SMTL ID : 3v4k.3 (3 other biounits)

First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase APOBEC3G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-tetramer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: V.35, R.36, G.37, R.38, W.108 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: V.35, R.36, G.37, R.38, W.108 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain C: V.35, R.36, G.37, R.38, W.108 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain D: V.35, R.36, G.37, R.38, W.108 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.32, H.190 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.32, A:H.190, H2O.2, H2O.2, H2O.9, H2O.9 MG.6: 3 residues within 4Å: Chain B: E.32, P.33, H.190 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.190, H2O.12, H2O.13, H2O.15, H2O.17 MG.10: 2 residues within 4Å: Chain C: E.32, H.190 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.32, C:H.190, H2O.21, H2O.21, H2O.28, H2O.28 MG.14: 3 residues within 4Å: Chain D: E.32, P.33, H.190 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:H.190, H2O.31, H2O.32, H2O.34, H2O.36

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.71, H.73 Chain D: C.84 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:C.84, A:H.71, A:H.73, H2O.9 ZN.4: 4 residues within 4Å: Chain A: H.80, E.82, C.111, C.114 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.80, A:C.111, A:C.114, H2O.2 ZN.7: 2 residues within 4Å: Chain B: H.71, H.73 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.71, B:H.73, H2O.18 ZN.8: 4 residues within 4Å: Chain B: H.80, E.82, C.111, C.114 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.80, B:C.111, B:C.114, H2O.13 ZN.11: 2 residues within 4Å: Chain C: H.71, H.73 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.71, C:H.73, H2O.28 ZN.12: 4 residues within 4Å: Chain C: H.80, E.82, C.111, C.114 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.80, C:C.111, C:C.114, H2O.21 ZN.15: 3 residues within 4Å: Chain A: C.84 Chain D: H.71, H.73 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:C.84, D:H.71, D:H.73, H2O.37 ZN.16: 4 residues within 4Å: Chain D: H.80, E.82, C.111, C.114 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.80, D:C.111, D:C.114, H2O.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G. Acs Chem.Biol. (2012)

Release Date

2012-01-25

Peptides

DNA dC->dU-editing enzyme APOBEC-3G: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

DNA dC->dU-editing enzyme APOBEC-3G

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