PDB 3sdk structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

2.7Å resolution

Structure of yeast 20S open-gate proteasome with Compound 34

Released: 13 Jun 2012

DOI: 10.2210/pdb3sdk/pdb

Source organism: Saccharomyces cerevisiae S288C

Primary publication:
Optimization of a series of dipeptides with a P3 threonine residue as non-covalent inhibitors of the chymotrypsin-like activity of the human 20S proteasome.

Blackburn C, Barrett C, Blank JL, Bruzzese FJ, Bump N, Dick LR, Fleming P, Garcia K, Hales P, Hu Z, Jones M, Liu JX, Sappal DS, Sintchak MD, Tsu C, Gigstad KM

Bioorg Med Chem Lett 20 6581-6 (2010)

PMID: 20875739

Function and Biology Details

Reaction catalysed:

Cleavage of peptide bonds with very broad specificity.

Biochemical function:

protein binding

Biological process:

proteolysis involved in protein catabolic process

Cellular component:

proteasome core complex

Sequence domains:

Structure analysis Details

Assembly composition:

hetero 28-mer (preferred)

Assembly name:

Proteasome complex (preferred)

PDBe Complex ID:

PDB-CPX-149135 (preferred)

Entry contents:

14 distinct polypeptide molecules

Macromolecules (14 distinct):

Proteasome subunit alpha type-2 Chains: A, O

Molecule details ›

Chains: A, O
Length: 250 amino acids
Theoretical weight: 27.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P23639 (Residues: 1-250; Coverage: 100%)

Gene names: PRE8, PRS4, YML092C
Sequence domains:

Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit alpha type-3 Chains: B, P

Molecule details ›

Chains: B, P
Length: 235 amino acids
Theoretical weight: 25.97 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P23638 (Residues: 11-245; Coverage: 91%)

Gene names: PRE9, PRS5, YGR135W
Sequence domains:

Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit alpha type-4 Chains: C, Q

Molecule details ›

Chains: C, Q
Length: 241 amino acids
Theoretical weight: 26.9 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P40303 (Residues: 3-243; Coverage: 95%)

Gene names: PRE6, YOL038W
Sequence domains:

Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit alpha type-5 Chains: D, R

Molecule details ›

Chains: D, R
Length: 260 amino acids
Theoretical weight: 28.65 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P32379 (Residues: 1-260; Coverage: 100%)

Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains:

Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit alpha type-6 Chains: E, S

Molecule details ›

Chains: E, S
Length: 233 amino acids
Theoretical weight: 25.5 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P40302 (Residues: 2-234; Coverage: 100%)

Gene names: PRE5, YM9924.06, YMR314W
Sequence domains:

Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Probable proteasome subunit alpha type-7 Chains: F, T

Molecule details ›

Chains: F, T
Length: 242 amino acids
Theoretical weight: 26.73 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P21242 (Residues: 7-248; Coverage: 84%)

Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Sequence domains:

Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit alpha type-1 Chains: G, U

Molecule details ›

Chains: G, U
Length: 243 amino acids
Theoretical weight: 27.32 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P21243 (Residues: 10-252; Coverage: 96%)

Gene names: PRC2, PRS2, SCL1, YGL011C
Sequence domains:

Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit beta type-2 Chains: H, V

Molecule details ›

Chains: H, V
Length: 222 amino acids
Theoretical weight: 23.99 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P25043 (Residues: 30-251; Coverage: 85%)

Gene names: PUP1, YOR157C
Sequence domains:

Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit beta type-3 Chains: I, W

Molecule details ›

Chains: I, W
Length: 204 amino acids
Theoretical weight: 22.5 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P25451 (Residues: 2-205; Coverage: 100%)

Gene names: PUP3, YER094C
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit beta type-4 Chains: J, X

Molecule details ›

Chains: J, X
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P22141 (Residues: 1-198; Coverage: 100%)

Gene names: PRE1, YER012W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit beta type-5 Chains: K, Y

Molecule details ›

Chains: K, Y
Length: 212 amino acids
Theoretical weight: 23.33 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P30656 (Residues: 76-287; Coverage: 74%)

Gene names: DOA3, P8283.10, PRE2, PRG1, YPR103W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit beta type-6 Chains: L, Z

Molecule details ›

Chains: L, Z
Length: 222 amino acids
Theoretical weight: 24.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P23724 (Residues: 20-241; Coverage: 92%)

Gene names: PRE7, PRS3, PTS1, YBL0407, YBL041W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit beta type-7 Chains: 1, M

Molecule details ›

Chains: 1, M
Length: 233 amino acids
Theoretical weight: 25.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P30657 (Residues: 34-266; Coverage: 88%)

Gene names: PRE4, YFR050C
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Proteasome subunit beta type-1 Chains: 2, N

Molecule details ›

Chains: 2, N
Length: 196 amino acids
Theoretical weight: 21.52 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:

Canonical: P38624 (Residues: 20-215; Coverage: 91%)

Gene names: J1407, PRE3, YJL001W
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores

X-ray source: APS BEAMLINE 31-ID

Spacegroup: P2₁

Unit cell:

a: 136.121Å b: 299.404Å c: 146.236Å

α: 90° β: 112.92° γ: 90°

R-values:

R R_work R_free

0.224 0.223 0.258

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Citations

3 review citations

Exploiting nature's rich source of proteasome inhibitors as starting points in drug development.

Gräwert et al. (2012)

2 more

2 mentions without citation

Computational Approaches for the Discovery of Human Proteasome Inhibitors: An Overview.

Guedes et al. (2016)

1 more