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Yeast 20S proteasome in complex with the vinyl sulfone LU122

X-ray diffraction
2.9Å resolution
PDB entry 4int coloured by chain, front view.
PDB entry 4int coloured by chain, side view.
PDB entry 4int coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Assembly composition:
hetero 28-mer (preferred)
Entry contents: 14 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Proteasome complex
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Multimeric state: hetero 28-mer
Accessible surface area: 214975.35 Å2
Buried surface area: 120889.43 Å2
Dissociation area: 6,696.92 Å2
Dissociation energy (ΔGdiss): 44.05 kcal/mol
Dissociation entropy (TΔSdiss): 28.61 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-149135

Macromolecules

Proteasome subunit alpha type-2
Chains: A, O
Length: 250 amino acids
Theoretical weight: 27.19 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23639 (Residues: 1-250; Coverage: 100%)
Gene names: PRE8, PRS4, YML092C
Pfam:
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-2 in PDB entry 4int, assembly 1, front view.
Proteasome subunit alpha type-2 in PDB entry 4int, assembly 1, side view.
Proteasome subunit alpha type-2 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit alpha type-3
Chains: B, P
Length: 258 amino acids
Theoretical weight: 28.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23638 (Residues: 1-258; Coverage: 100%)
Gene names: PRE9, PRS5, YGR135W
Pfam:
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-3 in PDB entry 4int, assembly 1, front view.
Proteasome subunit alpha type-3 in PDB entry 4int, assembly 1, side view.
Proteasome subunit alpha type-3 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit alpha type-4
Chains: C, Q
Length: 254 amino acids
Theoretical weight: 28.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40303 (Residues: 1-254; Coverage: 100%)
Gene names: PRE6, YOL038W
Pfam:
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-4 in PDB entry 4int, assembly 1, front view.
Proteasome subunit alpha type-4 in PDB entry 4int, assembly 1, side view.
Proteasome subunit alpha type-4 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit alpha type-5
Chains: D, R
Length: 260 amino acids
Theoretical weight: 28.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32379 (Residues: 1-260; Coverage: 100%)
Gene names: DOA5, G9155, PUP2, YGR253C
Pfam:
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-5 in PDB entry 4int, assembly 1, front view.
Proteasome subunit alpha type-5 in PDB entry 4int, assembly 1, side view.
Proteasome subunit alpha type-5 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit alpha type-6
Chains: E, S
Length: 234 amino acids
Theoretical weight: 25.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40302 (Residues: 1-234; Coverage: 100%)
Gene names: PRE5, YM9924.06, YMR314W
Pfam:
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-6 in PDB entry 4int, assembly 1, front view.
Proteasome subunit alpha type-6 in PDB entry 4int, assembly 1, side view.
Proteasome subunit alpha type-6 in PDB entry 4int, assembly 1, top view.
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Probable proteasome subunit alpha type-7
Chains: F, T
Length: 288 amino acids
Theoretical weight: 31.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21242 (Residues: 1-288; Coverage: 100%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Pfam:
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Probable proteasome subunit alpha type-7 in PDB entry 4int, assembly 1, front view.
Probable proteasome subunit alpha type-7 in PDB entry 4int, assembly 1, side view.
Probable proteasome subunit alpha type-7 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit alpha type-1
Chains: G, U
Length: 252 amino acids
Theoretical weight: 28.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21243 (Residues: 1-252; Coverage: 100%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Pfam:
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-1 in PDB entry 4int, assembly 1, front view.
Proteasome subunit alpha type-1 in PDB entry 4int, assembly 1, side view.
Proteasome subunit alpha type-1 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit beta type-2
Chains: H, V
Length: 232 amino acids
Theoretical weight: 25.11 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25043 (Residues: 30-261; Coverage: 89%)
Gene names: PUP1, YOR157C
Pfam:
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-2 in PDB entry 4int, assembly 1, front view.
Proteasome subunit beta type-2 in PDB entry 4int, assembly 1, side view.
Proteasome subunit beta type-2 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit beta type-3
Chains: I, W
Length: 205 amino acids
Theoretical weight: 22.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25451 (Residues: 1-205; Coverage: 100%)
Gene names: PUP3, YER094C
Pfam: Proteasome subunit
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-3 in PDB entry 4int, assembly 1, front view.
Proteasome subunit beta type-3 in PDB entry 4int, assembly 1, side view.
Proteasome subunit beta type-3 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit beta type-4
Chains: J, X
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22141 (Residues: 1-198; Coverage: 100%)
Gene names: PRE1, YER012W
Pfam: Proteasome subunit
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-4 in PDB entry 4int, assembly 1, front view.
Proteasome subunit beta type-4 in PDB entry 4int, assembly 1, side view.
Proteasome subunit beta type-4 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit beta type-5
Chains: K, Y
Length: 212 amino acids
Theoretical weight: 23.33 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30656 (Residues: 76-287; Coverage: 74%)
Gene names: DOA3, P8283.10, PRE2, PRG1, YPR103W
Pfam: Proteasome subunit
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-5 in PDB entry 4int, assembly 1, front view.
Proteasome subunit beta type-5 in PDB entry 4int, assembly 1, side view.
Proteasome subunit beta type-5 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit beta type-6
Chains: L, Z
Length: 222 amino acids
Theoretical weight: 24.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23724 (Residues: 20-241; Coverage: 92%)
Gene names: PRE7, PRS3, PTS1, YBL0407, YBL041W
Pfam: Proteasome subunit
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-6 in PDB entry 4int, assembly 1, front view.
Proteasome subunit beta type-6 in PDB entry 4int, assembly 1, side view.
Proteasome subunit beta type-6 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit beta type-7
Chains: M, a
Length: 233 amino acids
Theoretical weight: 25.95 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30657 (Residues: 34-266; Coverage: 88%)
Gene names: PRE4, YFR050C
Pfam: Proteasome subunit
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-7 in PDB entry 4int, assembly 1, front view.
Proteasome subunit beta type-7 in PDB entry 4int, assembly 1, side view.
Proteasome subunit beta type-7 in PDB entry 4int, assembly 1, top view.
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Proteasome subunit beta type-1
Chains: N, b
Length: 196 amino acids
Theoretical weight: 21.52 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38624 (Residues: 20-215; Coverage: 91%)
Gene names: J1407, PRE3, YJL001W
Pfam: Proteasome subunit
InterPro:
CATH: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit beta type-1 in PDB entry 4int, assembly 1, front view.
Proteasome subunit beta type-1 in PDB entry 4int, assembly 1, side view.
Proteasome subunit beta type-1 in PDB entry 4int, assembly 1, top view.
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