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EPHA3_HUMAN_604_947_pep

Ephrin type-A receptor 3 [Protein kinase superfamily. Tyr protein kinase family. Ephrin receptor subfamily]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (EPHA3_HUMAN):D: Protein kinase (746, 750, 767, 784:788, 790, 796, 823, 827, 830, 831, 834)746, 750, 767, 784:788, 790, 796, 823, 827, 830, 831, 834
A2 (EPHA3_HUMAN):894:900894:900

Full PDB list

2gsf, 2qo2, 2qo7, 2qo9, 2qob, 2qoc, 2qod, 2qof, 2qoi, 2qok, 2qol, 2qon, 2qoo, 2qoq, 3dzq, 3fxx, 3fy2, 4g2f, 4gk2, 4gk3, 4gk4, 4p4c, 4p5q, 4p5z, 4twn, 4two (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
D
7
4
6
R
7
5
0
L
7
6
7
G
7
8
4
K
7
8
5
I
7
8
6
P
7
8
7
I
7
8
8
W
7
9
0
I
7
9
6
R
8
2
3
N
8
3
0
I
8
3
4
A
8
9
5
A
8
9
6
R
8
9
7
P
8
9
8
S
8
9
9
N
9
0
0
[1]2qoc.a none . . . - . . . . . . . . . . . . . . .
[1]3fxx.a QWDNYEptrIW98 . . . . . . . . . . . . . . . . . . .
[1]3fy2.a WDNYEFIW84 . . . . . . . . . . . . . - . . . . .

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

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PDB.ch
A1 A2
D
7
4
6
R
7
5
0
L
7
6
7
G
7
8
4
K
7
8
5
I
7
8
6
P
7
8
7
I
7
8
8
W
7
9
0
I
7
9
6
R
8
2
3
E
8
2
7
N
8
3
0
Q
8
3
1
I
8
3
4
A
8
9
4
A
8
9
5
A
8
9
6
R
8
9
7
P
8
9
8
S
8
9
9
N
9
0
0
[1]2qoc.a . . . - * . . . . . . . . . . . . . . . . .
[1]3fxx.a . . . . . . . . . . . . . . . - . . . . . .
[1]3fy2.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
2qoc.a is apo
3fxx.a:QWDNYEptrIW
3fy2.a:WDNYEFIW
[1] 2qoc.a
-
2.7 2.6
[1] 3fxx.a -
0.1
0.1
[1] 3fy2.a - 0.5
0.2
[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
2qoc.a
3fxx.a
3fy2.a
[1] 2qoc.a
0
.12 .12
[1] 3fxx.a .12
0
.02
[1] 3fy2.a .12 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
2qoc.a
3fxx.a
3fy2.a
[1] 2qoc.a
0
0.8 0.6
[1] 3fxx.a 0.8
0
0.3
[1] 3fy2.a 0.6 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2qoc.a
3fxx.a
3fy2.a
[1] 2qoc.a
0
1.3 1.2
[1] 3fxx.a 1.3
0
0.7
[1] 3fy2.a 1.2 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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