1G65

Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity of alpha,beta-epoxyketone proteasome inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.336
  • R-Value Work: 0.283

Literature

Macromolecules
Sequence Display for 1G65

Classification: HYDROLASE / HYDROLASE inhibitor

Total Structure Weight: 705540.00

Macromolecule Entities
Molecule Chains Length Organism Details
Proteasome component Y7 A, O 250 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE8 PRS4 YML092C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component Y13 B, P 244 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE9 PRS5 YGR135W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE6 C, Q 241 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE6 YOL038W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PUP2 D, R 242 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP2 DOA5 YGR253C G9155
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE5 E, S 233 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE5 YMR314W YM9924.06
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component C1 F, T 244 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE10 PRC1 Gene View PRS1 YOR362C O6650
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component C7-alpha G, U 243 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): SCL1 PRC2 PRS2 YGL011C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PUP1 H, V 222 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP1 YOR157C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PUP3 I, W 204 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP3 YER094C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component C11 J, X 198 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE1 YER012W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE2 K, Y 212 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE2 DOA3 PRG1 YPR103W P8283.10
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component C5 L, Z 222 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE7 PRS3 PTS1 YBL041W YBL0407
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE4 1, M 233 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE4 YFR050C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE3 2, N 196 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE3 YJL001W J1407
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
EPOXOMICIN (peptide inhibitor) 3, 4 5 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

D, F, G, H, I, K, L, N MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
3, 4 NON-POLYMER C2 H4 O --
IML
Query on IML
3, 4 L-PEPTIDE LINKING C7 H15 N O2 ILE
04D
Query on 04D
3, 4 NON-POLYMER C9 H21 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.336
  • R-Value Work: 0.283
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 135.20 α = 90.00
b = 300.20 β = 112.98
c = 144.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-11-03
  • Released Date: 2000-11-27
  • Deposition author(s): Groll, M., Kim, K.B., Kairies, N., Huber, R., Crews, C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4