4KSJ: OTU domain of Gumby/Fam105B

Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom. Determined by X-ray diffraction at 1.6 Å resolution. Released 5 Jun 2013.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,326
Mol. weight: 32.76 kDa
Released: 5 Jun 2013

Explore 4KSJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KSJ contains 19 α-helices and 11 β-strands across 1 chain. 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: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	1
α-helix	83-85	3
β-strand	86-87	2	2
α-helix	88-95	8
α-helix	101-114	14
β-strand	119-121	3	2
α-helix	122	1
β-strand	123	1	1
α-helix	124	1
α-helix	129-140	12
α-helix	147-150	4
α-helix	153-164	12
α-helix	166-170	5
α-helix	184-203	20
α-helix	208-218	11
α-helix	223-248	26
α-helix	255-262	8
α-helix	269-275	7
α-helix	277-279	3
β-strand	280	1	3
β-strand	284	1	3
α-helix	288-298	11
β-strand	301-306	6	4
α-helix	307-309	3
α-helix	313-315	3
β-strand	316-319	4	4
α-helix	328	1
β-strand	329-334	6	4
β-strand	340-341	2	4
β-strand	342-344	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein FAM105B	A	protein	276	Homo sapiens	Q96BN8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4KSJ_1 Protein FAM105B (chains A)
GSRLSVAPEMDIMDYCKKEWRGNTQKATCMKMGYEEVSQKFTSIRRVRGDNYCALRATLF
QAMSQAVGLPPWLQDPELMLLPEKLISKYNWIKQWKLGLKFDGKNEDLVDKIKESLTLLR
KKWAGLAEMRTAEARQIACDELFTNEAEEYSLYEAVKFLMLNRAIELYNDKEKGKEVPFF
SVLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEMFLLAYAVRHTIQVYRLSKYNTEEFI
TVYPTDPPKDWPVVTLIAEDDRHYNIPVRVCEETSL

Primary citation

The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis. Rivkin, E., Almeida, S.M., Ceccarelli, D.F. et al. Nature (2013) 498:318-324. DOI 10.1038/nature12296 · PubMed

Other PDB entries of the same protein (UniProt Q96BN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZNV 1.3 Å, Crystal structure of the OTU domain of OTULIN at 1.3 Angstroms.
3ZNX 1.35 Å, Crystal structure of the OTU domain of OTULIN D336A mutant
6I9C 1.77 Å, Structure of the OTU domain of OTULIN G281R mutant
3ZNZ 1.9 Å, Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin
6SAK 2.0 Å, Structure of the OTULINcat C129A - SNX27 PDZ domain complex.
9LZX 2.0 Å, Crystal structure of the OTU domain of OTULIN in complex with 11B6
4OYK 2.0 Å, Structure of HOIP PUB domain bound to OTULIN PIM
4KSK 2.4 Å, Gumby/Fam105B in complex with ubiquitin
4P0B 2.7 Å, Crystal structure of HOIP PUB domain in complex with OTULIN PIM
4KSL 2.83 Å, Gumby/Fam105B in complex with linear di-ubiquitin
5OE7 2.95 Å, Structure of OTULIN bound to the Met1-linked diubiquitin activity probe

Browse structure collections

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