SMTL ID : 6ki3.1 (1 other biounit)

The crystal structure of AsfvAP:dF commplex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x DG- DC- DA- DG- DC- DG- DT- DC- DC: DNA (5'-D(*GP*CP*AP*GP*CP*GP*TP*CP*C)-3')(Non-covalent)

DG-DC-DA-DG-DC-DG-DT-DC-DC.1: 15 residues within 4Å: Chain A: R.55, Y.86, D.236, R.237 Chain B: G.10, G.11, A.12, C.13, G.14, C.15, T.16, G.17 Ligands: 3DR-DC-DG-DA-DC-DG-DA-DG.2, 3DR-DC-DG-DA-DC-DG-DA-DG.2, ZN.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.19, A:R.55, A:R.55, A:A.57, A:K.152, A:H.153 Water bridges: A:A.123 Salt bridges: A:H.153, A:H.153, A:H.154, A:H.154

1 x 3DR- DC- DG- DA- DC- DG- DA- DG: DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*AP*G)-3')(Non-covalent)

3DR-DC-DG-DA-DC-DG-DA-DG.2: 31 residues within 4Å: Chain A: F.10, S.12, H.13, R.14, F.50, G.53, P.54, R.55, N.60, H.83, Y.86, H.120, E.147, D.184, H.187, D.236, H.238, E.276, N.278 Chain B: C.1, C.2, T.3, C.4, G.5, T.6, C.7, G.8 Ligands: DG-DC-DA-DG-DC-DG-DT-DC-DC.1, ZN.3, ZN.4, ZN.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.10, A:F.50 Hydrogen bonds: A:Y.86, A:N.278 Salt bridges: A:H.120, A:H.187, A:H.238

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.187, D.236, H.238 Ligands: DG-DC-DA-DG-DC-DG-DT-DC-DC.1, 3DR-DC-DG-DA-DC-DG-DA-DG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.187, A:D.236, A:D.236, A:H.238 ZN.4: 7 residues within 4Å: Chain A: E.147, D.184, H.187, H.223, E.276 Ligands: 3DR-DC-DG-DA-DC-DG-DA-DG.2, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.147, A:D.184, A:H.223, A:E.276 ZN.5: 5 residues within 4Å: Chain A: H.83, H.120, E.147 Ligands: 3DR-DC-DG-DA-DC-DG-DA-DG.2, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.83, A:H.120, A:E.147, A:E.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., A unique DNA-binding mode of African swine fever virus AP endonuclease. Cell Discov (2020)

Release Date

2020-05-27

Peptides

Probable AP endonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable AP endonuclease

Related Entries With Identical Sequence