SMTL ID : 6khy.3 (2 other biounits)

The crystal structure of AsfvAP:AG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.187, D.236, H.238 Ligands: MES.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.187, A:D.236, A:D.236, A:H.238 ZN.2: 7 residues within 4Å: Chain A: E.147, D.184, H.187, H.223, E.276 Ligands: ZN.3, MES.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.147, A:D.184, A:H.223, A:E.276 ZN.3: 5 residues within 4Å: Chain A: H.83, H.120, E.147 Ligands: ZN.2, MES.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.83, A:H.120, A:E.147, A:E.147 ZN.5: 4 residues within 4Å: Chain D: H.187, D.236, H.238 Ligands: MES.8 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.187, D:D.236, D:D.236, D:H.238 ZN.6: 7 residues within 4Å: Chain D: E.147, D.184, H.187, H.223, E.276 Ligands: ZN.7, MES.8 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.147, D:D.184, D:H.223, D:E.276 ZN.7: 5 residues within 4Å: Chain D: H.83, H.120, E.147 Ligands: ZN.6, MES.8 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.83, D:H.120, D:E.147, D:E.147

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 14 residues within 4Å: Chain A: H.83, H.120, E.147, D.184, H.187, H.223, D.236, H.238, E.276 Chain B: C.16 Chain C: C.17 Ligands: ZN.1, ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:H.83, A:H.120, A:H.187, A:H.238 MES.8: 14 residues within 4Å: Chain D: H.83, H.120, E.147, D.184, H.187, H.223, D.236, H.238, E.276 Chain E: C.16 Chain F: C.17 Ligands: ZN.5, ZN.6, ZN.7 4 PLIP interactions: 4 interactions with chain D Salt bridges: D:H.83, D:H.120, D:H.187, D:H.238

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

2020-06-03

Peptides

Probable AP endonuclease: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D
D

Probable AP endonuclease

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