7 1.3 1.3 1.4
[1] 1xz0.a 0.6
0
1.4 1.7 1.4 1.3 1.4
[1] 4x6d.a 1.5 1.4
0
1.3 1.6 1.4 1.5
[1] 4x6d.c 1.7 1.7 1.3
0
1.7 1.6 1.8
[1] 4x6e.a 1.3 1.4 1.6 1.7
0
0.9 1.4
[1] 4x6f.a 1.3 1.3 1.4 1.6 0.9
0
1.1
[1] 5j1a.a 1.4 1.4 1.5 1.8 1.4 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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