3BY4: Ovarian Tumor (OTU) domain

Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin. Determined by X-ray diffraction at 1.55 Å resolution. Released 19 Feb 2008.

Method: X-ray diffraction
Resolution: 1.55 Å
Organisms: Saccharomyces cerevisiae, Homo sapiens
Chains: 2
Atoms: 2,104
Mol. weight: 32.45 kDa
Ligands: 3CN
Released: 19 Feb 2008

Explore 3BY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BY4 contains 11 α-helices and 15 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	93-95	3
β-strand	98-100	3	1
β-strand	108-112	5	1
α-helix	120-130	11
α-helix	136-148	13
α-helix	155-158	4
α-helix	162-168	7
α-helix	175-176	2
α-helix	178-188	11
β-strand	191-196	6	1
β-strand	201-205	5	1
β-strand	212-218	7	1
β-strand	223-228	6	1
β-strand	232	1	1
β-strand	235-236	2	1
α-helix	242-258	17

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	2
β-strand	12-16	5	2
β-strand	22	1	3
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	2
β-strand	48-49	2	2
β-strand	55	1	3
α-helix	56-59	4
β-strand	66-71	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin thioesterase OTU1	A	protein	212	Saccharomyces cerevisiae	P43558 (AlphaFold model)
Ubiquitin	B	protein	75	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3BY4_1 Ubiquitin thioesterase OTU1 (chains A)
MKRVLKSTEMSIGGSGENVLSVHPVLDDNSCLFHAIAYGIFKQDSVRDLREMVSKEVLNN
PVKFNDAILDKPNKDYAQWILKMESWGGAIEIGIISDALAVAIYVVDIDAVKIEKFNEDK
FDNYILILFNGIHYDSLTMNEFKTVFNKNQPESDDVLTAALQLASNLKQTGYSFNTHKAQ
IKCNTCQMTFVGEREVARHAESTGHVDFGQNR

Sequence of entity 2 (B), FASTA

>3BY4_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
3CN	3-aminopropane	C3 H9 N	1

Primary citation

Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. Messick, T.E., Russell, N.S., Iwata, A.J. et al. J Biol Chem (2008) 283:11038-11049. DOI 10.1074/jbc.M704398200 · PubMed

Other PDB entries of the same protein (UniProt P43558 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4KDL 1.81 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
4KDI 1.86 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
3C0R 2.31 Å, Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin

Browse structure collections

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