3V6E: USP2 and a mutant form of Ubiquitin

Crystal Structure of USP2 and a mutant form of Ubiquitin. Determined by X-ray diffraction at 2.1 Å resolution. Released 19 Dec 2012.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,644
Mol. weight: 52.74 kDa
Ligands: ZN
Released: 19 Dec 2012

Explore 3V6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V6E contains 20 α-helices and 28 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: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	268-269	2	1
α-helix	276-286	11
α-helix	289-296	8
α-helix	300-303	4
α-helix	314-325	12
α-helix	328-329	2
β-strand	333-334	2	1
α-helix	337-346	10
α-helix	348-350	3
α-helix	358-373	16
α-helix	392-404	13
α-helix	410-415	6
β-strand	417-425	9	2
β-strand	431-438	8	2
β-strand	441-443	3	3
β-strand	454	1	4
α-helix	455-463	9
β-strand	466-468	3	2
α-helix	470-472	3
α-helix	473-474	2
β-strand	475-476	2	5
β-strand	481-482	2	5
β-strand	485-493	9	2
β-strand	497-502	6	3
β-strand	505-506	2	6
β-strand	513-514	2	6
β-strand	520	1	4
β-strand	526-527	2	3
α-helix	529-531	3
β-strand	532	1	2
β-strand	540-550	11	3
β-strand	557-563	7	3
β-strand	570-574	5	3
β-strand	577-581	5	3
α-helix	583-585	3
β-strand	591-598	8	3

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	-4--1	4
β-strand	1-6	6	7
β-strand	12-17	6	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	7
β-strand	48-49	2	7
α-helix	50	1
β-strand	55	1	8
α-helix	57-59	3
β-strand	66-70	5	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 2	A	protein	367	Homo sapiens	O75604 (AlphaFold model)
Ubiquitin	B	protein	91	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3V6E_1 Ubiquitin carboxyl-terminal hydrolase 2 (chains A)
MGSSHHHHHHSSGLVPRGSMNSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQR
LYMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDA
QEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQ
LKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCR
CRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNH
AVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYEL
ASPPSRM

Sequence of entity 2 (B), FASTA

>3V6E_2 Ubiquitin (chains B)
MAHHHHHHSSGLVPRGSMQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEGIPPDQQRL
IFAGKQLEDGRTLSDYNIQKESTLHLVLRLR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

A strategy for modulation of enzymes in the ubiquitin system. Ernst, A., Avvakumov, G., Tong, J. et al. Science (2013) 339:590-595. DOI 10.1126/science.1230161 · 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
5XU8 1.81 Å, Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine
2HD5 1.85 Å, USP2 in complex with ubiquitin
2IBI 2.2 Å, Covalent Ubiquitin-USP2 Complex
6DGF 2.34 Å, Ubiquitin Variant bound to USP2

Browse structure collections

About this viewer

MolViewer shows 3V6E 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.