6LYD: Mimivirus UNG Y322L

Crystal Structure of mimivirus UNG Y322L in complex with UGI. Determined by X-ray diffraction at 2.6 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Acanthamoeba polyphaga mimivirus, Bacillus phage PBS2
Chains: 2
Atoms: 2,986
Mol. weight: 41.15 kDa
Released: 8 Jul 2020

Explore 6LYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LYD contains 22 α-helices and 17 β-strands across 2 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: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	105	1	1
α-helix	111-113	3
α-helix	114-117	4
α-helix	126-128	3
α-helix	132-134	3
α-helix	135-142	8
α-helix	146-159	14
β-strand	164-165	2	2
α-helix	168-170	3
α-helix	173-177	5
α-helix	180-182	3
β-strand	185-189	5	3
α-helix	192-193	2
β-strand	196	1	4
β-strand	202	1	4
β-strand	213	1	1
α-helix	219-230	12
α-helix	244-248	5
β-strand	251-255	5	3
β-strand	260-261	2	2
α-helix	273-286	14
β-strand	291-295	5	3
α-helix	297-302	6
α-helix	303-305	3
β-strand	312-316	5	3
β-strand	328-331	4	5
β-strand	339-342	4	5
α-helix	343-344	2
α-helix	345-347	3
α-helix	350-360	11
α-helix	364-367	4

Chain I: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	18-24	7	6
α-helix	26-33	8
β-strand	41-48	8	6
β-strand	53-60	8	6
β-strand	67-73	7	6
α-helix	78	1
β-strand	79-83	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable uracil-DNA glycosylase	A	protein	276	Acanthamoeba polyphaga mimivirus	Q5UPT2
Uracil-DNA glycosylase inhibitor	I	protein	83	Bacillus phage PBS2	P14739 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6LYD_1 Probable uracil-DNA glycosylase (chains A)
NRIITEYILIDANNYHFKSWIECFPDCKVNLKLLLFRPEWFDFFKYVESKTYFPQLESKL
SSYLEKRQRIVPYPELLFNTMNVLPPGKIKVVILGQDPYPGSCISGVPYAMGCSFSVPLN
CPVPKSLANIYTNLIKFNHMRKAPKHGCLASWILQGTFMINSAFTTVLNESGVHARTWES
FTADLIDYLTDNYDDLIFVAWGAHAHKLCQRVDPKKHYIITSSHPSPLSVSNTMTSMSYG
PNPKKVTYPSFNSVDHFGKINEHLKSRNKKPIFWDL

Sequence of entity 2 (I), FASTA

>6LYD_2 Uracil-DNA glycosylase inhibitor (chains I)
TNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSD
APEYKPWALVIQDSNGENKIKML

Primary citation

Selective interactions between mimivirus uracil-DNA glycosylase and inhibitory proteins determined by a single amino acid. Pathak, D., Kwon, E., Kim, D.Y. J Struct Biol (2020) 211:107552-107552. DOI 10.1016/j.jsb.2020.107552 · PubMed

Other PDB entries of the same protein (UniProt Q5UPT2), best resolution first:

5X55 2.3 Å, Crystal structure of mimivirus uracil-DNA glycosylase
6LYE 3.1 Å, Crystal Structure of mimivirus UNG Y322F in complex with UGI

Browse structure collections

About this viewer

MolViewer shows 6LYD 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.