SMTL ID : 8uuc.1

Crystal structure of a bacterial clusterless MutYX bound to an Abasic site analog (THF) opposite d(8-oxo-G)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: K.187, A.188, V.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.188 Water bridges: A:N.192 NA.2: 3 residues within 4Å: Chain A: A.66, S.67, D.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.67, A:S.67

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain A: Q.110, L.112, I.115 Chain C: C.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Q.110, A:L.112, A:I.115 MG.17: 1 residues within 4Å: Chain C: C.5 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: S.209, R.210 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: H.145, V.190, A.191, P.193, R.196 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.191 Salt bridges: A:H.145, A:R.196

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

EDO.6: 10 residues within 4Å: Chain A: N.81, R.82, R.214, A.215, V.218, L.260, E.263, F.265 Chain B: C.5, G.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.81, A:N.81, A:R.82, A:R.214 EDO.7: 7 residues within 4Å: Chain A: S.194, H.199, H.200, T.201 Chain C: C.5, A.6 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.200, A:T.201, A:T.201 Water bridges: A:S.194 EDO.8: 5 residues within 4Å: Chain A: S.67, T.68, A.69, R.267, A.275 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.68, A:T.68, A:T.68, A:A.69, A:A.275 Water bridges: A:S.67 EDO.9: 7 residues within 4Å: Chain A: Q.39, R.82, R.83, A.86, G.114 Chain C: T.9, C.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.39, A:R.82, A:R.82 EDO.10: 3 residues within 4Å: Chain A: K.48, Y.49, R.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.48, A:R.52 EDO.11: 6 residues within 4Å: Chain A: R.140, S.194, S.197, H.199, H.200 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.140, A:S.194 Water bridges: A:T.137, A:R.140, A:H.199 EDO.12: 5 residues within 4Å: Chain A: T.68, L.85, K.88, R.89, E.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.85, A:E.92 EDO.13: 3 residues within 4Å: Chain A: G.208, K.213, E.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.213, A:K.213 Water bridges: A:G.208 EDO.14: 5 residues within 4Å: Chain A: L.25, A.30, W.50, N.51, M.54 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.51 EDO.15: 5 residues within 4Å: Chain A: Q.203, S.204, R.211 Chain B: A.4, C.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.204, A:S.204, A:R.211 EDO.16: 2 residues within 4Å: Chain A: R.268, D.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.268, A:R.268, A:D.271 EDO.18: 1 residues within 4Å: Chain C: C.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trasvina-Arenas, C.H. et al., Crystal structure of MutYX: A novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-Oxoguanine recognition sphere. Biorxiv (2025)

Release Date

2025-01-22

Peptides

Adenine DNA glycosylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenine DNA glycosylase