4ZD5: Catalytic domain of Sst2 F403A mutant

Catalytic domain of Sst2 F403A mutant. Determined by X-ray diffraction at 2.07 Å resolution. Released 14 Oct 2015.

Method: X-ray diffraction
Resolution: 2.07 Å
Organism: Schizosaccharomyces pombe
Chains: 2
Atoms: 3,043
Mol. weight: 44.38 kDa
Ligands: ZN
Released: 14 Oct 2015

Explore 4ZD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZD5 contains 13 α-helices and 26 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: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	252-253	2	1
β-strand	259-260	2	1
β-strand	263-266	4	2
α-helix	269-276	8
α-helix	278-282	5
β-strand	288-296	9	2
β-strand	299-307	9	2
β-strand	310-312	3	3
β-strand	317-319	3	3
α-helix	322-331	10
β-strand	335-342	8	2
α-helix	352-364	13
β-strand	369-374	6	2
α-helix	375-377	3
β-strand	379-385	7	2
α-helix	389-395	7
β-strand	411-413	3	2
α-helix	414-415	2
β-strand	420-423	4	2
β-strand	428-431	4	2

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	252-253	2	4
β-strand	259-260	2	4
β-strand	263-266	4	5
α-helix	269-282	14
β-strand	288-296	9	5
β-strand	299-307	9	5
β-strand	310-312	3	6
β-strand	317-319	3	6
α-helix	322-331	10
β-strand	335-342	8	5
α-helix	352-364	13
β-strand	369-374	6	5
α-helix	375-377	3
β-strand	379-385	7	5
α-helix	389-396	8
β-strand	411-413	3	5
α-helix	414-415	2
β-strand	420-423	4	5
β-strand	428-431	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AMSH-like protease sst2	A, B	protein	197	Schizosaccharomyces pombe	Q9P371 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4ZD5_1 AMSH-like protease sst2 (chains A, B)
GPLGSMAGTFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQN
AFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTH
CSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLAHPHEGKVYTMVAQPG
HVREINSKLQVVDLRVK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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

Primary citation

Structure of the catalytic domain of Sst2 F403A mutant at 2.07 Angstoms resolution. Shrestha, R.K. To be published.

Other PDB entries of the same protein (UniProt Q9P371 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JXE 1.45 Å, Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain
4K1R 1.63 Å, Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin
4ZD4 1.63 Å, Catalytic domain of Sst2 F403W mutant
4MS7 1.67 Å, Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain
4ZFR 1.72 Å, Catalytic domain of Sst2 F403A mutant bound to ubiquitin
4MSM 1.74 Å, Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant…
4MSJ 1.8 Å, Crystal structure of S. pombe AMSH-like protease SST2 catalytic domain from P212121…
4MSD 1.9 Å, Crystal structure of Schizosaccharomyces pombe AMSH-like protein SST2 T319I mutant
4MSQ 1.95 Å, Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain…
4PQT 2.05 Å, Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal…
4NQL 2.3 Å, The crystal structure of the DUB domain of AMSH orthologue, Sst2 from S. pombe, in…
4ZFT 2.3 Å, Catalytic domain of Sst2 F403W mutant bound to ubiquitin

Browse structure collections

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