5X55: Mimivirus uracil-DNA glycosylase

Crystal structure of mimivirus uracil-DNA glycosylase. Determined by X-ray diffraction at 2.3 Å resolution. Released 9 Aug 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Acanthamoeba polyphaga mimivirus
Chains: 2
Atoms: 4,814
Mol. weight: 84.55 kDa
Released: 9 Aug 2017

Explore 5X55 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X55 contains 36 α-helices and 25 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: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	98-102	5
β-strand	105	1	1
α-helix	106-108	3
α-helix	114-117	4
α-helix	125-128	4
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
β-strand	196	1	4
β-strand	202	1	4
β-strand	213	1	1
α-helix	216-218	3
α-helix	219-230	12
α-helix	244-248	5
β-strand	251-255	5	3
β-strand	260-261	2	2
β-strand	264	1	2
α-helix	273-286	14
β-strand	291-295	5	3
α-helix	297-303	7
β-strand	312-316	5	3
β-strand	328-332	5	5
β-strand	338-342	5	5
α-helix	345-347	3
α-helix	350-360	11
α-helix	363-365	3

Chain B: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	98-102	5
β-strand	105	1	6
α-helix	114-117	4
α-helix	125-128	4
α-helix	132-134	3
α-helix	135-143	9
α-helix	146-159	14
β-strand	164-165	2	7
α-helix	168-171	4
α-helix	173-177	5
α-helix	180-182	3
β-strand	185-189	5	8
β-strand	196	1	9
β-strand	202	1	9
β-strand	213	1	6
α-helix	216-218	3
α-helix	219-230	12
α-helix	244-248	5
β-strand	251-255	5	8
β-strand	260-261	2	7
α-helix	269-286	18
β-strand	291-295	5	8
α-helix	297-303	7
β-strand	312-316	5	8
β-strand	328-332	5	10
β-strand	338-342	5	10
α-helix	343-344	2
α-helix	345-347	3
α-helix	350-360	11
α-helix	364-366	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable uracil-DNA glycosylase	A, B	protein	370	Acanthamoeba polyphaga mimivirus	Q5UPT2

Sequence of entity 1 (A, B), FASTA

>5X55_1 Probable uracil-DNA glycosylase (chains A, B)
MSKKNVDPFSDSDSSSEPPSIFSSDNEENSDVDNSVIINDKNTKSDEADIKYMDEDESSD
SESESESKKKSKKSKKSKKSKKSVTKKKNNLLVGNRIITEYILIDANNYHFKSWIECFPD
CKVNLKLLLFRPEWFDFFKYVESKTYFPQLESKLSSYLEKRQRIVPYPELLFNTMNVLPP
GKIKVVILGQDPYPGSCISGVPYAMGCSFSVPLNCPVPKSLANIYTNLIKFNHMRKAPKH
GCLASWILQGTFMINSAFTTVLNESGVHARTWESFTADLIDYLTDNYDDLIFVAWGAHAH
KLCQRVDPKKHYIITSSHPSPYSVSNTMTSMSYGPNPKKVTYPSFNSVDHFGKINEHLKS
RNKKPIFWDL

Primary citation

Crystal structure of mimivirus uracil-DNA glycosylase. Kwon, E., Pathak, D., Chang, H.W. et al. PLoS One (2017) 12:e0182382-e0182382. DOI 10.1371/journal.pone.0182382 · PubMed

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

6LYD 2.6 Å, Crystal Structure of mimivirus UNG Y322L in complex with UGI
6LYE 3.1 Å, Crystal Structure of mimivirus UNG Y322F in complex with UGI

Browse structure collections

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