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ARF6_HUMAN_9_175

ADP-ribosylation factor 6 [Small GTPase superfamily. Arf family]

Composition of the binding site

Protein chains monomer
A1 (ARF6_HUMAN):22:28, 41:44, 63, 65:67, 122, 123, 125, 126, 155:15722:28, 41:44, 63, 65:67, 122, 123, 125, 126, 155:157
Metals (Me):Mg

Full PDB list

1e0s, 2a5d, 2a5f, 2a5g, 2j5x, 2w83, 3n5c, 3pcr, 3vhx, 4kax (redundant Pocketome entry); 3lvq, 3lvr (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
D
2
2
A
2
3
A
2
4
G
2
5
K
2
6
T
2
7
T
2
8
T
4
1
P
4
3
T
4
4
G
6
5
G
6
6
Q
6
7
N
1
2
2
K
1
2
3
D
1
2
5
L
1
2
6
C
1
5
5
A
1
5
6
T
1
5
7
[1]1e0s.a gdp28 . . . . . . . . . . . . . . . . . . . .
[1]2j5x.a gsp32 . . . . . . . . . . . . . . . . . . . . Mg
[1]2w83.a gtp32 . . . . . . . . . . . . L . . . . . . . Mg
[1]3n5c.a gdp28 . . . . . . . - - - . . . . . . . . . .
[1]3pcr.b gtp32 . . . . . . . . . . . . . . . . . . . . Mg

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 Me
D
2
2
A
2
3
A
2
4
G
2
5
K
2
6
T
2
7
T
2
8
T
4
1
I
4
2
P
4
3
T
4
4
D
6
3
G
6
5
G
6
6
Q
6
7
N
1
2
2
K
1
2
3
D
1
2
5
L
1
2
6
C
1
5
5
A
1
5
6
T
1
5
7
[1]1e0s.a . . . . . . . . . . . * . . . . . . . . . .
[1]2j5x.a . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2w83.a . . . . . . . . . . . . . . L . . . . . . . Mg
[1]3n5c.a . . . . . . . - - - - * . . . . . . . . . .
[1]3pcr.b . . . . . . . . . . . . . . . . . . . . . . Mg

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
1e0s.a:gdp
2j5x.a:gsp
2w83.a:gtp
3n5c.a:gdp
3pcr.b:gtp
[1] 1e0s.a
0
1.0 0.8 0 0.4
[1] 2j5x.a 0.1
0
0 0 0.6
[1] 2w83.a 0.4 0.2
0
0.3 0.3
[1] 3n5c.a 0 1.0 0.7
0
0.6
[1] 3pcr.b 0.5 0.8 0.6 0.3
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
1e0s.a
2j5x.a
2w83.a
3n5c.a
3pcr.b
[1] 1e0s.a
0
.08 .06 0 .08
[1] 2j5x.a .08
0
.04 .08 .09
[1] 2w83.a .06 .04
0
.07 .06
[1] 3n5c.a 0 .08 .07
0
.08
[1] 3pcr.b .08 .09 .06 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.3 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
1e0s.a
2j5x.a
2w83.a
3n5c.a
3pcr.b
[1] 1e0s.a
0
7.5 7.6 1.8 7.9
[1] 2j5x.a 7.5
0
0.3 3.4 0.8
[1] 2w83.a 7.6 0.3
0
3.4 0.7
[1] 3n5c.a 1.8 3.4 3.4
0
3.3
[1] 3pcr.b 7.9 0.8 0.7 3.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.8 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
1e0s.a
2j5x.a
2w83.a
3n5c.a
3pcr.b
[1] 1e0s.a
0
7.8 7.9 2.3 8.2
[1] 2j5x.a 7.8
0
0.5 3.1 0.9
[1] 2w83.a 7.9 0.5
0
3.0 0.8
[1] 3n5c.a 2.3 3.1 3.0
0
3.0
[1] 3pcr.b 8.2 0.9 0.8 3.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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