5XU8: Human USP2

Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine. Determined by X-ray diffraction at 1.81 Å resolution. Released 28 Feb 2018.

Method: X-ray diffraction
Resolution: 1.81 Å
Organisms: Homo sapiens, Bos taurus
Chains: 2
Atoms: 3,568
Mol. weight: 50.31 kDa
Ligands: DX4, ZN
Released: 28 Feb 2018

Explore 5XU8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XU8 contains 20 α-helices and 30 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: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	268-269	2	1
α-helix	276-286	11
α-helix	289-296	8
α-helix	305-306	2
α-helix	312-325	14
α-helix	329	1
β-strand	333-334	2	1
α-helix	337-346	10
α-helix	348-350	3
β-strand	356-357	2	2
α-helix	358-373	16
α-helix	392-404	13
α-helix	410-415	6
β-strand	417-425	9	3
β-strand	431-438	8	3
β-strand	441-443	3	4
α-helix	444-446	3
β-strand	453-454	2	5
α-helix	455-463	9
β-strand	466-468	3	3
α-helix	470-472	3
α-helix	473-474	2
β-strand	475-476	2	6
β-strand	481-482	2	6
β-strand	485-493	9	3
β-strand	497-502	6	4
β-strand	505	1	7
β-strand	514	1	7
β-strand	519-520	2	5
β-strand	526-527	2	4
α-helix	529-531	3
β-strand	532	1	3
β-strand	540-551	12	4
β-strand	556-563	8	4
β-strand	570-574	5	4
β-strand	577-581	5	4
α-helix	583-585	3
β-strand	591-598	8	4

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	8
β-strand	48-49	2	8
β-strand	55	1	9
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-70	5	8
β-strand	74-75	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 2	A	protein	356	Homo sapiens	O75604 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a	B	protein	76	Bos taurus	P62992 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5XU8_1 Ubiquitin carboxyl-terminal hydrolase 2 (chains A)
MNSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEE
FAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVT
LRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDP
FWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKI
LVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMGGH
YTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPSRMLEHHHHHH

Sequence of entity 2 (B), FASTA

>5XU8_2 Ubiquitin-40S ribosomal protein S27a (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
DX4	2-amino-1,9-dihydro-6H-purine-6-thione	C5 H5 N5 S	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

6-Thioguanine is a noncompetitive and slow binding inhibitor of human deubiquitinating protease USP2. Chuang, S.J., Cheng, S.C., Tang, H.C. et al. Sci Rep (2018) 8:3102-3102. DOI 10.1038/s41598-018-21476-w · PubMed

Other PDB entries of the same protein (UniProt O75604 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XVE 1.24 Å, Crystal structure of human USP2 C276S mutant in complex with ubiquitin
3NHE 1.26 Å, High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin
3V6C 1.7 Å, Crystal Structure of USP2 in complex with mutated ubiquitin
2HD5 1.85 Å, USP2 in complex with ubiquitin
3V6E 2.1 Å, Crystal Structure of USP2 and a mutant form of Ubiquitin
2IBI 2.2 Å, Covalent Ubiquitin-USP2 Complex
6DGF 2.34 Å, Ubiquitin Variant bound to USP2

Browse structure collections

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