5OHK: PDB entry 5OHK

Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution). Determined by X-ray diffraction at 2.34 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 2.34 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,017
Mol. weight: 47.15 kDa
Ligands: AYE, ZN
Released: 20 Sept 2017

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

Secondary structure: helices and β-sheets

5OHK contains 14 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: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	69-70	2	1
α-helix	77-87	11
α-helix	90-100	11
α-helix	101-104	4
α-helix	116-127	12
β-strand	137-138	2	1
α-helix	141-150	10
α-helix	162-178	17
α-helix	220-222	3
β-strand	226-234	9	2
β-strand	240-248	9	2
β-strand	251-254	4	3
β-strand	259	1	4
β-strand	262	1	4
β-strand	265	1	5
α-helix	266-274	9
β-strand	277-282	6	2
β-strand	306-316	11	2
β-strand	320-326	7	3
β-strand	328-330	3	6
β-strand	336-338	3	6
β-strand	344	1	5
β-strand	348-350	3	3
α-helix	352-354	3
β-strand	355	1	2
β-strand	435-445	11	3
β-strand	452-458	7	3
α-helix	459-460	2
β-strand	473-477	5	3
β-strand	480-484	5	3
α-helix	486-491	6
β-strand	494-501	8	3

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	12-16	5	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	50-51	2
β-strand	52	1	9
β-strand	54	1	9
β-strand	55	1	8
β-strand	66-70	5	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin…	A	protein	336	Homo sapiens	Q70CQ3 (AlphaFold model)
Polyubiquitin-B	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5OHK_1 Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30 (chains A)
GPKGLVPGLVNLGNTCFMNSLLQGLSACPAFIRWLEEFTSQYSRDQKEPPSHQYLSLTLL
HLLKALSCQEVTDDEVLDASCLLDVLRMYRWQISSFEEQDAHELFHVITSSLEDERDGSG
SHWKSQHPFHGRLTSNMVCKHCEHQSPVRFDTFDSLSLSIPAATWGHPLTLDHCLHHFIS
SESVRDVVCDNCTKIEAKGTLNGEKVEHQRTTFVKQLKLGKLPQCLCIHLQRLSWSSHGT
PLKRHEHVQFNEDLSMDEYKYHSNASTYLFRLMAVVVHHGDMHSGHFVTYRRSPPSARNP
LSTSNQWLWVSDDTVRKASLQEVLSSSAYLLFYERV

Sequence of entity 2 (B), FASTA

>5OHK_2 Polyubiquitin-B (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGX

Ligands and cofactors

ID	Name	Formula	Copies
AYE	prop-2-en-1-amine	C3 H7 N	1
ZN	Zinc ion	Zn	1

Primary citation

Mechanism and regulation of the Lys6-selective deubiquitinase USP30. Gersch, M., Gladkova, C., Schubert, A.F. et al. Nat Struct Mol Biol (2017) 24:920-930. DOI 10.1038/nsmb.3475 · PubMed

Other PDB entries of the same protein (UniProt Q70CQ3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
9LYF 2.58 Å, Structure-based Discovery of Novel non-Covalent Small Molecule Inhibitors of USP30
9F19 2.75 Å, Human USP30 chimera in complex with NK036 inhibitor
5OHP 2.8 Å, Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin
8D1T 2.94 Å, Crystal structure of human USP30 in complex with a covalent inhibitor 552 and a Fab
8D0A 3.19 Å, Crystal structure of human USP30 in complex with a covalent inhibitor 829 and a Fab
5OHN 3.6 Å, Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low…

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