SMTL ID : 7uxd.1

Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy Zebularine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x DA- DA- DT- DC- DC- DDN- DA- DA- DA: DNA (5'-D(*AP*AP*TP*CP*CP*(DDN)P*AP*AP*A)-3')(Non-covalent)

DA-DA-DT-DC-DC-DDN-DA-DA-DA.1: 25 residues within 4Å: Chain A: W.26, V.27, R.28, G.29, R.30, H.31, E.32, T.33, N.59, A.61, K.62, H.63, H.72, A.73, E.74, W.100, S.101, P.102, C.103, C.106, Y.130, D.131, D.132, K.133 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.33, A:H.72, A:A.73, A:E.74, A:C.103 Water bridges: A:N.59, A:N.59, A:Y.130 Salt bridges: A:H.31 pi-Stacking: A:H.72, A:Y.130

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.72, E.74, C.103, C.106 Ligands: DA-DA-DT-DC-DC-DDN-DA-DA-DA.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.72, A:C.103, A:C.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maiti, A. et al., Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state. Nat Commun (2022)

Release Date

2022-12-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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