PDBe 2gpl

X-ray diffraction
2.81Å resolution

TMC-95 based biphenyl-ether macrocycles: specific proteasome inhibitors

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Probable proteasome subunit alpha type-7 Chains: F, T
Molecule details ›
Chains: F, T
Length: 244 amino acids
Theoretical weight: 26.89 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21242 (Residues: 5-248; Coverage: 85%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Sequence domains:
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
Expression system: Saccharomyces cerevisiae
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 alpha type-2 Chains: A, O
Molecule details ›
Chains: A, O
Length: 250 amino acids
Theoretical weight: 27.19 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
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 beta type-4 Chains: J, X
Molecule details ›
Chains: J, X
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
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 alpha type-3 Chains: B, P
Molecule details ›
Chains: B, P
Length: 244 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23638 (Residues: 2-245; Coverage: 95%)
Gene names: PRE9, PRS5, YGR135W
Sequence domains:
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
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30656 (Residues: 76-287; Coverage: 74%)
Gene names: DOA3, P8283.10, PRE2, PRG1, YPR103W
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
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38624 (Residues: 20-215; Coverage: 91%)
Gene names: J1407, PRE3, YJL001W
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
Expression system: Saccharomyces cerevisiae
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 alpha type-6 Chains: E, S
Molecule details ›
Chains: E, S
Length: 233 amino acids
Theoretical weight: 25.5 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40302 (Residues: 2-234; Coverage: 100%)
Gene names: PRE5, YM9924.06, YMR314W
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
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40303 (Residues: 3-243; Coverage: 95%)
Gene names: PRE6, YOL038W
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
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25043 (Residues: 30-251; Coverage: 85%)
Gene names: PUP1, YOR157C
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Proteasome subunit alpha type-5 Chains: D, R
Molecule details ›
Chains: D, R
Length: 242 amino acids
Theoretical weight: 26.54 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32379 (Residues: 9-250; Coverage: 93%)
Gene names: DOA5, G9155, PUP2, YGR253C
Sequence domains: Proteasome subunit
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
Expression system: Saccharomyces cerevisiae
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 alpha type-1 Chains: G, U
Molecule details ›
Chains: G, U
Length: 243 amino acids
Theoretical weight: 27.32 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21243 (Residues: 10-252; Coverage: 96%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Sequence domains:
Structure domains: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P21
Unit cell:
a: 136.425Å b: 300.962Å c: 144.762Å
α: 90° β: 113.17° γ: 90°
R-values:
R R work R free
0.282 0.217 0.241
Expression system: Saccharomyces cerevisiae