4INR

Yeast 20S proteasome in complex with the vinyl sulfone LU102

Structural Biology Knowledgebase: 4INR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.224

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4INR

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 731168.42

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
Proteasome component Y13 B, P 258 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE9 PRS5 YGR135W
Proteasome component PRE6 C, Q 254 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE6 YOL038W
Proteasome component PUP2 D, R 260 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP2 DOA5 YGR253C G9155
Proteasome component PRE5 E, S 234 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE5 YMR314W YM9924.06
Proteasome component C1 F, T 288 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE10 PRC1 Gene View PRS1 YOR362C O6650
Proteasome component C7-alpha G, U 252 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): SCL1 PRC2 PRS2 YGL011C
Proteasome component PUP1 H, V 232 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP1 YOR157C
Proteasome component PUP3 I, W 205 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP3 YER094C
Proteasome component C11 J, X 198 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE1 YER012W
Proteasome component PRE2 K, Y 212 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE2 DOA3 PRG1 YPR103W P8283.10
Proteasome component C5 L, Z 222 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE7 PRS3 PTS1 YBL041W YBL0407
Proteasome component PRE4 M, a 233 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE4 YFR050C
Proteasome component PRE3 N, b 196 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE3 YJL001W J1407

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1G1
Query on 1G1

H, K, V, Y N3Phe-Leu-Leu-Phe(4-NH2CH2)-methyl vinyl sulfone, bound form
C33 H49 N7 O5 S
NBVHKDCONVHHDW-RYTSNQFKSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1G1 N/A in BindingDB
N/A in BindingMoad
IC50: 2600 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000979 H, K, V, Y N3PHE-LEU-LEU-PHE(4-NH2CH2)-METHYL VINYL SULFONE, BOUND FORM Peptide-like /
Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.224
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 136.32 α = 90.00
b = 301.05 β = 113.13
c = 144.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-06
  • Released Date: 2013-01-30
  • Deposition author(s): Geurink, P.P., van der Linden, W.A., Mirabella, A.C., Gallastegui, N., de Bruin, G., Blom, A.E.M., Voges, M.J., Mock, E.D., Florea, B.I., van der Marel, G.A., Driessen, C., van der Stelt, M., Groll, M., Overkleeft, H.S., Kisselev, A.F.

Revision History

  • 2013-02-27
    Type: Citation | Details: Citation update