SMTL ID : 8ftj.1

Crystal structure of human NEIL1 (P2G (242K) C(delta)100) glycosylase bound to DNA duplex containing urea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: Q.138, E.139, Y.140, Q.141, Q.142 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.140, A:Q.141, A:Q.142, A:Q.142 Water bridges: A:Q.138 EDO.2: 3 residues within 4Å: Chain A: G.125, G.126, K.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.126, A:K.127 EDO.3: 2 residues within 4Å: Chain A: H.229, K.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.233 Water bridges: A:L.137

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: R.184, R.260 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.184, A:R.260 SO4.5: 2 residues within 4Å: Chain A: P.93, R.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.94 Salt bridges: A:R.94 SO4.6: 2 residues within 4Å: Chain A: R.56, W.128 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tomar, R. et al., Base excision repair of the N-(2-deoxy-d-erythro-pentofuranosyl)-urea lesion by the hNEIL1 glycosylase. Nucleic Acids Res. (2023)

Release Date

2023-04-26

Peptides

Endonuclease 8-like 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endonuclease 8-like 1