6DGF: Ubiquitin Variant

Ubiquitin Variant bound to USP2. Determined by X-ray diffraction at 2.34 Å resolution. Released 13 Feb 2019.

Method: X-ray diffraction
Resolution: 2.34 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,339
Mol. weight: 53.34 kDa
Ligands: ZN
Released: 13 Feb 2019

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

Secondary structure: helices and β-sheets

6DGF 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: 16 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	299-302	4
α-helix	313-325	13
α-helix	329	1
β-strand	333-334	2	1
α-helix	337-346	10
α-helix	348-350	3
α-helix	358-372	15
α-helix	392-404	13
α-helix	412-415	4
β-strand	417-425	9	2
β-strand	431-438	8	2
β-strand	441-444	4	3
β-strand	452-454	3	4
α-helix	455-462	8
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	497-503	7	3
β-strand	505-508	4	6
β-strand	511-514	4	6
β-strand	518-520	3	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
α-helix	599-604	6

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
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	370	Homo sapiens	O75604 (AlphaFold model)
Polyubiquitin-B	B	protein	93	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6DGF_1 Ubiquitin carboxyl-terminal hydrolase 2 (chains A)
HHHHHHSSGLVPRGSSSPGRDGMNSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYC
LQRLYMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQ
QDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLF
VGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPT
CCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASEN
TNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLF
YELASPPSRM

Sequence of entity 2 (B), FASTA

>6DGF_2 Polyubiquitin-B (chains B)
MAHHHHHHVTSLYKKAGSTMCIFVCTLTGRCITLEVEPSDTIENVKAKIQDKEGIPPDQQ
RLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Yeast Two-Hybrid Analysis for Ubiquitin Variant Inhibitors of Human Deubiquitinases. Pascoe, N., Seetharaman, A., Teyra, J. et al. J Mol Biol (2019) 431:1160-1171. DOI 10.1016/j.jmb.2019.02.007 · 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
3V6E 2.1 Å, Crystal Structure of USP2 and a mutant form of Ubiquitin
2IBI 2.2 Å, Covalent Ubiquitin-USP2 Complex

Browse structure collections

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