5NNH: KSHV uracil-DNA glycosylase, apo form

KSHV uracil-DNA glycosylase, apo form. Determined by X-ray diffraction at 2.2 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Human herpesvirus 8
Chains: 1
Atoms: 1,825
Mol. weight: 27.32 kDa
Released: 21 Mar 2018

Explore 5NNH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NNH contains 13 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	29-35	7
α-helix	39-55	17
β-strand	61-62	2	1
α-helix	65-67	3
α-helix	70-74	5
α-helix	77-79	3
β-strand	82-86	5	2
β-strand	95	1	3
β-strand	102	1	3
α-helix	110-122	13
α-helix	135-139	5
β-strand	142-146	5	2
β-strand	151-152	2	1
α-helix	165-178	14
β-strand	183-187	5	2
α-helix	189-192	4
α-helix	195-197	3
β-strand	204-208	5	2
α-helix	232-242	11
α-helix	246-248	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uracil-DNA glycosylase	A	protein	240	Human herpesvirus 8	F5HFA1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5NNH_1 Uracil-DNA glycosylase (chains A)
SASGVDDRDLLLAPKWISFLSLSSFLKQKLLSLLRQIRELRLTTTVYPPQDKLMWWSHCC
DPEDIKVVILGQDPYHKGQATGLAFSVDPQCQVPPSLRSIFRELEASVPNFSTPSHGCLD
SWARQGVLLLNTVLTVEKGRAGSHEGLGWDWFTSFIISSISSKLEHCVFLLWGRKAIDRT
PLINAQKHLVLTAQHPSPLASLGGRHSRWPRFQGCNHFNLANDYLTRHRRETVDWGLLEQ

Primary citation

A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping. Earl, C., Bagneris, C., Zeman, K. et al. Nucleic Acids Res (2018) 46:4286-4300. DOI 10.1093/nar/gky217 · PubMed

Other PDB entries of the same protein (UniProt F5HFA1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NN7 2.5 Å, KSHV uracil-DNA glycosylase, apo form
6LYV 2.7 Å, The crystal structure of SAUGI/KSHVUDG complex
5NNU 2.97 Å, KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide…

Browse structure collections

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