4KSK: Gumby/Fam105B

Gumby/Fam105B in complex with ubiquitin. Determined by X-ray diffraction at 2.4 Å resolution. Released 5 Jun 2013.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,501
Mol. weight: 87.6 kDa
Released: 5 Jun 2013

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

Secondary structure: helices and β-sheets

4KSK contains 46 α-helices and 34 β-strands across 4 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: 17 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	117-121	5	2
β-strand	123	1	1
α-helix	129-140	12
α-helix	147-150	4
α-helix	152-154	3
α-helix	157-164	8
α-helix	166-170	5
α-helix	184-202	19
α-helix	208-216	9
α-helix	223-248	26
α-helix	255-261	7
α-helix	269-272	4
α-helix	273-277	5
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
β-strand	329-336	8	4
β-strand	339-341	3	4
β-strand	342-345	4	2

Chain B: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	82	1	5
α-helix	83-85	3
β-strand	86-87	2	6
α-helix	88-95	8
α-helix	101-114	14
β-strand	119-121	3	6
α-helix	122	1
β-strand	123	1	5
α-helix	124	1
α-helix	129-140	12
α-helix	147-150	4
α-helix	154-156	3
α-helix	157-164	8
α-helix	166-170	5
α-helix	184-202	19
α-helix	208-218	11
α-helix	223-247	25
α-helix	256-260	5
α-helix	264-266	3
α-helix	269-272	4
α-helix	273-277	5
β-strand	280	1	7
β-strand	284	1	7
α-helix	288-298	11
β-strand	301-306	6	8
α-helix	307-309	3
β-strand	316-319	4	8
α-helix	328	1
β-strand	329-336	8	8
β-strand	339-341	3	8
β-strand	342-344	3	6

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	9
β-strand	12-17	6	9
β-strand	22	1	10
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	9
β-strand	48-49	2	9
α-helix	50-51	2
β-strand	55	1	10
α-helix	57-59	3
β-strand	66-69	4	9
α-helix	71-73	3

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	11
β-strand	12-17	6	11
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	11
β-strand	48-49	2	11
α-helix	50-51	2
β-strand	65-69	5	11
α-helix	71-73	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein FAM105B	A, B	protein	300	Homo sapiens	Q96BN8 (AlphaFold model)
Polyubiquitin-C	C, D	protein	80	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4KSK_1 Protein FAM105B (chains A, B)
GSMYRAADEIEKEKELLIHERGASEPRLSVAPEMDIMDYCKKEWRGNTQKATCMKMGYEE
VSQKFTSIRRVRGDNYSALRATLFQAMSQAVGLPPWLQDPELMLLPEKLISKYNWIKQWK
LGLKFDGKNEDLVDKIKESLTLLRKKWAGLAEMRTAEARQIACDELFTNEAEEYSLYEAV
KFLMLNRAIELYNDKEKGKEVPFFSVLLFARDTSNDPGQLLRNHLNQVGHTGGLEQVEMF
LLAYAVRHTIQVYRLSKYNTEEFITVYPTDPPKDWPVVTLIAEDDRHYNIPVRVCEETSL

Sequence of entity 2 (C, D), FASTA

>4KSK_2 Polyubiquitin-C (chains C, D)
GAMGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGG

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
4KSJ 1.6 Å, Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom
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
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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