6GH9: USP15 catalytic domain

USP15 catalytic domain in complex with small molecule. Determined by X-ray diffraction at 2.09 Å resolution. Released 26 Sept 2018.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,319
Mol. weight: 84.08 kDa
Ligands: MIX, ZN
Released: 26 Sept 2018

Explore 6GH9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GH9 contains 25 α-helices and 36 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	1
α-helix	271-279	9
α-helix	282-289	8
α-helix	294-296	3
α-helix	308-320	13
β-strand	327-328	2	1
α-helix	331-340	10
α-helix	355-366	12
α-helix	373-375	3
α-helix	386-400	15
α-helix	404-409	6
β-strand	411-419	9	2
β-strand	424-432	9	2
β-strand	435-437	3	3
β-strand	757-758	2	4
α-helix	759-766	8
β-strand	770-771	2	2
β-strand	778-780	3	5
β-strand	785-787	3	5
β-strand	790-797	8	2
β-strand	801-806	6	3
β-strand	823-824	2	4
β-strand	830-831	2	3
α-helix	833-835	3
β-strand	836	1	2
β-strand	845-857	13	3
β-strand	860-868	9	3
β-strand	875-879	5	3
β-strand	882-886	5	3
α-helix	888-891	4
β-strand	896-903	8	3
α-helix	904-906	3

Chain B: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	6
α-helix	271-279	9
α-helix	282-289	8
α-helix	294-296	3
α-helix	308-320	13
β-strand	327-328	2	6
α-helix	331-340	10
α-helix	355-366	12
α-helix	373-375	3
α-helix	386-400	15
α-helix	404-409	6
β-strand	411-419	9	7
β-strand	424-432	9	7
β-strand	435-437	3	8
β-strand	756-758	3	9
α-helix	759-766	8
β-strand	770	1	7
β-strand	790-797	8	7
β-strand	801-806	6	8
β-strand	822-824	3	9
β-strand	830-831	2	8
β-strand	836	1	7
β-strand	845-854	10	8
β-strand	863-868	6	8
β-strand	875-879	5	8
β-strand	882-886	5	8
α-helix	888-890	3
β-strand	896-903	8	8
α-helix	904-906	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 15	A, B	protein	365	Homo sapiens	Q9Y4E8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6GH9_1 Ubiquitin carboxyl-terminal hydrolase 15 (chains A, B)
MEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSY
AELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKK
PYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFC
YLTLPLASTSKVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVH
LKRFSYSRYMRDKLDTLVDFPINDLDMSEFLINPNAGPCRYNLIAVSNHYGGMGGGHYTA
FAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDTFSGTGFFPLDRETAAALEH
HHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MIX	1,4-dihydroxy-5,8-BIS({2-[(2-hydroxyethyl)amino]ethyl}amino)-9,10-anthracenedio…	C22 H28 N4 O6	1
ZN	Zinc ion	Zn	1

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

Primary citation

The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel. Ward, S.J., Gratton, H.E., Indrayudha, P. et al. J Biol Chem (2018) 293:17362-17374. DOI 10.1074/jbc.RA118.003857 · PubMed

Other PDB entries of the same protein (UniProt Q9Y4E8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4A3P 1.4 Å, Structure of USP15 DUSP-UBL deletion mutant
3T9L 1.5 Å, Structure of N-terminal DUSP-UBL domains of human USP15
6ML1 1.9 Å, Structure of the USP15 deubiquitinase domain in complex with an affinity-matured…
6GHA 1.98 Å, USP15 catalytic domain structure
7R2G 1.98 Å, USP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2)
6CPM 2.01 Å, Structure of the USP15 deubiquitinase domain in complex with a third-generation…
3LMN 2.15 Å, Oligomeric structure of the DUSP domain of human USP15
4A3O 2.2 Å, Crystal structure of the USP15 DUSP-UBL monomer
9VVV 2.3 Å, Crystal structure of USP15 catalytic domain in complex with Ub-PA
3PPA 2.35 Å, Structure of the Dusp-Ubl domains of Usp15
6CRN 2.5 Å, Structure of the USP15 deubiquitinase domain in complex with a high-affinity…
3PV1 2.6 Å, Crystal structure of the USP15 DUSP-UBL domains

Browse structure collections

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