3RII: Ubiquitin carboxyl-terminal hydrolase isozyme L5

Name: PDB 3RII: Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme
Published: 2011-11-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Nov 2011.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,634
Mol. weight: 52.81 kDa
Ligands: MG
Released: 9 Nov 2011

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

Secondary structure: helices and β-sheets

3RII contains 27 α-helices and 18 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-24	10
β-strand	28	1	1
β-strand	30-34	5	2
α-helix	47	1
β-strand	49-56	8	2
α-helix	62-64	3
β-strand	67-68	2	2
α-helix	69	1
α-helix	72-75	4
α-helix	85-87	3
α-helix	88-98	11
β-strand	106	1	1
α-helix	109-118	10
α-helix	123-131	9
α-helix	134-142	9
α-helix	159-162	4
β-strand	164-171	8	2
β-strand	174-178	5	2
α-helix	185	1
β-strand	186-190	5	2
α-helix	197-213	17
β-strand	218-225	8	2

Chain B: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	15-24	10
β-strand	28	1	3
β-strand	30-34	5	4
α-helix	47	1
β-strand	49-56	8	4
β-strand	67-68	2	4
α-helix	69	1
α-helix	72-75	4
α-helix	85-87	3
α-helix	88-99	12
β-strand	106	1	3
α-helix	109-118	10
α-helix	123-131	9
α-helix	134-143	10
α-helix	156-158	3
α-helix	159-162	4
β-strand	164-171	8	4
β-strand	174-178	5	4
α-helix	185	1
β-strand	186-190	5	4
α-helix	197-212	16
β-strand	218-225	8	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase isozyme L5	A, B	protein	233	Homo sapiens	Q9Y5K5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3RII_1 Ubiquitin carboxyl-terminal hydrolase isozyme L5 (chains A, B)
GPLGSMTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFL
FKWQPGEEPAGSVVQDSRLDTIFFAKQVINNASATQAIVSVLLNCTHQDVHLGETLSEFK
EFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRL
YELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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

Primary citation

Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme. Maiti, T.K., Permaul, M., Boudreaux, D.A. et al. FEBS J (2011) 278:4917-4926. DOI 10.1111/j.1742-4658.2011.08393.x · PubMed

Other PDB entries of the same protein (UniProt Q9Y5K5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3A7S 2.2 Å, Catalytic domain of UCH37
3TB3 2.3 Å, Crystal structure of the UCH domain of UCH-L5 with 6 residues deleted
4UEL 2.3 Å, UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
3RIS 2.4 Å, Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human…
9E7K 2.41 Å, Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in…
4UEM 2.82 Å, UCH-L5 in complex with the RPN13 DEUBAD domain
3IHR 2.95 Å, Crystal Structure of Uch37
4WLP 3.1 Å, Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex
4UF6 3.69 Å, UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G
4UF5 3.7 Å, Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G

Browse structure collections

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