SMTL ID : 5vhv.1 (1 other biounit)

Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an oxocarbenium-intermediate analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: R.157, L.158, P.159, W.160, R.163 Chain B: C.5 Chain C: G.8, G.9, A.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.163, A:R.163 Water bridges: A:W.160

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

MES.2: 6 residues within 4Å: Chain A: R.97, D.98, D.99, F.100, K.101, R.130 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.98, A:D.98, A:F.100 Water bridges: A:R.102, A:R.130 Salt bridges: A:D.98, A:D.99, A:R.130

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

NA.3: 4 residues within 4Å: Chain B: T.9, C.10 Chain C: A.4, T.6 No protein-ligand interaction detected (PLIP)

1 x 9B4: (2R,5R,13R,16R)-9-(hydroxymethyl)-9-{[(2R)-2-hydroxypropoxy]methyl}-5,13-dimethyl-4,7,11,14-tetraoxaheptadecane-2,16-diol(Non-covalent)

9B4.4: 17 residues within 4Å: Chain A: L.5, G.82, F.83, L.86, G.114, S.115, E.117, F.118, P.159, W.160 Chain B: A.6, X.7, G.8, T.9 Chain C: C.5, T.6, T.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.86 Hydrogen bonds: A:W.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, R. et al., Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO J. (2018)

Release Date

2017-10-25

Peptides

alkylpurine DNA glycosylase AlkC: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

alkylpurine DNA glycosylase AlkC

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