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ABC3G_HUMAN_191_383

DNA dC->dU-editing enzyme APOBEC-3G [Cytidine and deoxycytidylate deaminase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ABC3G_HUMAN):R: Necessary for homooligomerization (278, 280, 307, 308, 310, 334)
D: CMP/dCMP-type deaminase 2 (278, 280, 307, 308, 310)
278, 280, 307, 308, 310, 334

Full PDB list

3e1u, 3iqs, 3ir2, 3v4j, 3v4k, 4rov, 4row (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
2
7
8
T
2
8
0
C
3
0
8
F
3
1
0
K
3
3
4
[1]3v4j.a pqr12 . . * K .
[1]3v4k.a none . . . K .
[1]4row.a none . . . . .

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
R
2
7
8
T
2
8
0
L
3
0
7
C
3
0
8
F
3
1
0
K
3
3
4
[1]3v4j.a . . . * K .
[1]3v4k.a . . . * K *
[1]4row.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
3v4j.a:pqr
3v4k.a is apo
4row.a is apo
[1] 3v4j.a
0.6
- -
[1] 3v4k.a 1.8
-
-
[1] 4row.a 2.0 -
-
[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
3v4j.a
3v4k.a
4row.a
[1] 3v4j.a
0
.20 .23
[1] 3v4k.a .20
0
.03
[1] 4row.a .23 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3v4j.a
3v4k.a
4row.a
[1] 3v4j.a
0
0.2 0.2
[1] 3v4k.a 0.2
0
0.2
[1] 4row.a 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3v4j.a
3v4k.a
4row.a
[1] 3v4j.a
0
1.4 1.5
[1] 3v4k.a 1.4
0
0.4
[1] 4row.a 1.5 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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