1JD2

Crystal Structure of the yeast 20S Proteasome:TMC-95A complex: A non-covalent Proteasome Inhibitor

Structural Biology Knowledgebase: 1JD2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.336
  • R-Value Work: 0.251

Literature

Macromolecules
Sequence Display for 1JD2

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 705815.94

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEASOME COMPONENT Y7 A, V 250 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE8 PRS4 YML092C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT Y13 B, W 244 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE9 PRS5 YGR135W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT PRE6 C, X 241 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE6 YOL038W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT PUP2 D, Y 242 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Mutation: A125E, A126R, A127L
Details: part of 20S subunit
Gene Name(s): PUP2 DOA5 YGR253C G9155
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT PRE5 E, Z 233 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Mutation: A127Y
Details: part of 20S subunit
Gene Name(s): PRE5 YMR314W YM9924.06
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT C1 1, F 244 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE10 PRC1 Gene View PRS1 YOR362C O6650
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT C7-ALPHA 2, G 243 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): SCL1 PRC2 PRS2 YGL011C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT PUP1 H, O 222 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PUP1 YOR157C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT PUP3 I, P 204 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PUP3 YER094C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT C11 J, Q 198 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE1 YER012W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT PRE2 K, R 212 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE2 DOA3 PRG1 YPR103W P8283.10
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT C5 L, S 222 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE7 PRS3 PTS1 YBL041W YBL0407
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT PRE4 M, T 233 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE4 YFR050C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEASOME COMPONENT PRE3 N, U 196 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Details: part of 20S subunit
Gene Name(s): PRE3 YJL001W J1407
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
TMC-95A inhibitor 8, 9 5 Arthrinium arundinis

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

D, F, G, H, I, L, N, P MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001096
Query on PRD_001096
8, 9 TMC-95A Cyclic peptide /
Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.336
  • R-Value Work: 0.251
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 135.20 α = 90.00
b = 301.30 β = 112.60
c = 144.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-06-12
  • Released Date: 2002-02-13
  • Deposition author(s): Groll, M., Koguchi, Y., Huber, R., Kohno, J.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4