SMTL ID : 6w0r.1

Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DG-DT-DC.1: 19 residues within 4Å: Chain A: S.140, N.141, L.235, P.236, G.237, V.238, G.239, T.240, K.241, V.242, D.260, V.261 Ligands: DC-DC-DT-DG-DG.2, DC-DC-DT-DG-DG.2, DC-DC-DT-DG-DG.2, DC-DC-DT-DG-DG.2, DC-DC-DT-DG-DG.2, NA.3, S5Y.7 Protein-ligand interaction information (PLIP) not available

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

DC-DC-DT-DG-DG.2: 10 residues within 4Å: Chain A: N.141, N.143, R.146, Y.195, R.196 Ligands: DC-DA-DG-DG-DT-DC.1, DC-DA-DG-DG-DT-DC.1, DC-DA-DG-DG-DT-DC.1, DC-DA-DG-DG-DT-DC.1, S5Y.7 Protein-ligand interaction information (PLIP) not available

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: C.233, L.235, V.238 Ligands: DC-DA-DG-DG-DT-DC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.238, A:V.238

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 5 residues within 4Å: Chain A: V.50, A.52, Y.91, D.128, E.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.52, A:D.128 Water bridges: A:D.128, A:E.131 NO3.5: 5 residues within 4Å: Chain A: R.89, K.90, Q.93, L.94, D.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.89, A:Q.93, A:L.94, A:D.95 NO3.6: 4 residues within 4Å: Chain A: Y.225, H.229, D.244, R.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.225 Water bridges: A:R.296, A:R.296, A:R.296

1 x S5Y: 2-(2-ethoxyethoxy)ethanethiol(Non-covalent)

S5Y.7: 10 residues within 4Å: Chain A: Y.195, R.196, C.199, G.237 Ligands: DC-DA-DG-DG-DT-DC.1, DC-DA-DG-DG-DT-DC.1, DC-DA-DG-DG-DT-DC.1, DC-DA-DG-DG-DT-DC.1, DC-DC-DT-DG-DG.2, DC-DC-DT-DG-DG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shigdel, U.K. et al., The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase. Nat Commun (2020)

Release Date

2020-09-23

Peptides

N-glycosylase/DNA lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-glycosylase/DNA lyase