› 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
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
Molecule details ›
Chains: C, Q
Length: 248 amino acids
Theoretical weight: 27.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14818 (Residues: 1-248; Coverage: 100%)
Gene names: HSPC, PSMA7
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-5 Chains: D, R
Molecule details ›
Chains: D, R
Length: 241 amino acids
Theoretical weight: 26.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28066 (Residues: 1-241; Coverage: 100%)
Gene name: PSMA5
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-1 Chains: E, S
Molecule details ›
Chains: E, S
Length: 263 amino acids
Theoretical weight: 29.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25786 (Residues: 1-263; Coverage: 100%)
Gene names: HC2, NU, PROS30, PSC2, PSMA1
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-3 Chains: F, T
Molecule details ›
Chains: F, T
Length: 255 amino acids
Theoretical weight: 28.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25788 (Residues: 1-255; Coverage: 100%)
Gene names: HC8, PSC8, PSMA3
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-6 Chains: G, U
Molecule details ›
Chains: G, U
Length: 246 amino acids
Theoretical weight: 27.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60900 (Residues: 1-246; Coverage: 100%)
Gene names: PROS27, PSMA6
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-7 Chains: H, V
Molecule details ›
Chains: H, V
Length: 234 amino acids
Theoretical weight: 25.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99436 (Residues: 44-277; Coverage: 85%)
Gene names: PSMB7, Z
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-3 Chains: I, W
Molecule details ›
Chains: I, W
Length: 205 amino acids
Theoretical weight: 22.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49720 (Residues: 1-205; Coverage: 100%)
Gene name: PSMB3
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-2 Chains: J, X
Molecule details ›
Chains: J, X
Length: 201 amino acids
Theoretical weight: 22.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49721 (Residues: 1-201; Coverage: 100%)
Gene name: PSMB2
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Z-LLY-ketoaldehyde peptide Chains: c, d
Molecule details ›
Chains: c, d
Length: 4 amino acids
Theoretical weight: 576 Da
Source organism: Homo sapiens
Expression system: Not provided
Proteasome subunit beta type-5 Chains: K, Y
Molecule details ›
Chains: K, Y
Length: 204 amino acids
Theoretical weight: 22.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28074 (Residues: 60-263; Coverage: 78%)
Gene names: LMPX, MB1, PSMB5, X
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-1 Chains: L, Z
Molecule details ›
Chains: L, Z
Length: 213 amino acids
Theoretical weight: 23.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P20618 (Residues: 29-241; Coverage: 88%)
Gene names: PSC5, PSMB1
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-4 Chains: M, a
Molecule details ›
Chains: M, a
Length: 219 amino acids
Theoretical weight: 24.41 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28070 (Residues: 46-264; Coverage: 83%)
Gene names: PROS26, PSMB4
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-6 Chains: N, b
Molecule details ›
Chains: N, b
Length: 205 amino acids
Theoretical weight: 21.92 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28072 (Residues: 35-239; Coverage: 86%)
Gene names: LMPY, PSMB6, Y
Sequence domains: Proteasome subunit
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

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

Entry percentile scores
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