5JKN: Deubiquitinase MINDY-1

Crystal structure of deubiquitinase MINDY-1. Determined by X-ray diffraction at 3.0 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,022
Mol. weight: 32.44 kDa
Ligands: HG, PO4
Released: 22 Jun 2016

Explore 5JKN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JKN contains 11 α-helices and 18 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: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	113-121	9	1
β-strand	124-130	7	1
β-strand	131	1	2
α-helix	139-148	10
β-strand	160-162	3	1
α-helix	163-175	13
α-helix	187-200	14
α-helix	203-206	4
β-strand	212	1	3
β-strand	213	1	4
β-strand	220	1	3
α-helix	226-232	7
β-strand	236-238	3	5
β-strand	239	1	6
α-helix	247-253	7
β-strand	257	1	4
α-helix	258-269	12
α-helix	274-289	16
β-strand	294	1	6
α-helix	296-305	10
α-helix	307	1
β-strand	311-316	6	5
β-strand	319-326	8	5
β-strand	329-333	5	5
β-strand	336	1	2
α-helix	337-339	3
β-strand	347-349	3	5
β-strand	359-360	2	5
β-strand	366	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein FAM63A	A	protein	289	Homo sapiens	Q8N5J2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5JKN_1 Protein FAM63A (chains A)
GPLGSPEFPGRLEMEPDFYCVKWIPWKGEQTPIITQSTNGPCPLLAIMNILFLQWKVKLP
PQKEVITSDELMAHLGNCLLSIKPQEKSEGLQLNFQQNVDDAMTVLPKLATGLDVNVRFT
GVSDFEYTPECSVFDLLGIPLYHGWLVDPQSPEAVRAVGKLSYNQLVERIITCKHSSDTN
LVTEGLIAEQFLETTAAQLTYHGLCELTAAAKEGELSVFFRNNHFSTMTKHKSHLYLLVT
DQGFLQEEQVVWESLHNVDGDSCFCDSDFHLSHSLGKGPGAEGGSGSPE

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	1
PO4	Phosphate ion	O4 P	1

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

Primary citation

MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Abdul Rehman, S.A., Kristariyanto, Y.A., Choi, S.Y. et al. Mol Cell (2016) 63:146-155. DOI 10.1016/j.molcel.2016.05.009 · PubMed

Other PDB entries of the same protein (UniProt Q8N5J2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MN9 2.05 Å, Crystal structure of MINDY-1 tMIU in complex with K48-diUb
6TUV 2.16 Å, Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin
6TXB 2.18 Å, Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin
5JQS 2.65 Å, Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin
6YJG 3.28 Å, Crystal structure of MINDY1 mutant-Y114F
6Y6R 3.32 Å, Crystal structure of MINDY1 T335D mutant
6Z90 3.59 Å, Crystal structure of MINDY1 mutant-P138A

Browse structure collections

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