3TB3: UCH domain of UCH-L5 with 6 residues deleted

Name: PDB 3TB3: Crystal structure of the UCH domain of UCH-L5 with 6 residues deleted
Published: 2012-02-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Crystal structure of the UCH domain of UCH-L5 with 6 residues deleted. Determined by X-ray diffraction at 2.3 Å resolution. Released 22 Feb 2012.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,275
Mol. weight: 51.45 kDa
Ligands: CA
Released: 22 Feb 2012

Explore 3TB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3TB3 contains 23 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: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	15-24	10
β-strand	28	1	1
β-strand	30-35	6	2
α-helix	40-42	3
α-helix	47	1
β-strand	49-56	8	2
β-strand	67-68	2	2
α-helix	69	1
α-helix	73-76	4
α-helix	85-87	3
α-helix	88-97	10
β-strand	106	1	1
α-helix	108-118	11
α-helix	123-131	9
α-helix	134-143	10
β-strand	164-171	8	2
β-strand	174-178	5	2
β-strand	186-190	5	2
α-helix	197-212	16
β-strand	218-225	8	2

Chain B: 11 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	30-35	6	4
α-helix	40-42	3
β-strand	49-56	8	4
β-strand	67-68	2	4
α-helix	69	1
α-helix	73-76	4
α-helix	85-87	3
α-helix	88-97	10
β-strand	106	1	3
α-helix	109-117	9
α-helix	123-131	9
α-helix	134-143	10
β-strand	164-171	8	4
β-strand	174-179	6	4
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	229	Homo sapiens	Q9Y5K5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3TB3_1 Ubiquitin carboxyl-terminal hydrolase isozyme L5 (chains A, B)
GSMTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKW
QPGEEPAGSVVQDSRLDTIFFAKQVINNAAATQAIVSVLLNCTHQDVHLGETLSEFKEFS
QSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYEL
DGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

Length of the active-site crossover loop defines the substrate specificity of ubiquitin C-terminal hydrolases for ubiquitin chains. Zhou, Z.R., Zhang, Y.H., Liu, S. et al. Biochem J (2012) 441:143-149. DOI 10.1042/BJ20110699 · PubMed

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

3RII 2.0 Å, Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human…
3A7S 2.2 Å, Catalytic domain of UCH37
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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