5NNU: Uracil-DNA glycosylase

KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping. Determined by X-ray diffraction at 2.97 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 2.97 Å
Organisms: synthetic construct, Human gammaherpesvirus 8
Chains: 12
Atoms: 8,844
Mol. weight: 135.29 kDa
Released: 21 Mar 2018

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

Secondary structure: helices and β-sheets

5NNU contains 54 α-helices and 24 β-strands across 4 chains. 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: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	32-38	7
α-helix	42-61	20
β-strand	64-65	2	1
α-helix	68-70	3
α-helix	73-77	5
β-strand	85-89	5	2
α-helix	113-125	13
α-helix	138-142	5
β-strand	145-149	5	2
β-strand	154-155	2	1
α-helix	168-181	14
β-strand	186-190	5	2
α-helix	192-195	4
α-helix	198-200	3
β-strand	207-211	5	2
α-helix	216-219	4
α-helix	228-229	2
α-helix	235-245	11
α-helix	249-251	3

Chains B and D: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	32-38	7
α-helix	42-61	20
β-strand	64-65	2	3
α-helix	68-70	3
α-helix	73-77	5
β-strand	85-89	5	4
α-helix	113-125	13
α-helix	138-142	5
β-strand	145-149	5	4
β-strand	154-155	2	3
α-helix	168-181	14
β-strand	186-190	5	4
α-helix	192-195	4
α-helix	198-200	3
β-strand	207-211	5	4
α-helix	216-219	4
α-helix	228-229	2
α-helix	235-245	11
α-helix	249-251	3

Chain E: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	32-38	7
α-helix	42-61	20
β-strand	64-65	2	7
α-helix	68-70	3
α-helix	73-77	5
α-helix	80-82	3
β-strand	85-89	5	8
α-helix	113-125	13
α-helix	138-142	5
β-strand	145-149	5	8
β-strand	154-155	2	7
α-helix	168-181	14
β-strand	186-190	5	8
α-helix	192-195	4
α-helix	198-200	3
β-strand	207-211	5	8
α-helix	216-219	4
α-helix	228-229	2
α-helix	235-245	11
α-helix	249-251	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA containing an abasic site	S, U, W, Y	DNA	11	synthetic construct
Uracil-DNA glycosylase	A, B, D, E	protein	240	Human gammaherpesvirus 8	F5HFA1 (AlphaFold model)
DNA	T, V, X, Z	DNA	11	synthetic construct

Sequence of entity 1 (S, U, W, Y), FASTA

>5NNU_1 DNA containing an abasic site (chains S, U, W, Y)
AATGTXATCTT

Sequence of entity 2 (A, B, D, E), FASTA

>5NNU_2 Uracil-DNA glycosylase (chains A, B, D, E)
SASGVDDRDLLLAPKWISFLSLSSFLKQKLLSLLRQIRELRLTTTVYPPQDKLMWWSHCC
DPEDIKVVILGQDPYHKGQATGLAFSVDPQCQVPPSLRSIFRELEASVPNFSTPSHGCLD
SWARQGVLLLNTVLTVEKGRAGSHEGLGWDWFTSFIISSISSKLEHCVFLLWGRKAIDRT
PLINAQKHLVLTAQHPSPLASLGGRHSRWPRFQGCNHFNLANDYLTRHRRETVDWGLLEQ

Sequence of entity 3 (T, V, X, Z), FASTA

>5NNU_3 DNA (chains T, V, X, Z)
AAGATAACATT

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:

5NNH 2.2 Å, KSHV uracil-DNA glycosylase, apo form
5NN7 2.5 Å, KSHV uracil-DNA glycosylase, apo form
6LYV 2.7 Å, The crystal structure of SAUGI/KSHVUDG complex

Browse structure collections

About this viewer

MolViewer shows 5NNU directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.