4PIH: K33S mutant of ubiquitin

X-ray crystal structure of the K33S mutant of ubiquitin. Determined by X-ray diffraction at 1.5 Å resolution. Released 29 Oct 2014.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,342
Mol. weight: 17.26 kDa
Ligands: CA
Released: 29 Oct 2014

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

Secondary structure: helices and β-sheets

4PIH contains 8 α-helices and 14 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-71	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, B	protein	76	Homo sapiens	P62987 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4PIH_1 Ubiquitin (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDSEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

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

Primary citation

Enhancing ubiquitin crystallization through surface-entropy reduction. Loll, P.J., Xu, P., Schmidt, J.T. et al. Acta Crystallogr F Struct Biol Commun (2014) 70:1434-1442. DOI 10.1107/S2053230X14019244 · PubMed

Other PDB entries of the same protein (UniProt P62987 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
4PIJ 1.5 Å, X-ray crystal structure of the K11S/K63S double mutant of ubiquitin
5GOJ 1.55 Å, Lys63-linked di-ubiquitin
5J8P 1.55 Å, Lys27-linked diubiquitin
5GOI 1.59 Å, Lys48-linked di-ubiquitin
8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
5GOC 1.73 Å, Lys11-linked diubiquitin
29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
8QYX 1.78 Å, Human 60S ribosomal subunit
4HJK 1.78 Å, U7Ub7 Disulfide variant
5GO7 1.8 Å, Linear tri-ubiquitin

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