› 5lf6

X-ray diffraction
2.07Å resolution

Human 20S proteasome complex with Z-LLY-ketoaldehyde at 2.1 Angstrom

Released:
DOI: 10.2210/pdb5lf6/pdb
Model geometry
Fit model/data
PDB entry 5lf6 coloured by chain, front view.
PDB entry 5lf6 coloured by chain, side view.
PDB entry 5lf6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design.
Schrader J, Henneberg F, Mata RA, Tittmann K, Schneider TR, Stark H, Bourenkov G, Chari A
Science 353 594-8 (2016)
PMID: 27493187

Function and Biology Details

Reaction catalysed: 
Cleavage of peptide bonds with very broad specificity.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127167 (preferred)
Entry contents:
15 distinct polypeptide molecules
Macromolecules (15 distinct):
Proteasome subunit alpha type-2 Chains: A, O
Molecule details ›
Chains: A, O
Length: 234 amino acids
Theoretical weight: 25.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25787 (Residues: 1-234; Coverage: 100%)
Gene names: HC3, PSC3, PSMA2
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-4 Chains: B, P
Molecule details ›
Chains: B, P
Length: 261 amino acids
Theoretical weight: 29.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25789 (Residues: 1-261; Coverage: 100%)
Gene names: HC9, PSC9, PSMA4
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-7 Chains: C, Q
Proteasome subunit alpha type-5 Chains: D, R
Proteasome subunit alpha type-1 Chains: E, S
Proteasome subunit alpha type-3 Chains: F, T
Proteasome subunit alpha type-6 Chains: G, U
Proteasome subunit beta type-7 Chains: H, V
Proteasome subunit beta type-3 Chains: I, W
Proteasome subunit beta type-2 Chains: J, X
Z-LLY-ketoaldehyde peptide Chains: c, d
Proteasome subunit beta type-5 Chains: K, Y
Proteasome subunit beta type-1 Chains: L, Z
Proteasome subunit beta type-4 Chains: M, a
Proteasome subunit beta type-6 Chains: N, b

Ligands and Environments

5 bound ligands:
Ligand CL 55 x CL
Ligand NEN 8 x NEN
Ligand K 6 x K
Ligand MG 10 x MG
Ligand 1PE 9 x 1PE
1 modified residue:
Ligand YCM 4 x YCM

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P212121
Unit cell:
a: 113.87Å b: 203.48Å c: 315.63Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.227
Expression system: Not provided

Quick links

Citations

23 review citations

The versatility of boron in biological target engagement.
Diaz et al. (2017)
22 more