2HD5: USP2

USP2 in complex with ubiquitin. Determined by X-ray diffraction at 1.85 Å resolution. Released 15 Aug 2006.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, Bos taurus
Chains: 2
Atoms: 3,287
Mol. weight: 50.07 kDa
Ligands: ZN
Released: 15 Aug 2006

Explore 2HD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2HD5 contains 18 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: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	215-216	2	1
α-helix	223-233	11
α-helix	236-243	8
α-helix	244B-244E	4
α-helix	255-268	14
β-strand	273-274	2	1
α-helix	277-284	10
α-helix	286-288	3
β-strand	294	1	2
α-helix	296-310	15
α-helix	313Q-314C	13
α-helix	319-324	6
β-strand	326-334	9	3
β-strand	340-347	8	3
β-strand	350-353	4	4
β-strand	359	1	5
α-helix	360-367	8
β-strand	371-373	3	3
α-helix	375-377	3
α-helix	378-379	2
β-strand	380-381	2	6
β-strand	385-386	2	6
β-strand	389-397	9	3
β-strand	401-407	7	4
β-strand	409-410	2	7
β-strand	419-420	2	7
β-strand	426	1	5
β-strand	431-432	2	4
α-helix	434-436	3
β-strand	437	1	3
β-strand	447-458	12	4
β-strand	463-470	8	4
β-strand	477-481	5	4
β-strand	484-488	5	4
α-helix	490-492	3
β-strand	513-520	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
β-strand	42-45	4	8
β-strand	48-49	2	8
α-helix	50	1
β-strand	55	1	9
α-helix	56-59	4
α-helix	61-62	2
β-strand	66-70	5	8
β-strand	75	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 2	A	protein	359	Homo sapiens	O75604 (AlphaFold model)
Polyubiquitin	B	protein	76	Bos taurus	P0CH28 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2HD5_1 Ubiquitin carboxyl-terminal hydrolase 2 (chains A)
MNSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEE
FAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVT
LRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDP
FWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKI
LVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMGGH
YTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPSRMAAALEHHHHHH

Sequence of entity 2 (B), FASTA

>2HD5_2 Polyubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural Basis of Ubiquitin Recognition by the Deubiquitinating Protease USP2. Renatus, M., Parrado, S.G., D'Arcy, A. et al. Structure (2006) 14:1293-1302. DOI 10.1016/j.str.2006.06.012 · 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
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

About this viewer

MolViewer shows 2HD5 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.